Marsupial phyloSNPs

Introduction to Marsupial phyloSNPs

In this project, new genomic data from the Tasmanian devil (Sarcophilus harrisii), Tasmanian tiger (Thylacinus cynocephalus), and echidna (Tachyglossus aculeatus) are analyzed for significant changes at the protein coding level. The goal is to find single amino acid changes in one of these species at a highly invariant residue in a well-conserved exon in a gene with known or predictable tertiary structure. Such changes are thought to enrich for genetic changes with significant, adaptive biochemical or phenotypic consequences (1,2,3,4), in contrast to ordinary SNPs at positions of low conservation. Thus phyloSNPs are informative to the distinctive biology of the species carrying them and suggest a focus for subsequent experiment.

It is also of particular interest to determine the levels of variation within the Tasmanian devil population as a whole because the number of individuals have become low and possibly inbreed with adverse sequelae. For this it will be necessary to first determine sites of variation and then to genotype them across a large number of individuals.

Marsupial genomic and cDNA data to date has been quite limited compared to placental mammal. Yet as outgroup, metatheran animals provide important context to placentals and represent important context in understanding human protein evolution. The monotheres are inevitably limited by the paucity of extant species (basically platypus and echidna) and dim prospects for fossil DNA. Consequently echidna provides an important adjunct to the existing but incomplete platypus assembly. While extant birds and reptiles -- the preceding divergence node -- are abundant it must be remembered that a very considerable time elapsed (from 310 mry to 175 mry) prior to divergence of mammals with living representatives. This gap of 135 myr is comparable to the whole evolutionary record of theran mammals.

Assumed vertebrate phylogenetic tree

Marsupial relationships are taken from a 2009 paper establishing the mitochondrial genome sequences of the Tasmanian tiger (Thylacinus cynocephalus) and numbat (Myrmecobius fasciatus).

Newick tree that generates a marsupial-centric vertebrate phylogenetic tree:

((((((((((((sarHar,smiCra),myrFas),thyCyn),(macEug,triVul)),monDom),
((((loxAfr,proCap),echTel),(dasNov,choHof)),
((((((bosTau,turTru),susScr),vicPac),((equCab,(felCat,canFam)),(myoLuc,pteVam))),(eriEur,sorAra)),
(((((((((homSap,panTro),gorGor),ponPyg),macMul),calJac),tarSyr),(micMur,otoGar)),tupBel),
(((((musMus,ratNor),dipOrd),cavPor),speTri),(oryCun,ochPri)))))),
(ornAna,tacAcu)),
((galGal,taeGut),anoCar)),
xenTro),
(((tetNig,takRub),(gasAcu,oryLap)),danRer)),
calMil),
petMar);

Newick tree that generates the homo-centric vertebrate phylogenetic tree:

((((((((((((((((((homSap,panTro),gorGor),ponPyg),macMul),calJac),tarSyr),(micMur,otoGar)),tupBel),
(((((musMus,ratNor),dipOrd),cavPor),speTri),(oryCun,ochPri))),
(((((vicPac,susScr),turTru),bosTau),((equCab,(felCat,canFam)),(myoLuc,pteVam))),(eriEur,sorAra))),
(((loxAfr,proCap),echTel),(dasNov,choHof))),
(monDom,((macEug,triVul),(sarHar,thyCyn)))),
(ornAna,tacAcu)),
((galGal,taeGut),anoCar)),
xenTro),
(((tetNig,takRub),(gasAcu,oryLap)),danRer)),
calMil),
petMar);

Phylo-sorting data

This tab-delimited table enables four different sort orders. These are needed because data can be missing from species in a manner that varies by gene, making data alignment difficult. Some alignment tools also lose input order, so that needs to be recovered. The ordering here flattens the phylogenetic tree by taking human (arbitrarily) at the top and resolving ambiguous situations (eg mouse, rat) by putting species with the best assemblies first.

The first two columns provide sort order number for the 44 species alignment at UCSC as phylogenetic and alphabetic order respectively. The third and fourth columns do this for a larger set of 53 species for which data is commonly available (notably in marsupials). The fifth column supplies the genSpp acronym and the sixth the Newick tree format syntax. These two columns by themselves will correctly draw the vertebrate phylogenetic tree in all online software without further editing. The final columns provide genus, species, and common name.

..	..	..	..	......	((((((((((((			
46	10	54	10	anoCar	)),	Anolis	carolinensis	(lizard)
29	11	22	11	bosTau	,	Bos	taurus	(cow)
15	12	38	12	calJac	),	Callithrix	jacchus	(marmoset)
62	54	61	13	calMil	),	Callorhinchus	milii	(elephantfish)
32	13	28	14	canFam	)),(	Canis	familiaris	(dog)
23	14	46	15	cavPor	),	Cavia	porcellus	(guinea_pig)
41	15	21	16	choHof	)),((((((	Choloepus	hoffmanni	(sloth)
52	16	60	17	danRer	)),	Danio	rerio	(zebrafish)
40	17	20	18	dasNov	,	Dasypus	novemcinctus	(armadillo)
22	18	45	19	dipOrd	),	Dipodomys	ordii	(kangaroo_rat)
39	19	19	20	echTel	),(	Echinops	telfairi	(tenrec)
30	20	26	21	equCab	,(	Equus	caballus	(horse)
35	21	31	22	eriEur	,	Erinaceus	europaeus	(hedgehog)
31	22	27	23	felCat	,	Felis	catus	(cat)
44	23	52	24	galGal	,	Gallus	gallus	(chicken)
50	24	58	25	gasAcu	,	Gasterosteus	aculeatus	(stickleback)
12	25	35	26	gorGor	),	Gorilla	gorilla	(gorilla)
10	26	33	27	homSap	,	Homo	sapiens	(human)
37	27	17	28	loxAfr	,	Loxodonta	africana	(elephant)
58	56	14	29	macEug	,	Macropus	eugenii	(wallaby)
14	28	37	30	macMul	),	Macaca	mulatta	(rhesus)
17	29	40	31	micMur	,	Microcebus	murinus	(mouse_lemur)
42	30	16	32	monDom	),((((	Monodelphis	domestica	(opossum)
20	31	43	33	musMus	,	Mus	musculus	(mouse)
33	32	29	34	myoLuc	,	Myotis	lucifugus	(microbat)
56	57	12	35	myrFas	),	Myrmecobius	fasciatus	(numbat)
26	33	49	36	ochPri	)))))),(	Ochotona	princeps	(pika)
43	34	50	37	ornAna	,	Ornithorhynchus	anatinus	(platypus)
25	35	48	38	oryCun	,	Oryctolagus	cuniculus	(rabbit)
51	36	59	39	oryLap	)),	Oryzias	latipes	(medaka)
18	37	41	40	otoGar	)),	Otolemur	garnettii	(bushbaby)
11	38	34	41	panTro	),	Pan	troglodytes	(chimp)
53	39	62	42	petMar	)	Petromyzon	marinus	(lamprey)
13	40	36	43	ponPyg	),	Pongo	pygmaeus	(orang)
38	41	18	44	proCap	),	Procavia	capensis	(hyrax)
34	42	30	45	pteVam	))),(	Pteropus	vampyrus	(macrobat)
21	43	44	46	ratNor	),	Rattus	norvegicus	(rat)
54	58	10	47	sarHar	,	Sarcophilus	harrisii	(tasmanian_devil)
55	59	11	48	smiCra	),	Sminthopsis	crassicaudata	(dunnart)
36	44	32	49	sorAra	)),(((((((((	Sorex	araneus	(shrew)
24	45	47	50	speTri	),(	Spermophilus	tridecemlineatus	(squirrel)
60	60	24	51	susScr	),	Sus	scrofa	(pig)
61	61	51	52	tacAcu	)),((	Tachyglossus	aculeatus	(echidna)
45	46	53	53	taeGut	),	Taeniopygia	guttata	(finch)
49	47	57	54	takRub	),(	Takifugu	rubripes	(fugu)
16	48	39	55	tarSyr	),(	Tarsius	syrichta	(tarsier)
48	49	56	56	tetNig	,	Tetraodon	nigroviridis	(pufferfish)
57	62	13	57	thyCyn	),(	Thylacinus	cynocephalus	(tasmanian_tiger)
59	63	15	58	triVul	)),	Trichosurus	vulpecula	(bushytail_possum)
19	50	42	59	tupBel	),(((((	Tupaia	belangeri	(tree_shrew)
28	51	23	60	turTru	),	Tursiops	truncatus	(dolphin)
27	52	25	61	vicPac	),((	Vicugna	pacos	(lama)
47	53	55	62	xenTro	),(((	Xenopus	tropicalis	(frog)
								
44	44	53	53	genSpp	tree_syntax	genus	species	common
ph	al	ph	al

Candidate analysis

The first issue is error within the reads themselves; the second is whether the default 454 Newbler assembler correctly identified overelapping reads and put them together properly to give exon-spanning reads. Those issues are discussed elsewhere -- here it is assumed the data is correct, so the entire focus is on subsequent bioinformatics.

(methods explained more shortly)

Case of ERN2

chr6_5971 ERN2 4
contig00001  length=355   numreads=5
KLPFTIPELVHASPCRSSDGVLYT
.....................F..
               ^        
15      R=3(75) H=2(50

Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in
tasmanian  devil (in this case, both individuals differ from Monodelphis by L->F), then differences between the two thylacines
(here one individual has R at position 15, the other has H), and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler (the official 454 assembler) which uses 
lower-case letters for less confident calls.

Pseudogene issues: ERN2 has not generated potentially confusing recent processed pseudogenes in mammals (lack of human, opossum or platypus genome Blat matches to ERN2 query). The variation observed here between individual tasmanian devils is implausibly an early stage in the loss of parent gene because of ERN2 functional essentiality; the exon cannot come from a decaying segmental duplication because coverage is high enough to also detect the main gene.

Paralog issues: The GeneSorter tool at UCSC shows a single significant full-length paralog in human, ERN1, also with 22 coding exons. The genes reside on different chromosomes but in regions with local homology of synteny. However this particular exon is a good match (3 differences out of 23), so there is potential for experimental difficulties in distinguishing them in short reads (including the following exon readily resolves them bioinformatically). In any event, at positions 15 and 20, ERN1 is identical at the amino acid level to ERN2. The gene duplication appears to have occured subsequent to amphioxus divergence earlier diverging metazoans are single-copy.

Homoplasy (recurrent mutation) issues: This exon is very conserved and does not exhibit repetitive sequence, compositional simplicity, or indels in any species in either paralog that could foster experimental error or alignment ambiguity. At position 15, the ancestral value is arginine in both paralogs. The G--> A transition to histidine in one individual is conservative under most circumstances (still basic) and arises from an arginine codon CpG hotspot conserved back to lamprey in 30 of 32 species with available data, yet histidine is not observed part of a reduced alphabet (ie R/H) at this position over many billions of years of branch length. Consequently R-->H is a significant change in this individual tasmanian devil.

Known variations: No human disease variants have been reported for either ERN2 or ERN1, probably attributable to essentiality. Site-specific mutation close to the exon here have been generated for K121P, D123P, W125A, and Q105E but only for ERN1. Naturally occuring coding SNPs in the human population relevent to the ERN2 exon are not known but low frequency alleles could emerge from the 1000 Genomes Project.

Side issues: a very ancient conserved leucine at position 21 appears to be transitioning to phenylalanine at marsupial node but has not been fixed, so settles out as L or F depending on lineage-sorting on each terminal marsupial leaf whereas placentals are all changed to phenylalanine (a phyloSNP caught in mid-air). While L and F might seem about the 'same' as amino acids, the branch length conservation totals say both are important but for different reasons: this is not a waffle codon nor reduced alphabet situation. This raises the question -- given the extreme conservation of this exon otherwise -- of whether the L-->F change at position 21 in both individuals has 'enabled' (made neutral or adaptive) an otherwise unfavorable R-->H change at position 15 in one individual.

Structural significance: By good fortune, the crystal structure of ERN1 (alternately called IRE1) has been published. The PDB 2HZ6 structure has good coverage of this particular exon. Consequently the marsupial ERN2 could be very accurately modelled and the structural effects of L-->F with or without R-->H computed by submission to online SwissProt modelling service.

Monodelphis ERN2 (key exon: sarHar2) aligned to human ERN1 luminal domain 
 Expect = 5.8e-65 Identities = 109/180 (60%), Positives = 141/180 (78%)

ERN2_monDom   1  PESLLFISTLDGSLHAVSKKTGDIQWTLKDDPIIQGPVYATEPAFLPDPSDGSLYILGEE  60
                 PE+LLF+STLDGSLHAVSK+TG I+WTLK+DP++Q P +  EPAFLPDP+DGSLY LG +
ERN1_homSap   8  PETLLFVSTLDGSLHAVSKRTGSIKWTLKEDPVLQVPTHVEEPAFLPDPNDGSLYTLGSK  67

ERN2_monDom  61  SKQGLMKLPFTIPELVHASPCHSSDGVFYTGRKQDTWFMVDPKSGKKQTMLSTETWDGLY  120
                 + +GL KLPFTIPELV ASPCRSSDG+LY G+KQD W+++D  +G+KQ  LS+   D L 
ERN1_homSap  68  NNEGLTKLPFTIPELVQASPCRSSDGILYMGKKQDIWYVIDLLTGEKQQTLSSAFADSLC  127

ERN2_monDom  121 PSAPLLYIGRTQYTVTMYDPRSQALRWNTTYRGYSAPLLDHLPGYQVGHFTCSGEGLVVT  180
                 PS  LLY+GRT+YT+TMYD +++ LRWN TY  Y+A L +    Y++ HF  +G+GLVVT
ERN1_homSap  128 PSTSLLYLGRTEYTITMYDTKTRELRWNATYFDYAASLPEDDVDYKMSHFVSNGDGLVVT  187

Functional significance: A considerable amount is known about the paralog ERN1. Annotation transfer is likely applicable to ERN2. The two gene products differ primarily in expression -- ERN1 ubiquitious but ERN2 restricted to intestinal epithelial cells:

"The unfolded protein response (UPR) is an evolutionarily conserved mechanism by which all eukaryotic cells adapt to the accumulation of unfolded proteins in the endoplasmic reticulum (ER). Inositol-requiring kinase 1 (IRE1 or ERN1) and PKR-related ER kinase (PERK) are two type I transmembrane ER-localized protein kinase receptors that signal the UPR through a process that involves homodimerization and autophosphorylation... The monomer of the luminal domain comprises a unique fold of a triangular assembly of beta-sheet clusters. Structural analysis identified an extensive dimerization interface stabilized by hydrogen bonds and hydrophobic interactions... Mutations that disrupt the dimerization interface produced ERN1 protein that failed to either dimerize or activate the UPR upon ER stress."

"ERN1 is a type I transmembrane protein kinase receptor that also has a site-specific RNase activity that, upon activation, initiates a site-specific unconventional splicing reaction. The substrate for IRE1 RNase in metazoans is Xbp1 mRNA, which encodes a basic leucine zipper transcription factor of the ATF/CREB family. XBP1 controls expression of genes containing an X-box element or a UPR element in their promoter regions. The IRE1-mediated splicing reaction introduces into XBP1 an alternative C terminus, thereby generating an XBP1 molecule that is a more potent transcriptional activator. Therefore, activation of IRE1 and its RNase increases the transcription of genes encoding ER chaperones and folding catalysts... the ERN1 N-terminal luminal domain (NLD) functions as an ER stress sensor... under normal conditions IRE1 is maintained in a monomeric state through interaction of the NLD with the ER resident chaperone BiP. Upon ER stress, Grp78 binds to unfolded proteins as they accumulate, permitting the released NLD to form homodimers. Dimerization of the NLD in turn leads to the activation of the protein kinase and RNase activities in the cytosolic domain of ERN1."

ENR2 is readily distinguished from its ERN1 paralog at tBlastn by including the two following exons which bring percent identity to 62%:

ERN2_monDom KLPFTIPELVHASPCRSSDGVLYTGRKQDTWFMVDPKSGKKQTMLSTETWDGLYPSAPLLYIGRTQYTVTMYDPRSQALRWNTTYRGYSA
            KLPFTIPELV ASPCRSSDG+LY G+KQD W++VD  +G+KQ  LS+   + L PS  LLY+GRT+YT+TM+D +S+ LRWN TY  Y+A
ERN1_monDom KLPFTIPELVQASPCRSSDGILYMGKKQDIWYVVDLMTGEKQQTLSSAFAESLCPSTSLLYLGRTEYTITMFDTKSRELRWNATYFDYAA

The first alignment shows ERN2 orthologs in vertebrates, the second as difference relative to opossum, the third ERN1 orthologs.
The ancestral nature of the CpG hotspot is shown in nucleotides in the final columns.

                            ^     *                                ^     *                                 ^     *  
ERN2_homSap  KLPFTIPELVHASPCRSSDGVFYT   ERN2_homSa  .....................F..   ERN1_homSap  KLPFTIPELVQASPCRSSDGILYM  CG Human
ERN2_panTro  KLPFTIPELVHASPCRSSDGVFYT   ERN2_panTr  .....................F..   ERN1_panTro  KLPFTIPELVQASPCRSSDGILYM  CG Chimp
ERN2_ponAbe  KLPFTIPELVHASPCRSSDGVFYT   ERN2_ponAb  .....................F..   ERN1_ponAbe  KLPFTIPELVQASPCRSSDGILYM  -- Gorilla
ERN2_rheMac  KLPFTIPELVHASPCRSSDGVFYT   ERN2_rheMa  .....................F..   ERN1_rheMac  KLPFTIPELVQASPCRSSDGILYM  CG Orangutan
ERN2_calJac  KLPFTIPELVHASPCRSSDGVFYT   ERN2_calJa  .....................F..   ERN1_calJac  KLPFTIPELVQASPCRSSDGILYM  CG Rhesus
ERN2_tarSyr  KLPFTIPELVHASPCRSSDGVFYT   ERN2_tarSy  .....................F..   ERN1_tarSyr  KLPFTIPELVQASPCRSSDGILYM  CG Marmoset
ERN2_micMur  KLPFTIPELVHASPCRSSDGVFYT   ERN2_micMu  .....................F..   ERN1_micMur  KLPFTIPELVQASPCRSTDGILYM  CG Tarsier
ERN2_tupBel  KLPFTIPELVHASPCRSSDGVFYT   ERN2_tupBe  .....................F..   ERN1_otoGar  KLPFTIPELVQASPCRSSDGILYM  CG Mouse_lemur
ERN2_musMus  KLPFTIPELVHASPCRSSDGVFYT   ERN2_musMu  .....................F..   ERN1_tupBel  KLPFTIPELVQASPCRSSDGILYM  -- Bushbaby
ERN2_ratNor  KLPFTIPELVHASPCRSSDGVFYT   ERN2_ratNo  .....................F..   ERN1_musMus  KLPFTIPELVQASPCRSSDGILYM  CG TreeShrew
ERN2_cavPor  KLPFTIPELVHTSPCRSSDGVFYT   ERN2_cavPo  ...........T.........F..   ERN1_ratNor  KLPFTIPELVQASPCRSSDGILYM  CG Mouse
ERN2_speTri  KLPFTIPELVHASPCRSSDGVFYT   ERN2_speTr  .....................F..   ERN1_dipOrd  KLPFTIPELVQASPCRSSDGILYM  CG Rat
ERN2_oryCun  KLPFTIPELVHASPCRSSDGVFYT   ERN2_oryCu  .....................F..   ERN1_cavPor  KLPFTIPELVQASPCRSSDGILYM  -- Kangaroo_rat
ERN2_ochPri  KLPFSIPELVHASPCRSSDGVFYT   ERN2_ochPr  ....S................F..   ERN1_speTri  KLPFTIPELVQASPCRSSDGILYM  CG Guinea_pig
ERN2_turTru  RLPFTIPELVHASPCRSSDGVFYT   ERN2_turTr  R....................F..   ERN1_oryCun  KLPFTIPELVQASPCRSSDGILYM  CG Squirrel
ERN2_bosTau  RLPFTIPELVHASPCRSSDGVFYT   ERN2_bosTa  R....................F..   ERN1_vicPac  KLPFTIPELVQASPCRSSDGILYM  CG Rabbit
ERN2_equCab  KLPFTIPELVHASPCRSSDGVFYT   ERN2_equCa  .....................F..   ERN1_turTru  KLPFTIPELVQASPCRSSDGILYM  CG Pika
ERN2_felCat  RLPFTIPELVHASPCRSSDGVFYT   ERN2_felCa  R....................F..   ERN1_bosTau  KLPFTIPELVQASPCRSSDGILYM  -- Alpaca
ERN2_canFam  KLPFTIPELVHASPCRSSDGVFYT   ERN2_canFa  .....................F..   ERN1_equCab  KLPFTIPELVQASPCRSSDGILYM  CG Dolphin
ERN2_myoLuc  KLPFTIPELVHASPCRSSDGVFYT   ERN2_myoLu  .....................F..   ERN1_canFam  KLPFTIPELVQASPCRSSDGILYM  CG Cow
ERN2_eriEur  KLPFTVPELVHTSPCRSSDGVFYT   ERN2_eriEu  .....V.....T.........F..   ERN1_myoLuc  KLPFTIPELVQASPCRSSDGILYM  CG Horse
ERN2_sorAra  KLPFTIPELVHASPCRSSDGVFYT   ERN2_sorAr  .....................F..   ERN1_pteVam  KLPFTIPELVQASPCRSSDGILYM  CG Cat
ERN2_loxAfr  KLPFTIPELVHASPCRSSDGVFYT   ERN2_loxAf  .....................F..   ERN1_eriEur  KLPFTIPELVQASPCRSSDGILYM  CG Dog
ERN2_echTel  KLPFTIPELVLASPCRSSDGVFYT   ERN2_echTe  ..........L..........F..   ERN1_sorAra  KLPFTIPELVQASPCRSSDGILYM  CG Microbat
ERN2_dasNov  KLPFTIPELVHTSPCRSSDGIFYT   ERN2_dasNo  ...........T........IF..   ERN1_loxAfr  KLPFTIPELVQASPCRSSDGILYM  -- Megabat
ERN2_monDom  KLPFTIPELVHASPCRSSDGVLYT   ERN2_monDo  KLPFTIPELVHASPCRSSDGVLYT   ERN1_proCap  KLPFTIPELVQASPCRSSDGILYM  CG Hedgehog
ERN2_macEug  KLPFTIPELVHASPCRSSDGVFYT   ERN2_macEu  .....................F..   ERN1_echTel  KLPFTIPELVQASPCRSSDGILYM  CG Shrew
ERN2_sarHar1 KLPFTIPELVQASPCRSSDGIFYM   ERN2_sarHa  ..........Q.........IF.M   ERN1_dasNov  KLPFTIPELVQASPCRSSDGILYM  -- Elephant
ERN2_sarHar2 KLPFTIPELVQASPCHSSDGIFYM   ERN2_sarHa  ..........Q....H....IF.M   ERN1_choHof  KLPFTIPELVQASPCRSSDGILYM  -- Rock_hyrax
ERN2_ornAna  KLPFTIPELVQSSPCRSSDGILYT   ERN2_ornAn  ..........QS........I...   ERN1_monDom  KLPFTIPELVQASPCRSSDGILYM  CG Tenrec
ERN2_anoCar  KLPFTIPELVQSSPCRSSDGIIYT   ERN2_anoCa  ..........QS........II..   ERN1_ornAna  KLPFTIPELVHASPCRSSDGILYM  CG Armadillo
ERN2_taeGut  KLPFTIPELVQSSPCRSSDGVLYT   ERN2_taeGu  ..........QS............   ERN1_galGal  KLPFTIPELVQASPCRSSDGILYM  CG Opossum
ERN2_galGal  KLPFTIPELVQASPCRSSDGILYM   ERN2_galGa  ..........Q.........I..M   ERN1_taeGut  KLPFTIPELVQASPCRSSDGILYM  CG Platypus
ERN2_xenTro  KLPFTIPELVQSSPCRSSDGILYT   ERN2_xenTr  ..........QS........I...   ERN1_anoCar  KLPFTIPELVQASPCRSSDGILYM  CG Lizard
ERN2_xenLae  KLPFTIPELVQSSPCRSSDGILYT   ERN2_xenLa  ..........QS........I...   ERN1_xenTro  KLPFTIPELVQSSPCRSSDGILYT  CG Tetraodon
ERN2_tetNig  KLPFTIPELVQASPCRSSDGVLYM   ERN2_tetNi  ..........Q............M   ERN1_tetNig  KLPFTIPELVQASPCRSSDGVLYM  CG Fugu
ERN2_takRub  KLPFTIPELVQASPCRSSDGVLYM   ERN2_takRu  ..........Q............M   ERN1_takRub  KLPFTIPELVQASPCRSSDGVLYM  CT Stickleback
ERN2_gasAcu  KLPFTIPDLVQSAPCRSSDGILYT   ERN2_gasAc  .......D..QSA.......I...   ERN1_gasAcu  KLPFTIPELVQASPCRSSDGVLYM  CT Medaka
ERN2_oryLat  KLPFTIPELVQSAPCRSSDGILYT   ERN2_oryLa  ..........QSA.......I...   ERN1_oryLat  KLPFTIPELVQASPCRSSDGVLYM  CG Lamprey
ERN2_calMil  KLPFTIPELVQSSPCRSSDGILYT   ERN2_calMi  ..........QS........I...   ERN1_danRer  KLPFTIPELVQASPCRSSDGILYM  
ERN2_petMar  KLPFTIPELVHASPCRTSDGVLYT   ERN2_petMa  ................T.......    
ERN_braFlo   KLPFTIPELVNASPCKSSDGILYT   ERN_braFlo  ..........N....K....I...

Case of MGAT5

chr4_4859 MGAT5 12 
>contig00001  length=538   numreads=5 21 C=2(61) Y=2(56)
LFVGLGFPYEGPAPLEAIANGCAFLNVKFNPPKSSKNTDFFIGKPTLRE
.................................................
                     ^
Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in two
tasmanian  devil (here one is identical and the other differs from Monodelphis by C->Y) and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler (the official 454 assembler).

Pseudogene issues: No processed pseudogenes relevent to this exon are seen by Blat of human and opossum sequence. Some questionable sequence occurs in tarsier and sloth but may be due to low coverage read or assembly error. These fragmentary sequences also have cysteine at the position in question.

Paralog issues: This gene has a moderately similar paralog, MGAT5B, with a similar enzymatic role (beta1,6-N-acetylglucosaminyltransferase). The opossum MGAT5B protein differs at 12 positions out of 49 from opossum MGAT5, whereas human and marsupial MGAT5A differ at one residue. Consequently the two paralogs are readily distinguished within vertebrates. This is moot because 33 of 33 available MGAT5B also have cysteine at the position in question (data not shown).

Homoplasy (recurrent mutation) issues: The alignments below show tyrosine has never replaced cysteine in any other species. This cysteine is extremely invariant in both paralogs, tracing back to lophotrochozoa and cnidaria.

Known variations: No human disease alleles have been mapped to either paralog. None of 9 SNP tracks at the UCSC browser show human variation in this exon.

Side issues: The column marked with an asterisk in the difference alignment below indicates a non-conservative phyloSNP K-->I that occured in the theran mammal stem after platypus divergence. All three marsupial sequences including tasmanian devil have isoleucine in this position as do all 30 of the available placental mammal sequences, suggesting that both the lysine and the isoleucine continue to be under strong selection. No comparable shift occured in the theran stem for MGAT5B where the residue is arginine in all species, a basic residue similar to lysine.

Structural significance: The MGAT5 gene supposedly encodes a conventional enzyme, mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase involved in the synthesis of protein-bound and lipid-bound oligosaccharides. Yet surprisingly, no determined 3D structure exists at PDB relevent to the configuration of this exon -- nor indeed the large 741 residue protein. This is very peculiar because glycosyl transerfases are a well-studied group of enzymes (nearly 100 loci in human) and might be expected to bind UDP-GlcNAc (like MGAT4A or MGAT3).

Only a small region of the protein have a prediction at ModBase using 2f9fA, a remote mannosyltransferasee from Archaeoglobus fulgidus. Luckily the model covers the cysteine at issue, showing two helices and a beta sheet.

SwissProt does not annotate the cysteine at position 532 as part of a disulfide or active site; the predicted location (Golgi) can have homodimer disulfides of similar enzymes, though this is a complex topic. Although all 20 cysteines in this protein are conserved human to opossum, this could be a consequence of the overall sequence identity of 90%. Twelve of the cysteines, not including the Sarcophilus variant, are found in the last 140 residues, perhaps forming a disulfide knot. All but 1 of these cysteines is conserved in the pre-Bilateran anemone Nematostella (which enriches relative to overall percent identity of 43%).

Highest MGAT5 expression occurs in brain, heart, kidney, and placenta. No domains other than a signal peptide and 6 of its own glycosylation target sites are found by online tools such as SMART.

Although the bulky tyrosine substitution is conservative in the sense of polar nature and perhaps hydrogen-bonding capacity, it cannot replace these specialized functions of cysteine. Considering the extreme conservation of this cysteine, this substitution must have a substantial-- perhaps even disabling -- impact on enzymatic function.

Functional significance: In view of the facial tumor situation in tasmanian devils, OMIM's account of prior research in mouse on this gene is quite interesting. Less is known about MGAT5B though it also functions in the synthesis of complex cell surface N-glycans.

" Malignant transformation is accompanied by increased beta-1,6-GlcNAc branching of N-glycans attached to Asn-X-Ser/Thr sequences in mature glycoproteins... The amount of MGAT5 products correlates with disease progression... Mgat5-deficient mice, which are born healthy but develop various abnormalities as adults...Mgat5-deficient mice showed kidney autoimmune disease, enhanced delayed-type hypersensitivity, and increased susceptibility to experimental autoimmune encephalomyelitis...The Golgi enzyme beta1,6 N-acetylglucosaminyltransferase V (Mgat5) is up-regulated in carcinomas and promotes the substitution of N-glycan with poly N-acetyllactosamine, the preferred ligand for galectin-3 (Gal-3)...inhibitors of MGAT5 might be useful in the treatment of malignancies by targeting their dependency on focal adhesion signaling for growth and metastasis."

                                   ^                                                  ^                   *
MGAT5_homSap  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  homSap
MGAT5_panTro  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  panTro
MGAT5_gorGor  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  gorGor
MGAT5_ponAbe  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  ponAbe
MGAT5_rheMac  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  rheMac
MGAT5_calJac  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  calJac
MGAT5_micMur  LFVGLGFPYEGPAPLEAIANGCAFLNPKFSPPKSSKNTDFFIGKPTLRE  .............................S...................  micMur
MGAT5_otoGar  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  otoGar
MGAT5_tupBel  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  tupBel
MGAT5_musMus  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  musMus
MGAT5_ratNor  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  ratNor
MGAT5_criGri  LFVGLGFPYEGPAPLEAIANGCAFLNPKFSPPKSSKNTDFFIGKPTLRE  .............................S...................  criGri
MGAT5_dipOrd  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  dipOrd
MGAT5_cavPor  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  cavPor
MGAT5_speTri  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  speTri
MGAT5_oryCun  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  oryCun
MGAT5_ochPri  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  ochPri
MGAT5_vicPac  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  vicPac
MGAT5_susScr  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  susScr
MGAT5_turTru  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  turTru
MGAT5_bosTau  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  bosTau
MGAT5_equCab  LFAGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  ..A..............................................  equCab
MGAT5_felCat  lfvgLGFPYEGPAPLEAIANGCAFLNPKFSPPKSSKNTDFFIGKPTLRE  .............................S...................  felCat
MGAT5_canFam  LFVGLGFPYEGPAPLEAIANGCAFLNPKFSPPKSSKNTDFFIGKPTLRE  .............................S...................  canFam
MGAT5_myoLuc  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  myoLuc
MGAT5_eriEur  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  eriEur
MGAT5_sorAra  LFVGLGFPYEGPAPLEAIANGCAFLNPKFSPPKSSKNTDFFIGKPTLRE  .............................S...................  sorAra
MGAT5_loxAfr  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  loxAfr
MGAT5_proCap  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  proCap
MGAT5_echTel  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRE  .................................................  echTel
MGAT5_monDom  LFVGLGFPYEGPAPLEAIANGCAFLNVKFNPPKSSKNTDFFIGKPTLRE  ..........................V......................  monDom
MGAT5_macEug  LFVGLGFPYEGPAPLEAIANGCAFLNVKFNPPKSSKNTDFFIGKPTLRE  ..........................V......................  macEug
MGAT5_sarHar1 LFVGLGFPYEGPAPLEAIANGCAFLNVKFNPPKSSKNTDFFIGKPTLRE  ..........................V......................  sarHar1
MGAT5_sarHar2 LFVGLGFPYEGPAPLEAIANGYAFLNVKFNPPKSSKNTDFFIGKPTLRE  .....................Y....V......................  sarHar2
MGAT5_ornAna  LFVGLGFPYEGPAPLEAIANGCAFLNLKFNPPKSSKNTDFFKGKPTLRE  ..........................L..............K.......  ornAna
MGAT5_galGal  LFVGLGFPYEGPAPLEAIANGCAFLNLRFNPPKSSKNTEFFKGKPTLRE  ..........................LR..........E..K.......  galGal
MGAT5_taeGut  LFVGLGFPYEGPAPLEAIANGCAFLNLRFNPPKSSKNTDFFKGKPTLRE  ..........................LR.............K.......  taeGut
MGAT5_anoCar  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFKGKPTLRE  .........................................K.......  anoCar
MGAT5_xenTro  LFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSRNTDFFKGKPTLRE  ...................................R.....K.......  xenTro
MGAT5_tetNig  VFVGLSFPYEGPAPLEALANGCIFLNPRLKPPQSSLNSEFFKEKPNIRE  V....S...........L....I....RLK..Q..L.SE..KE..NI..  tetNig
MGAT5_takRub  LFVGLSFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFKGKPTLRE  .....S...................................K.......  takRub
MGAT5_gasAcu  LFVGLSFPYEGPAPLEAIANGCAFLNPKFSPAKSSKNTDFFKGKPTLRE  .....S.......................S.A.........K.......  gasAcu
MGAT5_oryLat  LFVGLSFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFKGKPTLRE  .....S...................................K.......  oryLat
MGAT5_danRer  LFVGLSFPYEGPAPLEAIANGCAFLNPRFDPAKSSKNTDFFKGKPTLRE  .....S.....................R.D.A.........K.......  danRer
MGAT5_oncMyk  LFVGLSFPYEGPAPLEAIANGCAFLNPKFTPPKSSKNTDFFKGKPTLRE  .....S.......................T...........K.......  oncMyk
MGAT5_pimPro  LFVGLSFPYEGPAPLEAIANGCAFLNPRFDPSKSSKNTDFFKGKPTLRE  .....S.....................R.D.S.........K.......  pimPro
MGAT5_calMil  LFVGLGFPYEGPAPLEAIANGCAFLNPRFNPPKSSKNTEFFKGKPTLRE  ...........................R..........E..K.......  calMil
MGAT5_petMar  LFVGLGFPYEGPAPLEAIANGCVFLNPRFRPPKSSKNTDFFKGKPTLRE  ......................V....R.R...........K.......  petMar
MGAT5_braFlo  LFVGLGFPYEGPAPLEAIASGCVFLNPKFTQPKSRLNTKFFEGKPTFRE  ...................S..V......TQ...RL..K..E....F..  braFlo
MGAT5_strPur  LFIGLGFPYEGPAPLEAVANGCVFLNPKFNPPKNYQNTKFFQGKPTSR.
MGAT5_helRob  LFIGLGFPYEGPAPLEAIAAGCVFINPKFNPPHSSLNTKFFKGKPTARE
MGAT5_nemVec  VFIGLGFPYEGPAPLEAIQSGCVFLNAKFDPPHDRVNTPFFKNKPTLRK

Note: the species with unfamiliar genSpp acronyms are Cricetulus griseus, Oncorhynchus mykiss, Pimephales promelas , Callorhinchus milii, Branchiostoma floridae, Strongylocentrotus purpuratus, Helobdella robusta, Nematostella vectensis, and Acropora millepora.

Here the opossum protein is broken into its 16 coding exons with phases (base overhangs at split codons) shown:

>MGAT5_monDom length=743
0 MAFFAPWKLSSQKLGFFLVTFGFIWGMMLLHFTIQQRTQHESSSMLREQILDLSKRYIKALAEENRNVVDGPYVGVMTAY 1
2 DLKKTLAVLLDNILQRIGKLESKVDNLVINGTGANSTNTTTTAAPSSIAAFEKISVA 1
2 DIINGAQEKCELPPMDGFPHCEGKIK 0
0 WMKDMWRTDPCYANYGVDGSTCSFFIYLSE 0
0 VENWCPHLPWRAKNPYEEPDQNSM 0
0 AEIRTDFNLLYGMMKRHEEFRWMILRIRRMADAWIEAIKSLAEKQNLEKRKRKK 0
0 ILVHLGLLTKESGFKIAENAFSGGPLGELVQWSDLITSLYLLGHDIRISASLAELKE 2
1 IMKRVVGNRSGCPTVGDRIVELIYIDIVGLAQFKKTLGPSWVHYQ 2
1 CMLRVLDSFGTEPEFNHANYAQSKGHKTPWGKWNLNPQQFYTMF 1
2 PHTPDNSFLGFVVEQHLNSSDIKHINEIKRQNQSLVYGKVDSFWK 0
0 NKKEYLDIIHTYMEVHATVYGSSTNHMPSYVKNHGILSGRDLQFLLRETK 0
0 LFVGLGFPYEGPAPLEAIANGCAFLNVKFNPPKSSKNTDFFIGKPTLRE 0
0 LTSQHPYAEVFIGRPHVWTVNPTDHREVENAVKAILNQK 0
0 IEPYMPYEFTCEGMLQRMNAFIEKQ 0
0 DFCHGQVMWPPLNALQVKLSEPGKSCKQVCQENQLICEPSFFQHLNKDKDVLK 2
1 YEVICHTTELANDILVPSYDDKKKHCVFQGDLLLFSCAGAHPKHKRICPCRDYIKGQVALCQDCL* 0

>MGAT5_sacHar Sarcophilus harrisii (tasmanian_devil) one match to exon 1: FPUIIJ301C96S1
0 MAFFAPWKLSSQN*GFSWLTFGFIWGMMLLHFTIQQRTQHESSSMLREQILDLSKRYIKALAEENRNVVDGPYVGVMTAY 1
2 DLKKTLAVLLDNILQRIGKLESKVDNLVINGTGANSTNTTTTAVPSSIAAFEKIsVA 1
2 DIINGAQEKCELPPMDGFPHCEGKIK 0
0  0
0  0
0 AEIRTDFHLLYGMMKRHEEFRWMILRIRRMADAWIEAIKSLAEKQNLEKRKRKK 0
0 ILVHLGLLTKESGFKIAENAFSGGPLGELVQWSDLITSLYLLGHDIRISASLAELKE 2
1 IMKRVVGNRSGCPTVGDRIVELIYIDIVGLAQFKKTLGPSWVHYQ 2
1 CMLRVLDSFGTEPEFNHANYAQSKGHKTPWGKWNLNPQQFYTMF 1
2 AHTPDNSFLGFVVEQHLNSSDIKHINEIKRQNQSLVYGKVDNFWK 0
0 NKKEYLDIIHTYMEVHATVYGSSTNHMPSYVKNHGILSGRDLQFLLRETK 0
0 LFVGLGFPYEGPAPLEAIANGYAFLNVKFNPPKSSKNTDFFIGKPTLRE 0
0  0
0 IEPYMPYEFTCEGMLQRMNAFIEKQ 0
0  2
1 YEVVCHTTELANDILVPSYDDRKKHCVFQGDLLLFSCAGAHPKHKRICPCRDYIKGQVALCQDCL* 0

The premature stop codon in the first exon is likely read error (1 bp dropped, 1 bp later added):

atggctttctttgctccatggaaattatcctctcagaaactagggtttttcctggtgact
 M  A  F  F  A  P  W  K  L  S  S  Q  K  L  G  F  F  L  V  T    correct monDom frame
  W  L  S  L  L  H  G  N  Y  P  L  R  N  -  G  F  S  W  -  L   6 residue observed frameshifts in sarHar N*GFSWL
   G  F  L  C  S  M  E  I  I  L  S  E  T  R  V  F  P  G  D  F  irrelevent 3rd reading frame

MGAT5 has 16 exons. The key one here is 12. Alignment of MGAT5_sarHar to opossum shows only 5 differences in 589 residues available for comparison. 
Alignment of Monodelphis to human establishes that MGAT5 is better conserved than the average gene: 

Identities = 673/744 (90%), Positives = 708/744 (95%), Gaps = 2/744 (0%)

monDo  1     MAFFAPWKLSSQKLGFFLVTFGFIWGMMLLHFTIQQRTQHESSSMLREQILDLSKRYIKA  60
             MA F PWKLSSQKLGFFLVTFGFIWGMMLLHFTIQQRTQ ESSSMLREQILDLSKRYIKA
homSa  146   MALFTPWKLSSQKLGFFLVTFGFIWGMMLLHFTIQQRTQPESSSMLREQILDLSKRYIKA  325

monDo  61    LAEENRNVVDGPYVGVMTAYDLKKTLAVLLDNILQRIGKLESKVDNLVINGTGANSTNTT  120
             LAEENRNVVDGPY GVMTAYDLKKTLAVLLDNILQRIGKLESKVDNLV+   G  + +T 
homSa  326   LAEENRNVVDGPYAGVMTAYDLKKTLAVLLDNILQRIGKLESKVDNLVV--NGTGTNSTN  499

monDo  121   TTAAPSSIAAFEKISVADIINGAQEKCELPPMDGFPHCEGKIKWMKDMWRTDPCYANYGV  180
             +T A  S+ A EKI+VADIINGAQEKC LPPMDG+PHCEGKIKWMKDMWR+DPCYA+YGV
homSa  500   STTAVPSLVALEKINVADIINGAQEKCVLPPMDGYPHCEGKIKWMKDMWRSDPCYADYGV  679

monDo  181   DGSTCSFFIYLSEVENWCPHLPWRAKNPYEEPDQNSMAEIRTDFNLLYGMMKRHEEFRWM  240
             DGSTCSFFIYLSEVENWCPHLPWRAKNPYEE D NS+AEIRTDFN+LY MMK+HEEFRWM
homSa  680   DGSTCSFFIYLSEVENWCPHLPWRAKNPYEEADHNSLAEIRTDFNILYSMMKKHEEFRWM  859

monDo  241   ILRIRRMADAWIEAIKSLAEKQNLEKRKRKKILVHLGLLTKESGFKIAENAFSGGPLGEL  300
              LRIRRMADAWI+AIKSLAEKQNLEKRKRKK+LVHLGLLTKESGFKIAE AFSGGPLGEL
homSa  860   RLRIRRMADAWIQAIKSLAEKQNLEKRKRKKVLVHLGLLTKESGFKIAETAFSGGPLGEL  1039

monDo  301   VQWSDLITSLYLLGHDIRISASLAELKEIMKRVVGNRSGCPTVGDRIVELIYIDIVGLAQ  360
             VQWSDLITSLYLLGHDIRISASLAELKEIMK+VVGNRSGCPTVGDRIVELIYIDIVGLAQ
homSa  1040  VQWSDLITSLYLLGHDIRISASLAELKEIMKKVVGNRSGCPTVGDRIVELIYIDIVGLAQ  1219

monDo  361   FKKTLGPSWVHYQCMLRVLDSFGTEPEFNHANYAQSKGHKTPWGKWNLNPQQFYTMFPHT  420
             FKKTLGPSWVHYQCMLRVLDSFGTEPEFNHANYAQSKGHKTPWGKWNLNPQQFYTMFPHT
homSa  1220  FKKTLGPSWVHYQCMLRVLDSFGTEPEFNHANYAQSKGHKTPWGKWNLNPQQFYTMFPHT  1399

monDo  421   PDNSFLGFVVEQHLNSSDIKHINEIKRQNQSLVYGKVDSFWKNKKEYLDIIHTYMEVHAT  480
             PDNSFLGFVVEQHLNSSDI HINEIKRQNQSLVYGKVDSFWKNKK YLDIIHTYMEVHAT
homSa  1400  PDNSFLGFVVEQHLNSSDIHHINEIKRQNQSLVYGKVDSFWKNKKIYLDIIHTYMEVHAT  1579

monDo  481   VYGSSTNHMPSYVKNHGILSGRDLQFLLRETKLFVGLGFPYEGPAPLEAIANGCAFLNVK  540
             VYGSST ++PSYVKNHGILSGRDLQFLLRETKLFVGLGFPYEGPAPLEAIANGCAFLN K
homSa  1580  VYGSSTKNIPSYVKNHGILSGRDLQFLLRETKLFVGLGFPYEGPAPLEAIANGCAFLNPK  1759

monDo  541   FNPPKSSKNTDFFIGKPTLRELTSQHPYAEVFIGRPHVWTVNPTDHREVENAVKAILNQK  600
             FNPPKSSKNTDFFIGKPTLRELTSQHPYAEVFIGRPHVWTV+  +  EVE+AVKAILNQK
homSa  1760  FNPPKSSKNTDFFIGKPTLRELTSQHPYAEVFIGRPHVWTVDLNNQEEVEDAVKAILNQK  1939

monDo  601   IEPYMPYEFTCEGMLQRMNAFIEKQDFCHGQVMWPPLNALQVKLSEPGKSCKQVCQENQL  660
             IEPYMPYEFTCEGMLQR+NAFIEKQDFCHGQVMWPPL+ALQVKL+EPG+SCKQVCQE+QL
homSa  1940  IEPYMPYEFTCEGMLQRINAFIEKQDFCHGQVMWPPLSALQVKLAEPGQSCKQVCQESQL  2119

monDo  661   ICEPSFFQHLNKDKDVLKYEVICHTTELANDILVPSYDDKKKHCVFQGDLLLFSCAGAHP  720
             ICEPSFFQHLNKDKD+LKY+V C ++ELA DILVPS+D K KHCVFQGDLLLFSCAGAHP
homSa  2120  ICEPSFFQHLNKDKDMLKYKVTCQSSELAKDILVPSFDPKNKHCVFQGDLLLFSCAGAHP  2299

monDo  721   KHKRICPCRDYIKGQVALCQDCL*  744
             +H+R+CPCRD+IKGQVALC+DCL 
homSa  2300  RHQRVCPCRDFIKGQVALCKDCL*  2371

Full length genes appear available from GenBank and genome projects for mouse, rat (NM_001107068), dog (wgs exons), horse (XM_001489091), wallaby (wgs exons), and platypus (XM_001520380). Because this gene is 90% conserved at marsupial, placental mammals will not be informative -- indeed it is necessary to go to greater phylogenetic depth than lamprey to define the ultra-conserved residues in this protein:

>MGAT5_macEug nearly identical to monDom; 3 exons are missing, 2 partial exons, exon 4 has frameshifts 
0 MAFFAPWKLSSQKLGFFL   1
2 DLKKTLAVLLDNILQRIGKLESKVDNLVINGTGANSTNTTTTAVPSSIAAFEKISVA 1
2 DIINGAQEKCELPPMDGFPHCEGKIK 0
0 WMKDiWRTDPCYANYGVDGSTCSFFIYLSE 0
0 VENWCPHLPWRAKNPYEEPDQNSM 0
0 0
0 ILVHLGLLTKESGFKIAENAFSGGPLGELVQWSDLITSLYLLGHDIRISASLAELKE 2
1 2
1    GTEPEFNHANYAQSKGHKTP    1
2 aHTPDNSFLGFVVEQHLNSSDIKHINEIKRQNQSLVYGKVDSFWK 0
0 NKKEYLDIIHTYMEVHATVYGSSTNHMPSYVKNHGILSGRDLQFLLRETK 0
0 LFVGLGFPYEGPAPLEAIANGCAFLNVKFNPPKSSKNTDFFIGKPTLRE 0
0 LTSQHPYAEVFIGRPHVWTVNPTDHREVENAVKAILNQK 0
0 IEPYMPYEFTCEGMLQRMNAFIEKQ 0
0 DFCHGQVMWPPLNALQVKLSEPGKSCKQVCQENQLICEPSFFQHLNKDKDVLK 2
1 YEVICHTTELANDILVPSYDDKKKHCVFQGDLLLFSCAGAHPKHKRICPCRDYIKGQVALCQDCL* 0

>MGAT5_galGal 87% identical to opossum
MAFPWKLSSQKLGFFLVTFGFIWGMMLLHFTIQQQTQHESSSVLREQILDLSKRYIKALAEENKNVVDGPYVGTVTAY
DLKKTLAVLLDNILQRIGKLESKVENLVLNGTGANSTNTTTPAPSLGAVEKLNVA
DLINGAQEQCELPPMDGFPHCEGKIK
WMKDMWRSDPCYASYGVDGSTCSFFIYLSE
VENWCPRLPWRAKNPNEETDQKTV
AEIRINFDPLYKMMSRHEEFRWMTLRIRRMADTWIEAIKSLAEKQNLENRKRKK
ILVHLGLLTKESGFKIAENAFSGGPLGELVQWSDLITSLYLLGHDIRISASLAELKE
IMKKVVGNRSGCPTQGDKVVELIYIDIVGLTQFKKTLGPSWVHYQ
CMLRVLDSFGTEPEFNHAHYAQSKGHKTPWGKWNLNPQQFYTMF
PHTPDNSFLGFVVEQHLNSSDIKHINDIKRQNQSLVYGKVDNFWK
DKKAYLDVIHTYMEVHGTVHGTSTIYIPGYVKNHGILSGRDLQFLLRETK
LFVGLGFPYEGPAPLEAIANGCAFLNLRFNPPKSSKNTEFFKGKPTLRE
LTSQHPYAEVYIGKPHVWTVDINNLSEVEKAVKSILNQK
IDPYLPYEFTCEGMLQRMNAFIERQ
DFCHGQVMWPPLSALQVKLAEPGKSCKQVCQESQLICEPSFFQHLNKDKALLK
HNIECLTTESANDILVPSFDGRRKHCVFQGDLLLFSCAGSHPTHRRICPCRDYIKGQVALCKDCL*

>MGAT5_nemVec Nematostella vectensis (sea anemone) XM_001641404 43% identical to opossum 19 of 20 cysteines conserved
MIATKGRPTFKLSAHRIGIVFIIISFIWGLYLIKIQLDERNSQPDYLKGRIIHLSKEYIRALAREKGVYGIDGQPSTQQGVGDLKKATAVLLQSMLERIHVL
EKQVEGVIVNSTLEFEILASQIKSLNTTFSLHLSNHSYVSANSCVIPDDPSYPECRQKVMWMRNFWKTHECYAKDHGVNGTICSFLVYLSEVENWCPKFPGRMKPTSRATTEGADL
HRSDVQGLLGLLNDQDPIKFKWIKNRINQMWPQWLSALEDLKKKRDLKKIKQKKILVHIGLLANERALHFAANADKGGPLGELVQWSDLIASLYLLGHDVTVTADIPRLQGIFGKL
RGPAKKPCPTTIKNDYDLIYLDYYGVKQMQTKVGQFTQSFKCKFRIVDSFGTEAQFNYAGFTEKVPGGSMALWGRHNLNLKQFMTMFPHSPDNSFLGFVVGEEPTPDPHPKKKKAR
ALVYGKHYYMWKDLKQRSFLDVINKYMEIHATVGGGIKKWVPSYVINHGVLPSLEVQKLLQDSMIFVGLGFPYEGPAPLEAIAHGCFFLNTKYHPPRNRINTPFFKDKPTLRQITS
QHPYAEDYIGQPYVYTVDINDLNKIEAVMKEIMMAEPVSPYLPYEFTHKGMLERLHVFIENQNFCGQNLWPPLNALQARKGAMGSSCKETCHSLGLVCEPQYFPAINTKERMTRSG
FPCNTTRVEDMPSLVAPGYRDDPPVCLRQAQNLLFSCTANSPTTKRLCPCRDFKKGQVALCSKC*

Case of ACTL6B

chr2_18546 ACTL6B 11  
>contig00001 length=502 numreads=11
GLSGNTMLGVGHVVTTSIGMCDIDIRP
...........................
   ^
3 G=4(94) R=7(213)

Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in
tasmanian  devil (in this case, one individual differs from Monodelphis by G->R), then differences between the two thylacines, and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler.

The change from small non-polar glycine to bulky positively charged lysine is highly non-conservative, especially at a highly conserved residue such as this. Again the change in Sarcophilus is at a CpG hotspot, this time with a mildly unusual transversion of the C to the purine G.

The well-studied protein here is a member of a family of actin-related proteins (ARPs) which have significant homology to conventional actins, in particular sharing the actin fold (an ATP-binding cleft) as common feature. ACTL6B and its 83% identical paralog ACTL6A are involved in diverse cellular processes such as vesicular transport, spindle orientation, nuclear migration and chromatin remodeling. Both have 14 coding exons. The entire exon containing the G-->R is highly conserved including the glycine.

Pseudogene issues: Blat of full length sequence to human shows no recent processed or segmental pseudogenes. However opossum assembly, which has all 14 exons, also contains a fairly recent processed pseudogene with 91.5% identity. This locus has internal stop codons and ELSD in place of GLSG for the key glycine. This pseudogene arose from ACTL6A, not ACTL6B.

Paralog issues: There is potential for confusion with the paralog ACTL6A. This wouldn't normally matter because all species in this gene too have glycine at the arginine-substituted site. However its pseudogene could present problems because its decay may have taken a different path in Sarcophilus than in Monodelphis giving the R (instead of D), assuming the pseudogene was formed prior to divergence of these species. Indeed, Macropus eugenii appears to have two processed pseudogenes; one of this has R in place of a glycine 4 residues earlier. It will prove necessary to consider adjacent regions in Sarcophilus reads to determine whether the feature is a pseudogene.

Comparison of gene to pseudogene in opossum:

000000889  E  R  L  R  I  P  E  G  L  F  D  P  S  N  V  K  G  L  S  G  000000948
<<<<<<<<<  |  X  |  K  |  |  |  |  |  |  |  |  |  |  |  |  E  |  |  D  <<<<<<<<<
250390825 gagtgactcaagattcctgaagggttatttgacccatctaatgtgaaggaattgtcagac 250390766

000000949  N  T  M  L  G  V  G  H  V  V  T  T  S  I  G  M  C  D  I  D  000001008
<<<<<<<<<  |  |  |  |  |  |  S  |  |  |  |  |  |  F  |  |  |  |  |  |  <<<<<<<<<
250390765 aacacaatgttgggagtcagtcatgttgttaccacaagctttgggatgtgtgacattgac 250390706

000001009  I  R  P  G  L  Y  G  S  V  I  V  T  G  G  N  T  L  000001059
<<<<<<<<<  F  |  |  |  |  |  D  N  M  L  G  A  |  |  |  I  |  <<<<<<<<<
250390705 tttagaccgggactttatgacaatatgttaggggcgggaggaaacattctg 250390655

Comparison of ACTL6A_homSap gene to pseudogenes in wallaby:

macEu:  1063 FPVGYNCNFGVEQLKITERLFDPSNVKRLSGNPMLGVSHVVTTRIGMCDIDIRPGLYGTV 1242
             FP GYNC+FG E+LKI E LFDPSNVK LSGN MLGVSHVVTT +GMCDIDIRPGLYG+V
homSa:   289 FPNGYNCDFGAERLKIPEGLFDPSNVKGLSGNTMLGVSHVVTTSVGMCDIDIRPGLYGSV 348
 
macEu:    48 PNVYKCGFGAEHFKIPEGLFDRSNMKGLSGNTMLGISHVVTKSTGMCDIDIRPGFYISVI 227
             PN Y C FGAE  KIPEGLFD SN+KGLSGNTMLG+SHVVT S GMCDIDIRPG Y SVI
homSa:   290 PNGYNCDFGAERLKIPEGLFDPSNVKGLSGNTMLGVSHVVTTSVGMCDIDIRPGLYGSVI 349

Homoplasy (recurrent mutation) issues:

Known variations:

Side issues:

Structural significance:

Functional significance:

                  *                            *                                            *
ACTL6B_homSap  GLSGNTMLGVGHVVTTSIGMCDIDIRP  GLSGNTMLGVGHVVTTSIGMCDIDIRP    ACTL6B_homSap GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_panTro  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_panTro GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_gorGor  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_gorGor GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_ponAbe  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_ponAbe GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_rheMac  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_rheMac GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_calJac  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_calJac GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_tarSyr  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_tarSyr GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_micMur  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_micMur GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_otoGar  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_otoGar GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_tupBel  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_tupBel GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_musMus  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_musMus GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_ratNor  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_ratNor GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_dipOrd  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_dipOrd GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_cavPor  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_cavPor GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_ochPri  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_ochPri GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_turTru  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_turTru GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_bosTau  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_bosTau GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_equCab  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_equCab GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_felCat  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_felCat GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_canFam  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_canFam GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_myoLuc  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_myoLuc GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_pteVam  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_pteVam GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_eriEur  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_eriEur GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_loxAfr  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_loxAfr GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_proCap  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_proCap GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_echTel  GLSGNTMLGVGHVVTTSIGMCDNDIRP  ......................N....    ACTL6B_echTel GLSGNTMLGVGHVVTTSIGMCDNDIRP
ACTL6B_monDom  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_monDom GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_ornAna  GLSGNTMLGVSHVVTTSVGMCDIDIRP  ..........S......V.........    ACTL6B_ornAna GLSGNTMLGVSHVVTTSVGMCDIDIRP
ACTL6B_galGal  GLSGNTMLGVSHVVTTSVGMCDIDIRP  ..........S......V.........    ACTL6B_galGal GLSGNTMLGVSHVVTTSVGMCDIDIRP
ACTL6B_taeGut  GLSGNTMLGVSHVVTTSVGMCDIDIRP  ..........S......V.........    ACTL6B_taeGut GLSGNTMLGVSHVVTTSVGMCDIDIRP
ACTL6B_anoCar  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_anoCar GLSGNTMLGVGHVVTTSIGMCDIDIRP
ACTL6B_xenTro  GLSGNTMLGVSHVVTTSVGMCDIDIRP  ..........S......V.........    ACTL6B_xenTro GLSGNTMLGVSHVVTTSVGMCDIDIRP
ACTL6B_tetNig  GLSGNTMLGVSHVVTTSVGMCDIDIRP  ..........S......V.........    ACTL6B_tetNig GLSGNTMLGVSHVVTTSVGMCDIDIRP
ACTL6B_takRub  GLSGNTMLGVSHVVTTSVGMCDIDIRP  ..........S......V.........    ACTL6B_takRub GLSGNTMLGVSHVVTTSVGMCDIDIRP
ACTL6B_gasAcu  GLSGNTMLGVGHVVTTSVGMCDIDIRP  .................V.........    ACTL6B_gasAcu GLSGNTMLGVGHVVTTSVGMCDIDIRP
ACTL6B_oryLat  GLSGNTMLGVGHVVTTSVGMCDIDIRP  .................V.........    ACTL6B_oryLat GLSGNTMLGVGHVVTTSVGMCDIDIRP
ACTL6B_danRer  GLSGNTMLGVGHVVTTSIGMCDIDIRP  ...........................    ACTL6B_danRer GLSGNTMLGVGHVVTTSIGMCDIDIRP
                  *                            *                                            *
Consensus      gLsGnTMlgvgHVVTts!g$CDi.Ir.  gLsGnTMlgvgHVVTts!g$CDi.Ir.  

(more shortly)

Case of IPO7

chr5_9037 IPO7 23 
>contig00001  length=680   numreads=8
SSQVEKHSCSLTEELGSDEDDIDEDGQEYLEILAKQAGEDGDDEEWEEDDAEETALEGYSTIIDDEENPVDEYQIFKAIFQ
....*N.....................................................F.....................
                                                           ^
59 F=2(72) S=3(53)

Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in
tasmanian  devil (in this case, both individuals differ from Monodelphis by  -> ), then differences between the two thylacines
(here one individual has   at position  , the other has  ), and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler (the official 454 assembler) which uses 
lower-case letters for less confident calls.

Pseudogene issues:

Paralog issues:

Homoplasy (recurrent mutation) issues:

Known variations:

Side issues:

Case of WDFY3

chr5_2532 WDFY3 19
>contig00001  length=482   numreads=8
DDFSEESSFYEILPCCARFRCGDLIVEGQWHHLVLVMSKGMLKNSTAALYIDGQLVSTVK
................T..............................T..L.....N...
                ^
16      T=3(117)        A=5(138)

Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in
tasmanian  devil (in this case, both individuals differ from Monodelphis by  -> ), then differences between the two thylacines
(here one individual has   at position  , the other has  ), and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler (the official 454 assembler) which uses 
lower-case letters for less confident calls.

Pseudogene issues:

Paralog issues:

Homoplasy (recurrent mutation) issues:

Known variations:

Side issues:

Structural significance:

Functional significance:

(more shortly)

Case of PPFIA3

chr4_22002 PPFIA3 15  incorrectly mapped from monDom5 to human
>contig00001  length=298   numreads=4
LIQEEKETTEQRAEELESRVSGSGLDSLGRYRASCSLPPSLTTSTLASPSPPSSGHSTPRPAPPSPAREAPANSTSNTAEKP
........................................................F..................G.V.
                                                        ^
 56 F=2(43) S=2(37)

Read data format: the top row gives project gene name, HGNC gene name and exon number from ENSEMBL monDom5
and human orthology predictions, then Monodelphis amino-acid segment, then sequence differences in
tasmanian  devil (in this case, both individuals differ from Monodelphis by  -> ), then differences between the two thylacines
(here one individual has   at position  , the other has  ), and finally the number of experimental reads that confirm the nucleotide
difference and the sum of the quality scores. The sequences were assembled by Newbler (the official 454 assembler) which uses 
lower-case letters for less confident calls.

Pseudogene issues:

Paralog issues:

Homoplasy (recurrent mutation) issues:

Known variations:

Side issues:

Structural significance:

Functional significance:

(more shortly)

Structural significance:

Functional significance:

(more shortly)

Other cases to be considered

chr6_2360 XYLT1 5  61 D=3(110) A=5(107)
>contig00001  length=488   numreads=10
RSNYMHRQVLQFAGQYQNVRVTSWRMATIWGGASLLSTYLQSMRDLMEMTDWPWDFFINLSAADYPI
 ...L........................................................D.....
                                                             ^

chr4_18550 ATP4A 6 16 C=4(130) R=3(74)
>contig00001  length=906   numreads=10
TAQGLVVNTGDRTIIGRIASLASGVENEKTPIAIEIEHFVDIIAGLAILFGATFFIVAMCIGYTFLRAMVFFMAIVVAYVPEGLLATVT
................C........................................................................
                ^

chr4_11174 FLI1 3  32 N=2(63) K=3(47)
>contig00001  length=575   numreads=9
ESPVDCSVNKCSKLVGGNESNPMNYNTYMDEKNGPPPNMTTNERRVIVPA
..................................................
                                ^

chr2_30280 VPS72 5  15 R=3(59) K=2(51)    
>contig00001  length=591   numreads=6
NYERLEADKKKQVHKKRKCPGPVITYHSMTVPLLAEPGPKEENVDVE
...............R..................T............
               ^

chr6_5144 ABCC1 23  4 Q=2(69) P=2(80) looks like a frame-shift problem in monDom5
>contig00001  length=802   numreads=10
HLCFPRLHLDLLHNVLRSPMSFFERTPSGNLVNRFSKEMDTVDSMIPQIIKMFMGSLFNVIGACIIILLATPIAAIIIPPLGLIYFFVQ
....Q....................................................................................
    ^

chr5_8347 SPON1 11  20 V=3(65) I=2(66) wobbly
>contig00001  length=433   numreads=5
GSTCTMSEWITWSPCSISCGVGMRSRERYVKQFPEDGSVCTVPTEETEKCTVNEEC
......................................I.N...............
                    ^

chr3_5872 ACOT12 14 14 I=3(95) V=3(110) wobbly
>contig00001  length=472   numreads=6
NTYVVAVKSVTLASIPPSPQYNRSEITCAGFLIRAVDSNSCT
.................................Q....S...
              ^

Other marsupial genes of interest

The collections below contain well-understood genes with very extensive comparative genomics. They can serve as a test bed for Sarcophilus assembly quality, a place where genuine anomalies or distinct adaptive features might surface (perhaps as phyloSNPs) and where marsupial phylogeny might be refined using rare genomic events in nuclear genes.

The gene sets contain all available marsupial orthologs plus for context one flanking gene each from placentals and monotremes. These genes are available in much broader hand-curated sets elsewhere on this site.

IRBP (96 marsupials)

Interphotoreceptor retinol-binding protein, poorly named by IGNC as RBP3 despite its complete lack of paralogs, is a 4 exon 1247 residue glycoprotein that shuttles retinoids between the photoreceptor cells and the retinal pigment epithelium. The protein's size results from four ancient internal tandem duplictions that became established prior to the intronation era.

The first three homology domains and part of the fourth are all encoded by the first large exon of 1090 amino acids. This exon has been much used in marsupial phylogeny (along with the first intron of transthyretin). Indeed the 96 marsupial species in 51 genera having determined IRBP sequences at GenBank include a Dec 2008 partial sequence for Thylacinus cynocephalus, as well as for Sarcophilus harrisii.

The closest matches to the thylacine IRBP are shown in the difference alignment of the first 60 residues below. These species all lie with the Dasyuromorphia. The indicated E-->K may be one of several phyloSNPs breaking this group into blue and green subclades.

The numbat Myrmecobius fits implausibly (its amino terminal sequence EF028750 needs verification) -- its affinities seem to lie with the Didelphimorphia. Thylacinus is not basal within Dasyuromorphia relative to Myrmecobius using IRBP. However this may be a case of mis-comparison of genes.

  *           *                                     *
STSKAPQHDSKFTNATQEELLALFQQIIKYQVLEGNVGYLRVDYIPGREMIEEVGEFLVN EU091365  0 Thylacinus cynocephalus
.........P..A..................I............................ AY532676  3 Myoictis wallacei
........NP..A............................................... AY532687  3 Neophascogale lorentzii
........NP..A........T...................................... AY532686  4 Phascolosorex dorsalis
.........P..V............................................... AY532670  2 Parantechinus apicalis
....V....P..A..................I.....................L...... AY532675  5 Myoictis melas
.........P..A...................................D........... AY532679  3 Dasyurus hallucatus
...E.....P..A............K........D.............D........... AY532685  6 Sarcophilus harrisii
...E.......RA..........L............................Q..K.... EF028748  6 Sminthopsis crassicaudata
.......R.P.LA.........SL.......................Q....Q....... EF028749  8 Planigale ingrami
..A......P.LA.V.....................................K....... EF028736  6 Antechinus stuartii
..A......P.L..V.....................................K....... EF028743  5 Micromurexia habbema
..A......P.LA.V.....................................K....... EF028744  6 Murexchinus melanurus
..A......P.L..V....V................................K....... EF028746  6 Paramurexia rothschildi
..A......P.LA.V.....................................K....... EF028747  6 Phascogale calura
..A......P.LA.V.....................................K....... EF028745  6 Phascomurexia naso
.SA......P.LA.V.....................................K....... AY532667  7 Murexia longicaudata
......K..PNLA........T.L..R....................Q.VV.K....... EF028750 12 Myrmecobius fasciatus
..PET...VP..A.V........L..M....................Q.VV.K....... AY233765 13 Caluromys philander
..PET...VP.LA.V.......QL..M....................Q.VV.K....... AF257675 15 Caluromysiops irrupta
..PET...VP.LA.V......T.L..M....................Q.VV.K....... AF257688 15 Glironia venusta  
.IPET...VP..A.V.R....T.L..M....................Q.VV.K....... AF257683 16 Didelphis albiventris
.IPE....VP.LA.I......T.L..M....................Q.VV.K....... AF257686 15 Gracilinanus microtarsus
.IPET...VP..A.V......T.L..M....................Q.VV.K....... AF257676 15 Marmosops noctivagus
.IPET...VP.LA.V........L..M....................Q.VV.K....... AY233788 15 Philander opossum
.IPET...VP.LA.I......T.L..M....................Q.VV.K....... AF257689 16 Thylamys pallidior

Using Sarcophilus as probe in a different region, 721-900, we find this peculiar outcome: what appears to be a second very odd gene, XY difference, pseudogene, weird balanced polymorphism, nonhomologous recombination, sequence submission error, frameshifts, or systemic experimental error (eg Dasyurus maculatus AY532680 is identical to AY243439 outside the 15 amino acid block). However the genomic reads from individual Sarcophilus used in this project show no sign of this gene despite excellent coverage of the second type of gene.

Macropus and Monodelphis genomes only contain the second type of gene. All Didelphimorphia and Diprotodontia are of this type, as are platypus and all placentals. With the Sarcophilus genome, this can be resolved as it should have both and be the such first genome. Perhaps the alignment above is a mixture of type 1 and type 2 genes (resp. alleles). The Myrmecobius anomaly makes it more likely two distinct genes are present.

A definite pecularity seen in blast searches is the occurence earlier in the sequence of a very homologous segment for this very block, likely the homologous part of another of the internal tandem repeats. It is seen in both types of genes. Possibly internal non-homologus recombination or gene conversion has inserted first repeat sequence again in this distal block in place of what was relatively diverged sequence. Internal gene conversion would make IRBP extremely difficult to use in alignment-based phylogeny. As rare genomic event, it unites the species that have it but species that don't have it would have to be re-examined to exclude the possiblity that only the type 2 gene happened to be sequenced.

It emerges from direct tblastn that the Sacrophilus individual sequenced was female. That is, ATRX is well represented but not ATRY (though the situation is somewhat confused due to additional paralogs). Marsupial XY are quite different from placentals:

"Many or most genes on the mammal Y chromosome evolved a testis-specific function after diverging from an X-borne copy with a general function in both sexes. In marsupial but not eutherian mammals, a testis-specific orthologue (ATRY) of the widely expressed X-borne ATRX gene lies on the Y chromosome. Since mutations in human ATRX cause sex reversal, it is possible that one function of ATRY in marsupials is testicular differentiation. We report here the isolation and sequencing of the tammar wallaby (Macropus eugenii) ATRY cDNA, and comparison of its sequence with that of tammar ATRX. The evolution of a testis-specific function for the ATRY protein distinct from the general role of ATRX in both sexes has been accompanied by sequence changes in many protein domains that would alter protein binding partners. A large open reading frame encodes a 1771 amino acid ATRY protein that has diverged extensively from ATRX. The conservation and loss of particular motifs identify those required for testicular function (ATRY) and function in other tissues (ATRX)."

AY532685 MEILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE Sarcophilus harrisii
AY532684 ....E................................S....................P. Dasyurus geoffroii
AY532681 ....E................................S....................P. Dasyurus albopunctatus
AY532683 ....E................................S....................P. Dasyurus viverrinus
AY532682 ....E........................P.......SE...................P. Dasyurus spartacus
AY532680 ....E..............R.................SR...................P. Dasyurus maculatus
AY532678 ..V..................................S....................P. Dasycercus cristicauda
AY532669 ..V..................................S....................P. Dasykaluta rosamondae
AY532676 ..V..................S...............S....................P. Myoictis wallacei
AY532675 ..V..................S...............S....................P. Myoictis melas
AY532687 ..V........N.L.......................S....................P. Neophascogale lorentzii
AY532671 ..V..................................S....................P. Parantechinus bilarni
AY532670 ..V.................................TS.........RG.........P. Parantechinus apicalis
AY532686 ..V..................................S........P...........p. Phascolosorex dorsalis
AY532674 ..V.......................................................P. Pseudantechinus ningbing
AY532672 ..V..................................S....................P. Pseudantechinus woolleyae
AY532673 ..V........N..R......................S...................SP. Pseudantechinus roryi
454 read MEILQKYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAMLQAVSEDP           Sarcophilus harrisii
EF028739 ............................V.TEEDLAAKLNAMLQA.............P. Antechinus minimus
AY243439 ....E..............R........V.TEEDLAAKLNAMLQA.............P. Dasyurus maculatus
EF028750 ....K................KT.....I.TEEDLAAKLNAILQA.............P. Myrmecobius fasciatus
EF028737 ..V.........................V.TEEDLAAKINAMLQA.............P. Antechinus flavipes
EF028748 ..V.........................V.TEEDLAAKLNA.LQA.............P. Sminthopsis crassicaudata
AY243438 ..V.........................V.TEEDLAAKLNA.LQA.............P. Planigale sp.
EF028749 ..V.........................V.TEEDLAAKLNA.LQA.............P. Planigale ingrami
AY532679 ..V.........................V.TEEDLAAKLNAMLQA............... Dasyurus hallucatus
AF025382 ..V.........................V.TEEDLAAKLNAMLQA.............P. Phascogale tapoatafa
EF028741 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus godmani
AY532666 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus swainsonii
EF028736 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus stuartii
EF028742 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus agilis
EF028738 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus bellus
EF028740 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus leo
EF028747 ..V.........................V.TEEDLAAKLNAMLQA.............P. Phascogale calura
EF028744 ..V.........................V.TEEDLAAKLNAMLQA.............P. Murexchinus melanurus
EF028743 ..V.........................V.TEEDLAAKLNAMLQA.............P. Micromurexia habbema
EU086688 ..V.........................V.TEEDLAAKLNAMLQA.............P. Pseudantechinus macdonnellensis
EU086689 ..V.........................V.TEEDLAAKLNAMLQA.............P. Pseudantechinus roryi
EU086686 ..V.........................V.TEEDLAAKLNAMLQA............SP. Pseudantechinus macdonnellensis
EU086687 ..V.........................V.TEEDLAAKLNAMLQA..........G..P. Pseudantechinus mimulus
AY532667 ..V.........................V.TEEDLAAKLNAMLQA.............P. Murexia longicaudata
EF028746 ..V.........................V.TEEDLAAKLNAMLQA.............P. Paramurexia rothschildi
AY532677 ..V.........................V.TEEDLAAKLNAMLQA.............P. Dasyuroides byrnei
EF028745 ..V..........I..............V.TEEDLAAKLNAMLQA.............P. Phascomurexia naso

Macropus eugenii assembly         
sacHar   MEILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE 
         ME+LQ YYTLVDRVPALLHHLTAIDYSS L  +   ++       VSEDPRLLVRVLR E
macEug   MEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPE  

Monodelphis domestica assembly     TSSLVLDLQHSSGGEISG 
sacHar   MEILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE  
         ME+LQ YYTLVDRVPALLHHLTAIDYSS L  +   ++       VSEDPRLLVRVLR E
monDom   MEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPE  

Ornithorhynchus anatinus assembly
sacHar    EILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE 
          ++L+ YY LVDRVPALL HL A+D SS L  +   SR        SEDPRLLVR L  E
ornAna    DLLRDYYALVDRVPALLRHLAALDLSSVLSEEDLTSRLNAGLQAASEDPRLLVRRLEPE  

Equus caballus assembly
sacHar    EILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE  
          E LQ YYTLVDRVPALLHHL ++D+SS +  D   ++       VSEDPRLLV V+RS+
equCab    EALQDYYTLVDRVPALLHHLASMDFSSVVSEDDLVAKLNAGLQAVSEDPRLLVWVVRSK

Rod rhodopsin RHO1 (4+ marsupials)

The optimal wavelength for scotopic (dim light) vision of Sarcophilus is easily predictable provided key tuning residues are covered by the assembly. The 97% match to Sminthopsis and agreement at tuning residues suggests this aspect of vision will be nearly identical between the two species.

>RHO1_homSap Homo sapiens (human)   
0 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG 1
2 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 2
1 YIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 0
0 FRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA* 0

>RHO1_monDom Monodelphis domesticus (opossum) Didelphimorphia
0 MNGTEGPNFYVPFSNKTGTVRSPFEEPQYYLADPWQFSCLAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLAIADLFMVFGGFTMTLYTSLHGYFVFGPTGCNLEGFFATLG 1
2 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIIGVAFTWVMALACAFPPLIGWSR 2
1 YIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPLIVIFFCYGQLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTIPAFFAKSSSVYNPVIYIMMNKQ 0
0 FRTCMITTLCCGKNPLGDDEASATASKTETSQVAPA* 0

>RHO1_macEug Macropus eugenii (wallaby) Diprotodontia frag, traces not yet consulted
0 MNGTEGPNFYVPFSNKTGVVRSPFEEPQYYLAEPWQFSCLAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLADADLFMDFGGFT       1
2 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACSTPPLLGWSR 2
1 0
0       ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKTSAVYNPVIYIMMNKQ 0
0 FRNCMITTLCCGKNPLGDDEASATTSKTETSQVAPA* 0

>RHO1_smiCra Sminthopsis crassicaudata (fat-tailed dunnart) Dasyuromorphia
0 MNGTEGPNFYVPYSNKSGVVRSPYEEPQYYLAEPWMFSCLAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLAVADLFMVICGFTTTLVTSLNGYFVFGTTGCLVEGFFATTG 1
2 GEVALWALVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWIMALACSVPPIFGWSR 2
1 YIPEGMQCSCGIDYYTLNPEFNNESFVIYMFVVHFIIPLTVIFFCYGQLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSDFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ 0
0 FRNCMITTLCCGKNPLGDDEASTTASKTETSQVAPA* 0

>RHO1_sacHar Sarcophilus harrisii (tasmanian_devil) 97% identity Sminthopsis crassicaudata
0 MNGTEGPNFYVPHSNKTGVVRSPYEEPQYYLAEPWMFSCLAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLAVADLFMVICGFTTTLVTSLNGYFVFGTTGCQIEGFFATTG 1
2 GEVALWALVVLAIERYIVVCKPMSNFRFGENHAIMGVVFTWIMALACSVPPLFGWSR 2
1 YIPEGMQCSCGIDYYTLNPEFNNESFVIYMFVVHFTIPLTVIFFCYGQLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSDFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ 0
0 FRTCMITTLCCGKNPLGDDEASATVSKTETSQVAPA* 0

>RHO1_calPhi Caluromys philander (woolly opossum) Didelphimorphia abstract:14659889
0 MNGTEGPNFYVPFSNKTGVVRSPFEEPQYYLAEPWQFSCLAAYMFMLIVLGFPINFLTLYVTIQHKKLRTPLNYILLNLAIADLFMVFGGFTTTLYTSLHGYFVFGPTGCDLEGFFATLG 1
2 GEIALWSLVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSR 2
1 YIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMVVIFFCYGQLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPILMTLPAFFAKTSAVYNPVIYIMLNKQ 0
0 FRTCMLTTLCCGKIPLGDDEASATASKTETSQVAPA*

>RHO1_ornAna Ornithorhynchus anatinus (platypus) 
0 MNGTEGQDFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSVLAAYMFMLIMLGFPINFLTLYVTIQHKKLRTPLNYILLNLAFANHFMVLGGFTTTLYTSLHGYFVFGPTGCNIEGFFATLG 1
2 GEIALWSLVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWIMALACALPPLVGWSR 2
1 YIPEGMQCSCGIDYYTLRPEVNNESFVIYMFVVHFTIPMTIIFFCYGRLVFTVKE 0
0 AAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTVPAFFAKSSAIYNPVIYIMMNKQ 0
0 FRNCMLTTICCGKNPLGDDEASATASKTEQSSVSTSQVSPA* 0

Cone rhodopsin SWS2 (9+ marsupials)

Cone rhodopsin RHO2 has been lost in all mammals and no debris from this gene is expected in Sacrophilus). The short wavelength cone opsin SWS2, while still present in platypus, has also been lost in all theran opsin too long ago to leave detectable remnants in syntenic position. Cone opsin SWS1 has this turned around, being present in theran mammals but only as debris in platypus. A nearly full length gene, most simiilar to Sminthopsis, can be recovered from Sarcophilus read coverage.

>SWS1_homSap Homo sapiens (human) Gt -FAM137A -CALU -NAG6 -FLNC 1385866 NP_990769 cone short   
0 MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVA 1
2 GLVTGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSR 2
1 FIPEGLQCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKA 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNPIIYCFMNKQ 0
0 FQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN* 0

>SWS1_monDom Monodelphis domesticus (opossum) Didelphimorphia
0 MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHFQTVFMGFVFCAGTPLNAVVLVATLRYKKLRQPLNYILVNVSLCGFIFCIFAVFTVFISSSQGYFIFGRHVCAMEAFLGSVA 1
2 GLVTGWSLAFLAFERFIVICKPFGNFRFNSKHAMMVVLATWVIGIGVSIPPFFGWSR 2
1 FIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIMPLFLICFSYSQLLRALRA 0
0 VAAQQQESATTQKAEREVSRMVVMMVGSFCLCYVPYAALAMYMVNNQNHGLDLRLVTIPAFFSKSACVYNPIIYCFMNKQ 0
0 FHACIMEMVCRKPMTDDSDVSSSQKTEVSAVSSSQVGPT* 0

>SWS1_thyEle Thylamys elegans (fat-tailed opossum) Didelphimorphia 
MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHLQTVFMGFVFC
AGTPLNAVVLVATLRYKKLRQPLNYILVNVSFSGFIFCIFAVFTVFISSSQGYFIFGH
HVCAMEAFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFNSKHAMMVVLATWVIGI
GVSIPPFFGWSRFIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIVPLFLICFSY
SQLLGALRAVAAQQQESATTQKAEREVSRMVVMMVGSFCLCYVPYAALAMYMVNNRNH
GLDLRLVTIPAFFSKSACVYNPIIYCFMNKQFHACIMEMVCRKPMTDDSDVSSSQKTE
VSAVSSSQVGPS

>SWS1_didAur Didelphis aurita (big-eared opossum) Didelphimorphia
MSGDEEFYLFKNISSVGPWDGPQHHIAPAWAFHFQTVFMGFVFC
AGTPLNAVVLVATLRYKKLRQPLNYILVNVSLSGFIFCIFAVFTVFISSSRGYFVFGR
HVCAMEAFLGSVAGLVMGWSLAFLAFERFVVICKPFGNFRFNAKHAMMVVLATWVIGI
GVSIPPFFGWSRFIPEGLQCSCGPDWYTVGTKYRSEYYAWFLFLSCFIGPLFLICFSY
AQLLGALRAVAAQQQESTTTQKAEREVSRMVVMMVGSFCLCYVPYAALGMYMINNRNH
GLDLRLVTIPAFFSKSACVYNPIIYCFMNKQFHACIMEMVCRKPMADDSDITSSQKTE
VSTVSSSQVGPS

>SWS1_macEug Macropus eugenii (wallaby) Diprotodontia
MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHCQTVFMGFVFFAGTPLNAVVLIATFRYKKLRQPLNYILVNISLAGFIYCIFSVFTVFISSSQGYFIFGR
HVCAMEGFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFNSKHSMMVVLATWVIGIGVSIPPFFGWSRYIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFILCFIMPLSLICFSY
SQLLGALRAVAAQQQESATTQKAEREVSRMVVMMVGSFCLCYVPYAALAMYMVNNRNHGIDLRLVTIPAFFSKSSCVYNPIIYCFMNKQFHACIMEMVCRKPMTDDSEASSSQKTEVSTVSSSQVGPS*

>SWS1_setBra Setonix brachyurus (quokka) Diprotodontia 
MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHCQTVFMGFVFF
AGTPLNAVVLIATFRYKKLRQPLNYILVNISLAGFIYCIISVFTVFISSSQGYFIFGR
HVCAMEGFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFNSKHSMMVVLATWVIGI
GVSIPPFFGWSRYIPEGLQCSCGPDWYTVGTKYHSEYYTWFLFILCFIMPLSLICFSY
SQLLGALRAVAAQQQESATTQKAEREVSRMVVMMVGSFCLCYVPYAALAMYMVNNRNH
GIDLRLVTIPAFFSKSACVYNPIIYCFMNKQFHACIMEMVCRKPMTDDSEASSSQKTE
VSTVSSSQVGPS

>SWS1_tarRos Tarsipes rostratus (honey possum) Diprotodontia
MSGDEEFYLFKDISSVGPWDGPQYHIAPAWAFHFQTTFMGFVFF
AGTPLNAVVLIATLRYKKLRQPLNYILVNISLAGFIFCVISVFTVFISSSQGYFIFGR
HVCAMEAFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFSSKHAMMVVLATWVIGI
GVSIPPFFGWSRYIPEGLQCSCGPDWYTVGTKYHSEYYTGFLFIFCFIVPLSLICFSY
SQLLGALRAVAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAALAMYMVNNRNH
GLDLRLVTIPAFFSKSACVYNPIVYWFMNKQFHACIMEMVCRKPMTDDSEISSSQKTE
VSTVSSSQVGPS

>SWS1_cerCon Cercartetus concinnus (pygmy possum) Diprotodontia
MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHFQTAFMGFVFF
VGTPLNAVVLVATLCYKKLRQPLNYILVNVSLAGFIFCIISVFTVFISSSQGYFIFGR
HVCAMEAFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFSSKHAMMVVLATWVIGI
GVSIPPFFGWSRYIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIVPLSLICFSY
SQLLGALRAVAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAALAMYMVNNRNH
GLDLRLVTIPACFSK 

>SWS1_smiCra Sminthopsis crassicaudata (dunnart) Dasyuromorphia
0 MSGDEEFYLFKNISLVGPWDGPQYHLAPAWAFHFQTAFMGFVFFAGTSLNGVVLIATLRYKKLRQPLNYILVNISLAGFIFCVFSVFTVFVSSSQGYFVFGRHVCAMEGFLGSVA 1
2 GLVTGWSLAFLAFERFIVICKPFGNFRFNSKHAMMVVLATWIIGIGVSIPPFFGWSR 2
1 YIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIVPLSLICFSYSQLLGALRA 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAAMAMYMVNNRNHGLDLRLVTIPAFFSKSACVYNPIIYCFMNKQ 0
0 FHACIMEMICKKPMTDDSETTSSQKTEVSTVSSSQVGPS* 0

>SWS1_sacHar Sarcophilus harrisii (tasmanian_devil) part of last exon missing 96% identity Sminthopsis crassicaudata
0 MSGDEEFYLFKNISPVGPWDGPQYHIAPAWAFHLQTAFMGFVFFAGTPLNGVVLIATLRYKKLRQPLNYILVNISLAGFIFCVFSVFTVFVSSSQGYFVFGRHVCAMEGFLGSVA 1
2 SGLVTGWSLAFLAFERFIVICKPFGNFRFHSKHATMVVLATWVIGIGVSIPPFFGWSR 2
1 YIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIVPLSLICFSYSQLLGALRAVS 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAALAMYMVNNRNHGLDLRLVTIPAFFSKSACVYNPIIYCFMNQ 0
0            KPMTDDSETTSSQKTEVSTVSSSQVGPS* 0
 
>SWS1_isoObe Isoodon obesulus (bandicoot) Peramelemorphia
MSGDEEFYLFKNISSVGPWDGPQYHIAPAWAFHCQTVFMGFVFF
AGTPLNAVVLIATLRYKKLRQPLNYILVNISLAGFIFCIFSVFTVFISSSQGYFIFGR
HVCAMEAFLGSVAGLVTGWSLAFLAFERFIVICKPFGNFRFHSKHAMMVVLATWVIGI
GVSIPPFFGWSRFIPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIIPLSLICFSY
SQLLRALRTVAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAALAMYMVNNRNH
GLDLRLVTIPAFFSKSACVYNPIIYCFMNKQFHACIMEMICRKPMTDDSETSSSQKTE
VSTVSSSQVSPS

>SWS1_galGal Gallus gallus (chicken) Gt 0...2.1.0.0 indel x x x x 348 aa 000 nm no_ref genome cone short1 violet   
0 MSSDDDFYLFTNGSVPGPWDGPQYHIAPPWAFYLQTAFMGIVFAVGTPLNAVVLWVTVRYKRLRQPLNYILVNISASGFVSCVLSVFVVFVASARGYFVFGKRVCELEAFVGTHG 1
2 GLVTGWSLAFLAFERYIVICKPFGNFRFSSRHALLVVVATWLIGVGVGLPPFFGWSR 2
1 YMPEGLQCSCGPDWYTVGTKYRSEYYTWFLFIFCFIVPLSLIIFSYSQLLSALRA 0
0 VAAQQQESATTQKAEREVSRMVVVMVGSFCLCYVPYAALAMYMVNNRDHGLDLRLVTIPAFFSKSACVYNPIIYCFMNKQ 0
0 FRACIMETVCGKPLTDDSDASTSAQRTEVSSVSSSQVGPT* 0

Cone rhodopsin LWS (9+ marsupials)

This basal long wavelength imaging opsin is available from 97 vertebrates and has already been analyzed for phyloSNPs and rare genomic events. The Didelphimorphia experienced a 3-4 residue insert in exon 1 that separates them from all other marsupials. Note this region has quite a complicated indel history. The extra residues have repeat character DVNE DDND suggesting replication slippage. The gene is present and intact in Sarcophilus though two exons are not currently available. LWS in tasmanian devil is identical to the Sminthopsis ortholog.

LWS_loxAfr  MAQQWGPHRLTGARLQDASE---DSTQASIFVYTNTNT  elephant
LWS_echTel  MAQRWGAHRLTGGQLQDTYE---GSTRTSIFVYTNSTS  tenrec
LWS_monDom  MTQAWDPAGFLARRRDVNEDDNDETTRSSLFVYTNSNN Didelphimorphia
LWS_didAur  MTQAWDPVGFLARRRDENEDDHDDTTRASLFVYTNSNN Didelphimorphia
LWS_tarRos  MTQAWDPAGFLAWRRDENE----ETTRASLFVYTNSNN Diprotodontia
LWS_macEug  MTQAWDPAGFLAWRRDENE----ETTRASLFVYTNSNN Diprotodontia
LWS_smiCra  MTQAWDPAGFLAWRRDENE----ETTRASLFVYTNSNN Dasyuromorphia
LWS_sacHar  MTQAWDPAGFLAWRRDENE----ETTRASLFVYTNSNN Dasyuromorphia
LWS_setBra  MTQAWDPAGFLAWRRDENE----ETTRASLFVYTNSNN Diprotodontia
LWS_cerCon  MTQAWDPAGFLAWQEDENE----ETTRASLFVYTNSNN Diprotodontia
LWS_myrFas  MTQAWDPAGFLAWRREENE----ETTRASLFTYTNSNN Dasyuromorphia
LWS_isoObe  MTQAWDPAGFLAWRRDENE----ETTRASLFVYTNSNN Peramelemorphia
LWS_ornAna  MTPAWNSGVYAARRRFEDEE---DTTRTSVFVYTNSNN  platupus
LWS_tacAcu  MTQAWDPAGFLAWRRDENEE---TTRASLFVYTNSNNT  echidna

>LWS_homSap Homo sapiens (human)   
0 MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTR 1
2 GPFEGPNYHIAPRWVYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFVLGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRA 0
0 VAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFHPLMAALPAFFAKSATIYNPVIYVFMNRQ 0
0 FRNCILQLFGKKVDDGSELSSASKTEVSSVSSVSPA* 0

>LWS_monDom Monodelphis domesticus (opossum) Didelphimorphia 4aa insert  
0 MTQAWDPAGFLARRRDVNEDDNDETTRSSLFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVYNLTSLWMVFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETVIASTISVINQIYGYFILGHPLCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIIFSWVWAAVWTAPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMATCCIFPLSIILLCYVQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTLFACFAAANPGYSFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSKTEGSSVSSVAPA* 0

>LWS_didAur Didelphis aurita (big-eared opossum) Didelphimorphia 4aa insert
0 MTQAWDPVGFLARRRDENEDDHDDTTRASLFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVYNLTSLWMVFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETVIASTISVINQIYGYFILGHPLCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIIFSWVWAAVWTSPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDLGVQSYMIVLMATCCIFPLSIILLCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTLFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSKTEVSSVSSVAPA* 0

>LWS_tarRos Tarsipes rostratus (honey possum) Diprotodontia ENED insert
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVFNLTSLWMVFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETIIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAIWTSPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGNSDPGIQSYMIVLMSTCCILPLSIILLCYVQVWRAIRA 2
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTLFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA* 0

>LWS_macEug Macropus eugenii (wallaby) Diprotodontia  
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTK 1
2 GPFEGPNYHIAPRWVFNLTSLWMIFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETLIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGNSDPGVQSYMIVLMSTCCILPLSVIFLCYIQVWLAIRS 2
0 VAKQQKESESTQKAEKEVSRMVVVMILAFCFCWGPYAIFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA* 0

>LWS_setBra Setonix brachyurus (quokka) Diprotodonti  
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTK 1
2 GPFEGPNYHIAPRWVFNLTSLWMIFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETMIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGNSDPGVQSYMIVLMSTCCILPLSVILLCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYAIFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVPA* 0

>LWS_cerCon Cercartetus concinnus (pygmy possum) Diprotodontia 
0 MTQAWDPAGFLAWQEDENEETTRASLFVYTNSNNTK 1
2 GPFEGPNYHIAPRWVFNLTSLWMVFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAIADLGETIIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAIWTSPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGNSDPGIQSYMIVLMSTCCILPLSIILLCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTFFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA*

>LWS_smiCra Sminthopsis crassicaudata (dunnart) Dasyuromorphia
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTK 1
2 GPFEGPNYHIAPRWVYNLTSLWMIFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETIIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMSTCCILPLSIIILCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVMVMILAFCFCWGPYALFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA* 0

>LWS_sacHar Sarcophilus harrisii (tasmanian_devil) half of exon 2, all of exon 4 missing frag 100% identical to Sminthopsis
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTK 1
2                                            FKKLRHPLNWILVNLAVADLGETIIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMSTCCILPLSIIILCYIQVWLAIRA 0
0 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA* 0

>LWS_myrFas Myrmecobius fasciatus (numbat) Dasyuromorphia
0 MTQAWDPAGFLAWRREENEETTRASLFTYTNSNNTK 1
2 GPFEGPNYHIAPRWVYNLTSFWMIFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETIIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMSTCCILPLSVILLCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYAIFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSRTEVSSVSSVAPA* 0

>LWS_isoObe Isoodon obesulus (bandicoot) Peramelemorphia  
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVYNLTSFWMFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETIIASTISVINQIYGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMTTCCILPLSIILLCYVQVWLAIRA 0
0 VAKQQKDSESTQKAEKEVSRMVVVMIRAYCFCWGPYTLFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSGTSRTEVSSVSSAPA* 0

>LWS_ornAna Ornithorhynchus anatinus (platypus)  
0 MTPAWNSGVYAARRRFEDEEDTTRTSVFVYTNSNNTR 1
2 DPFEGPNYHIAPRWAYNVTSLWMIFVVIASVFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETLIASTISVINQIFGYFILGHPMCVLEGYTVSLC 1
2 GITGLWSLSIISWERWIVVCKPFGNVKFDAKLAMVGIVFSWVWAAVWTAPPIFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMSTCCILPLSIIVLCYLQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTIFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQ 0
0 FRNCIMQLFGKKVDDGSELSSTSRTEVSSVSSVSPA* 0

>LWS_tacAcu Tachyglossus aculeatus (echidna)  
0 MTQAWDPAGFLAWRRDENEETTRASLFVYTNSNNTR 1
2 GPFEGPNYHIAPRWVFNLTSLWMVFVVIASIFTNGLVLVATMKFKKLRHPLNWILVNLAVADLGETIIASTISVINQIYGYFILGHPLCVLEGYTVSLC 1
2 GITGLWSLAIISWERWVVVCKPFGNVKFDAKLAMVGIIFSWVWAVWTSPPLFGWSR 2
1 YWPHGLKTSCGPDVFSGSSDPGVQSYMIVLMATCCIFPLSIILLCYIQVWLAIRA 0
0 VAKQQKESESTQKAEKEVSRMVVVMILAYCFCWGPYTLFACFAAANPGYAFHPLTASLPAYFAKSATIYNPIIYVFMNRQ 0
0 FRTCILQLFGKKVDDGSEVSSTSKTEVSSVSSVAPA* 0

Encephalopsin (2+ marsupials)

Pinopsin, parapinopsin, parietopsinand VA opsin all terminate in sauropods and are missing in all mammals. Encephalopsin has a very peculiar history of gene loss in tetrapods, requiring some seven independent and asynchronous events including platypus. While this limits the phylogenetic utility of any gene loss within marsupials, the status of the gene within Sarcophilus is still informative. A full length gene can be recovered with 94% identity to opossum, strongly indicating that encephalopsin is fully functional within Sarcophilus.

>ENCEPH_homSap Homo sapiens (human) OPN3 
0 MYSGNRSGGHGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0

>ENCEPH_monDom Monodelphis domestica (opossum) 
0 MYSDNSSDDGGGGYWGSGRAGGASGTGVTGEPGPEGSPRQAPLFSPGTYELLALLIATIGLLGLCNNLLVLVLYYKFQRLRTPTHLFLVNISFNDLLVSLFGVTFTFVSCLRSGWVWDSVGCAWDGFSNTLF 1
2 GIVSIMTLTVLAYERYNRIVHAKVINFSWAWRAITYIWLYSLVWTGAPLLGWNRYTLEIHGLGCSVDWKSKDPNDSSFVIFLFFGCLMLPVGVMAYCYGHILYAIRM
0 LRCVEELQTIQVIKILRYEKKVAKMCFLMIAIFLFCWMPYAVICLLVANGYGSLVTPTVAIIASLFAKSSTAYNPIIYIFMSRK 0
0 FRRCLLQLLCFRLLKFQQPKKDRPVIRTEKQIRPIVMSQKVGDRPKKKVTFSSSSIIFIITSDETQMIDENDKNSGTKVNVIQVRPL* 0

>ENCEPH_sacHar Sarcophilus harrisii (tasmanian_devil) 94% identity monDom
0 MYSGNSSDDAGGGYWGSGGTGGAGGTGVAGEPAPEGSPRPAPLFSPGTYELLALLIATIGLLGLCNNLLVLVLYYKFQRLRTPTHLFLVNISFSDLLVSLFGVTFTFVSCLRSGWVWDSVGCAWDGFSNTLF 1
2 GIVSIMTLTVLAYERYNRIVHAKVINFSWAWRAITYIWLYSLIWTGAPLLGWNRYTLEIHGLGCSVDWKSKDPNDSSFVLFLFLGCLVLPVGVMAYCYGHILYAIRM 0
0 FRCVEELQTLQVIKILRYEKKVAKMCFLMIATFLFCWMPHAVICFLVANGYGSLVTPTVAIIPSLFAKSSTAYNPIIYIFMSRK 0
0 FRRCLLQLLcFRQLKFQQPKKDRAIIRTEKQIRPIVMSQKVGDRPKKKVTFSSSSIIFIITSDETQMIDDNDKNSETKVNVIQVRPL* 0

>ENCEPH_macEug Macropus eugenii frag
0                         GALGCREPGQREPSSSAPFSPGTYELLALLIATIGLLGLCNNLLVLVLYYKFQRLRTPTHLLLVNISFSDLLVSLFGVTFTFVSCLRSGWVWHTVGCAWDGFSNSLF 1
2 GIVSIMTLTVLAYERYHRIVHAKVINFSWTWRAITYIWLYSLVWTGAPLLGWNRYTLEIHGLGCSVDWKSKDPNDSSFVLFLFLGCLVLPVGVMAYCYGHILYAIRM 0
0 0
0 FRRCLLQLLCFRQLKFQQPKKDRPVIRTEKQIRPIVMSQKVGDRPKKKVTFSSSSIIFIITSDETQMIDDNDKNNGTKVNVIQVRPL* 0

>ENCEPH_ornAna Ornithorhynchus anatinus pseudo
0 MVPWNGS-GRHLGAVR---GPE--SLPATPGAARPSRPGAGDGRL--LGLF-P-GVGGNLLVLLL--ALPGPPTTTDLYLASVAVSDLL--LL---LPFVYRLWRSRPWVFVCRLLGE-GGSLA 1
2 GIVSLISLAVLSYERYTLTLHPKQSNYQKAVLAVGASWIYSLIWTIPPLLGWSSYGTEGAGTSCSVHWSSKSVC-SYIVCLFI--CLVIPVLVMIYCYGRLLYAVKQ 0
0 LHCVKELQNIQVIGSLRYER*VTEMYFFTIAQFLVCQSPSALVSYPAAH-----VSPVVAKISPVFANSSFVYNPVISIFVRRK 0
0 KASR*KVNVIQVQPPS* 0

>ENCEPH_galGal Gallus gallus (chicken) 71%=homSap encephalopsin OPN3 full
0 MHSGNGTGATSRPQLAAAGHEVPGERPLFSAGTYELLALLIATIGTLGVCNNLLVLVLYYKFKRLRTPTNLFLVNISLSDLLVSVCGVSLTFMSCLRSRWVWDAAGCVWDGFSNSLF 1
2 GIVSIMTLTVLAYERYIRVVHAKVIDFSWSWRAITYIWLYSLAWTGAPLLGWNRYTLEIHGLGCSMDWKSKDPNDTSFVLLFFLGCLVAPVVIMAYCYGHILYAVRM 0
0 LRCVEDFQTSQVIKLLKYEKKVAKMCFLMISTFLICWMPYAVVSLLVTYGYSNLVTPTVAIIPSFFAKSSTAYNPVIYIFMSRK 0
0 FRQCLLQLLCFRLMRFQRIMKEPSGAGNVKPIRPIVMSQKVGDRPKKKVTFSSSSIIFIIASDDTQQIDDNSKHNGTKVNVIQVKPL* 0

TMT opsin (2+ marsupials)

TMT is an ancient locus that is present in monotremes and marsupials but lost in all placentals.

>TMT_monDom Monodelphis domestica shortened final exon 
0 MSNNLTTNLSLEALLSASEDKQRNGLSRTGHTIVAVFLGIILIFGSISNFIVLVLFCKFKVLRNPVNMLLLNISISDMLVCLSGTTLSFASSIQGRWIGGKHGCRWYGFANSCF 1
2 GIVSLISLAILSYERYRTLTLCPGQGADYQKALLAVAGSWLYSLVWTVPPLIGWSSYGTEGAGTSCSVHWTSKSVESVSYIMCLFIFCLVIPILVMVYFYGRLLYAVKQ 0
0 VGKIRKTAARKREYHVLFMVVTAVICYLICWVPYGMIALLATFGPPGVVSPVANVVPSILAKSSTVCNPIIYVLMNKQ 0
0 FYKCFLILFHCQPAQSGPDVSLCPSNVTVIQLGQRKNKDAPGSI*

>TMT_macEug Macropus eugenii frag
0 MSINLTANLSFGTLLPDSEEKQRSGLSRTGHTVTAVFLGLILILGVINNFIVLVLFCKFKVLRNPVNMLLLNISISDMLVCLTGTTLSFASSIRGRWIAGYHGCRWYGFANSCF 1
2 GIVSLISLAVLSYERYRTLTLCPRQGTDYHKALLAVAGSWLYSLIWTVPPLIGWSSYGTEGAGTSCSVHWTSKSVESVSYIMCLFIFCLVIPILFMVYFYGRLLYTVKQ 0
0 VGKIRKSAARKREYHVLFMVVTAVICYLICWVPYGMIALLATFGPPGVVSPVANVVPSILAKSSTVCNPIIYILMNKQ 0
0 FYKCFLILFHCQPASSASDASLCPSKMTVIQLGQRKDKEVPCAIQDLPEVSKKQLCLLSPESNVAPSSGHPQEKMEEKPLSE*  0

>TMT_sacHar Sarcophilus harrisii (tasmanian_devil) FP5MBH101BETOZ needed to finish
0 MSINLTTNLSFGPLLIDSEEKPRSGLSRTGHTVVAVFLGIILILGFINNFIVLILFCKFKVLRNPVNMLLLNISISDMLVCLSGTTLSFASSIRGRWIGGYHGCRWYGFANSCF 1
2 GIVSLISLAILSYERYRTLTLCPRRGADYQKALLAVAGSWLYSLIWTVPPLIGWSSYGTEGAGTSCSVHWTSKSVQSVSYIMCLFIFCLVIPILIMIYFYGRLLYTVKQ 0
0 VGKIRKTAARKREYHVLFMVVTAVICYLICWVPYGLIALVATFGPPGVVSPVANIVPSILAKSSTVCNPIIYILMNKQ 0
0 FYKCFLILFHCQPASSAPDASLCPSKVTVIQLGQR   * 0

>TMT_ornAna Ornithorhynchus anatinus frag
0                        GLSRTGHTMVAVFLGIILVFGFMNNLIVLILFCKFKALRNPVNMIMLNISASDMLVCVSGTTLSFASNISGRWIGGDPGCRWYGFVNSCL 1
2 GIVSLISLAVLSYERYRTLTLHPKQSTDYQKAVLAVGASWIYSLIWTIPPLLGWSSYGTEGAGTSCSVHWSSKSPVSVSYIVCLFIFCLVIPVLVMIYCYGRLLYAVKQ 0
0 IGKARKTAARKREYHVLFMVITTVICYLVCWMPYGVTALLATFGQPGTVSPEASVIPSILAKSSTVCNPIIYILMNKQ 0
0 FYKCFLILFHCQPPRAADAPSTYPSQVMVIQLNQRRSRETAGAPQVLLEMKHQTLHLLGPQLHETPSWERSTPVHPE* 0

>TMT_galGal Gallus gallus 
0 MNHTWTYNLSFGAPTDPVEPRAGLSRNGHTVVAVFLGFILFFGFLNNLIVLILFCKFKTLRNPVNMLLLNIhttp://genomewiki.ucsc.edu/index.php?title=Opsin_evolution:_Encephalopsin_gene_loss&action=editSISDMLVCISGTTLSFASNIHGKWIGGEHGCRWYGFVNSCF 1
2 GIVSLISLAVLSYERYSTLTLCNKRSDDYRKALLAVGGSWVYSLLWTVPPLLGWSSYGIEGAGTSCSVRWSSETAESTSYIICLFIFCLVIPVMVMMYCYGRLLYAVKQ 0
0 VGKIHKNTARKREYHVLFMVITTVICYLVCWIPYGVIALLATFGKPGVVTPVASIIPSILAKSSTVCNPIIYILMNKQ 0
0 FYKCFRQLFHCQPPSSTDGEPTCHSKVTVIQLNQKTDGGKLCNNKPRPETDNKVTSLLHPEPGLEPAAKTVPPM*  0

>TMT_taeGut Taeniopygia guttata 
0 MNHTWMYNLSFGAPAHPVEPRAGLSRSGHTVVAVFLGLILFFGFLNNLIVLILFCKFKTLRNPVNMLLLNISVSDMLVCISGTTLSFASNIRGKWIGGDHACRWYGFVNSCF 1
2 GVVSLISLAVLSYERYNTLTLCHKRSDDFRKALLAVAGSWIYSLVWTVPPLLGWSSYGVEGAGTSCSVRWSSESAESTSYIICLFVFCLVVPVMVMMYCYGRLLYAVKQ 0
0 VGKIHKNAARKREYHVLFMVIPTVICYLVCWIPYGVIALLATFGKPGAVTPITSIIPSILAKSSTVCNPIIYILMNKQ 0
0 FYKCFRQLFHCQPPSSTDGEPTCHSKVTVIQLDQRADGGNMCNNEPHPETDSKMTSLLCPETTSKATPPTS* 0

>TMT_anoCar full +TMT -ST6GAL2 (overlap) +SLC5A7
0 MSELSSNLTFNMSTSIEEPGSGLSRMGHNIVAVFLGLILVFGFLNNLVVLILFCKFKTLRNPVNMLLLNISASDMLVCISGTTLSFVSNIYGRWIGGEHGCRWYGFVNSCF 1
2 GIVSLISLAILSYERYSTLTQTNKRGSDYQKALLGVGGSWLYSLIWTVPPLIGWSSYGLEGAGTSCSVRWTSETLESVTYIICLFIFCLAIPVLVMIYCYARLFYAVKQ 0
0 VGKLRKTSARKREFHVLFMIITTIICYLICWMPYGVIALLATFGRPGLVSPVASVIPSILAKSSTVFNPIIYILMNKQ 0
0 FYKCFLMLLHCQPSSVADGETICQSKVMAIHQNQKAQGGVILKSQVVPQMDEKAICLLSPESSLDPVLESTPQLSKENSFL* 0

>TMT_xenTro full -UXS1 +TMT -ST6GAL2 (overlap) +SLC5A7
0 MSTIKNWTTNISVENSMSYIENDLSLPTEAVLSRTGHTVVAIFLGFILIFGFLNNFVVLILFCKFKTLRTPVNMMLLNISASDMLVCVSGTTLSFTSSIKGKWIGGEYGCQWYGFVNSCF 1
2 GIVSLISLAILSYERYSTLTLYNKGGPNFKKALLAVASSWLYSLVWTVPPLLGWSSYGREGAGTSCSVRWTSESVESVSYIICLFIFCLALPVFVMLYCYGRLLYAVKQ 0
0 VGKIRKIAARKREYHVLFMVITTVICYLLCWLPYGVVALLATFGRPGVISPVASVVPSILAKSSTVFNPIIYILMNKQ 0
0 FYKCFLILFHCHPTSSADGKSICQSNYTVIQLNQKLNNIVAIPGQTQIPESVDKMPCIHRQNNESPSDQMPQSTTEHLISGT* 0

RGR opsin (0 marsupials)

This gene has apparently been lost specifically in the marsupial clade, though support for that is only provided by the Monodelphis and Macropus genome projects. It would be of considerable interest to find the gene or a fragment thereof in syntenic position in Sarcophilus. However nothing can be found with tblastn of current reads.

>RGR1_homSap Homo sapiens (human) +PCDH21 -LRIT1 -GRID1 -WAPAL NM_001012720 retinal epithelium Mueller    
0 MAETSALPTGFGELEVLAVGMVLLVE 1
2 ALSGLSLNTLTIFSFCKTPELRTPCHLLVLSLALADSGISLNALVAATSSLLR 2
1 RWPYGSDGCQAHGFQGFVTALASICSSAAIAWGRYHHYCT 1
2 RSQLAWNSAVSLVLFVWLSSAFWAALPLLGWGHYDYEPLGTCCTLDYSKGDR 2
1 NFTSFLFTMSFFNFAMPLFITITSYSLMEQKLGKSGHLQ 0
0 VNTTLPARTLLLGWGPYAILYLYAVIADVTSISPKLQM 0
0 VPALIAKMVPTINAINYALGNEMVCRGIWQCLSPQKREKDRTK* 0

>RGR_dasNov Dasypus novemcinctus (armadillo) 
0 MAGSGVLPPGFGELEVLAVGTVLLVE 1
2 ALSGLVLNGLAIISFCKTPELRSPSRLLVLSLALADSGVSLNALVAATSSLLR 2
1 RWPYGSGGCQAHGFQGFVTALASISSSAAIAWERCHRHCI 1
2 GRRLAWSTAGCLVLCLWMAAAFWAALPLLGWGLYDYEPLGTCCTLDYSRGDR 2
1 NFISFLVTLALFNFFLPLLIMLTSYRLMAQKLKRSGHVQ 0
0 VSTALPGRLLLLGWGPYALLYLYAAVADATSLSPRLQM 0
0 VPALIAKTMPTVNALYYALGRESVHRNA* 0

>RGR_loxAfr Loxodonta africana (elephant) 
0 MAEPGHLPAGFQELEVLTVGTVLLLE 1
2 ALSGLSLNGLTILSFCKIPELRTPGHLLVLSLALADSGISLNALVAAMSSLRR 2
1 RWPYGSDGCQAHGFQGFVTALASICSCAAIAWERYHHYCT 1
2 RSRLAWSSASALVLFVWLSSAFWAALPLLGWGRYNYEPLGTCCTLDYSRGDR 2
1 NSTSFLLTMAFFNFLLPLFITLTSYRLMEQKLKKKGPLQ 0
0 VNTTLPARTLLLGWGPYALLYLCAAATDMTSISPRLQM 0
0 VPALVAKAVPVINACHYALGSEVVRGGIWQYLSRQRGESPLRARDRTH* 0

>RGR1_ornAna Ornithorhynchus anatinus (platypus) missing exon 1 DRY motif, afros ERY, other placentals GRY
0 1
2 ALLGLCLNGLTIASFRKIKELRTPSNLLVVSLALADSGICLNALMAALSSFLR 2
1 HWPYGAEGCRLHGFQGFATALASISLSAAIGWDRYLRHCS 1
2 RSKPQWGTAVSTVLFAWGFSAFWSMMPILGWGQYDYEPLRTCCTLDYSKGDR 2
1 NFTTYLFAVAFFNFVIPLFIMLTSYQSIEQRFKKSGLFK 0
0 LNTRLPTRTLLFCWGPYALLCFYATVENVTFISPKLRM 0
0 IPALIAKTVPVIDAFTYALRNEDYRGGIWQFLTGQKIERVEVENKIK* 0

>RGR1_galGal Gallus gallus (chicken) +PCDH21 -LRIT1 +CHAT -PARG 14985289 NM_001031216  
0 MVTSHPLPEGFTEIEVFAIGTALLVE 1
2 ALLGFCLNGLTIISFRKIKELRTPSNLLVLSIALADCGICINAFIAAFSSFLR 2
1 YWPYGSEGCQIHGFQGFLTALASISSSAAVAWDRYHHYCT 1
2 RSKLQWSTAISMMVFAWLFAAFWATMPLLGWGEYDYEPLRTCCTLDYSKGDR 2
1 NYITFLFALSIFNFMIPGFIMMTAYQSIHQKFKKSGHYK 0
0 FNTGLPLKTLVICWGPYCLLSFYAAIENVMFISPKYRM 0
0 IPAIIAKTVPTVDSFVYALGNENYRGGIWQFLTGQKIEKAEVDSKTK* 0

>RGR1_xenTro Xenopus tropicalis (frog) ?? 0.2.1.2.1.0.0 indel +PCDH21 -LRIT1 +CHAT -PARG 296 BC135113  
0 MVTSYPLPEGFTETEVFAIGTTLLVE 0
0 ALLGLLLNGLTLLSFYKIRELRTPSNLFIISLAVADTGLCLNAFVAAFSSFLR 2
1 YWPYGSEGCQIHGFQGFVAALSSIGSCAAIAWDRYHQYCT 1
2 RSKLHWSTAVSVVFFIWGFSAFWSAMPLFGWGEYDYEPLRTCCTLDYSKGDR 2
1 NYISYLFTMAFFEFLVPLFILMTAYQSIYQKMKKSGQIR 0
0 FNTSMPVKSLVFCWGPYCLLCFYAVIQDATILSPKLRM 0
0 IPALLAKTSPAVNAYVYGLGNENYRGGIWQYLTGQKLEKAETDNKTK* 0

Peropsin (2+ marsupials)

Sarophillus can be expected to have this gene. Further, the protein sequence should substantiate the 4 previously defined phyloSNPs characteristic of the marsupial/placental transition.

>PER_homSap Homo sapiens (human)
0 MLRNNLGNSSDSKNEDGSVFSQTEHNIVATYLIMA 1
2 GMISIISNIIVLGIFIKYKELRTPTNAIIINLAVTDIGVSSIGYPMSAASDLYGSWKFGYAGCQ 0
0 VYAGLNIFFGMASIGLLTVVAVDRYLTICLPDV 1
2 GRRMTTNTYIGLILGAWINGLFWALMPIIGWASYAPDPTGATCTINWRKNDR 2
1 SFVSYTMTVIAINFIVPLTVMFYCYYHVTLSIKHHTTSDCTESLNRDWSDQIDVTK 0
0 MSVIMICMFLVAWSPYSIVCLWASFGDPKKIPPPMAIIAPLFAKSSTFYNPCIYVVANKK 2
1 FRRAMLAMFKCQTHQTMPVTSILPMDVSQNPLASGRI* 0

>PER_loxAfr Loxodonta africana (elephant)
0 MLRNSLDNSSDSKNEDASVFSQTEHNIVATYLIMA 1
2 GMISILSNIIVLGIFIKYKELRTPTNAIIINLAVTDIGVSSIGYPMSAASDLHGRWKFGYTGCQ 0
0 IYAGLNIFFGMASIGLLTVVAVDRYLTICHPHI 1
2 GRRMTSNTYVSMILGAWINGLLWALLPITGWASYAPDPTGATCTINWRKNDA 2
1 SFVSYTMTVIVINFVVPLAVMFYCYYHVTRSIKRHTASNCAEYLNRDWSDQLDVTK 0
0 MSVIMILMFLVAWSPYSIVCLWASFGDSKKIPPSMAIIAPLFAKSSTFYNPCIYVVANKK 2
1 FRRAMFAMFKCQTHQAEPVTCILPMNVSQNPLAAGRI* 0

>PER_monDom Monodelphis domestica (opossum)
0 MFKNNSVKTLAPEKEGPSVFSPIEHKIVAAYLITA 1
2 GVISIVSNVIVLGIFVKYKALRTATNTIIINLAVTDIGVSSIGYPMSAASDLYGSWKFGYDGCQ 0
0 IYAGLNIFFGMASIGLLTAVAIDRYLTICQPDL 1
2 GGRMTSYNYTLMILTAWVNGFFWALMPIVGWAGYAPDPTGATCTINWRKNDV 2
1 SFVSYTMTVITINFAMPLGVMFYCYYNVSQKMKQYSPSNCPDHINRDWSNQVAVTK 0
0 MSVVMILMFLLAWSPYSIVCLWASFGDPKEIPPAMAIVAPLFAKSSTFYNPCIYVAANKK 2
1 FRRAISAMIRCQTHQSMPISNALPMN* 0

>PER_macEug Macropus eugenii (wallaby)
0 MFQNDSLEPEKESYSVFSPTEHNIVAAYLITA 1
2 GVISIPSNIIVLGIFVKYKELRTATNTIIINLAVTDIGVSSIGYPMSAASDLYGSWKFGYAGCQ 0
0 IYAGLNIFFGMASIGLLTAVAIDRYLTICQPDL 1
2 2
1 SFVSYTMTVIAINFVMPLVVMFYCYYNVSLKMKQYTRSSCPEHINRDWSNQVDVTK 0
0 MSVIMILMFLLAWSPYSVVCLWASFGDPKEIPPAMAIIAPLFAKSSTFYNPCIYVAANKK 2
1 FRRAISAMMRCETHQSMPVSNALPLNLT* 0

>PER_sarHar Sarcophilus harrisii (tasmanian_devil) 5.5 of 7 exons
0 MFKNDSFRSLEPEKEGHSVFSPAEHNIVAAYLITA 1
2   SILSNVIVLGIFVKFKELRTATNAIIINLA   0
0 1
2 GRRMTSFNYTIMILTAWVNGFFWALMPIVGWASYAPDPTGA   2
1 SFVSYTVTVIAINFVMPLVVMIYCYYNVSQKIKQYTPSNCPEYINRDWSNEVAVTK 0
0 MSVIMILMFLLAWSPYSVVCLWASFGDPKEIPPAMAIIAPLFAKSSTFYNPCIYVAANKK 2
1 FRrAISAMIQCQTHQSMSVSKALPMN* 0

>PER_ornAna Ornithorhynchus anatinus (platypus)
0 MRRNDSANLLESEHHDRSAFSQTDHNIVAAYLITA 1
2 GIMSIVSNVIVLGIFVKFEELRTATNAIIINLAVTDIGVSGIGYPMSAASDLHGSWKFGHAGCQ 0
0 IYAGLNIFFGMSSIGLLTVVAVDRYLTICRPAI 1
2 GRKMTRSNYTAMILAAWMNGFFWASMPLLGWASYASDPTGATCTINWRKNDA 2
1 SFISYTMTVIAVNFAVPLIVMFYCYYNVSKAMRQYPASRVLENLNIDWSEQVDVTK 0
0 MSVVMILMFLMAWSPYSIVCLWSSFGDPKKISPAVAIMAPLFAKSSTFYNPCIYVVANKK 2
1 FRRAMLSMVQCQTHREITITDVLPMNRSRSPLTL* 0

>PER_galGal Gallus gallus (chicken)
0 MHWNDSANSSESDAEAHSVFTQTEHNIVAAYLITA 1
2 GVISIFSNIVVLGIFVKYKELRTATNAIIINLAFTDIGVSGIGYPMSAASDLHGSWKFGYTGCQ 0
0 IYAALNIFFGMASIGLLTVVAVDRYLTICRPDI 1
2 GRRMTTRNYAALILAAWINAVFWASMPTVGWAGYASDPTGATCTANWRKNDV 2
1 SFVSYTMSVIAVNFVVPLTVMFYCYYNVSRTMKQYTSSNCLESINMDWSDQVDVTK 0
0 MSVVMIVMFLVAWSPYSIVCLWSSFGDPKKISPAMAIIAPLFAKSSTFYNPCIYVIANKK 2
1 FRRAILAMVRCQTRQEITISNALPMTVSLSALTS* 0

>PER_taeGut Taeniopygia guttata (finch)
0 MHWNDSSNSSESDDEAHSAFTQTEHNIVAAYLITA 1
2 GVISIFSNIVVLGIFVKYKELRTATNAIIINLAFTDIGVSGIGYPMSAASDLHGSWKFGYTGCQ 0
0 IYAALNIFFGMASIGLLTVVAVDRYLTICRPDI 1
2 GRRMTTRSYATLILAAWINAVFWSSMPTAGWASYAPDPTGATCTVNWRKNDA 2
1 SFISYTMSVIAVNFVVPLTVMFYCYYNVSRTMKQYASSNCLESINIDWSDQVDVTK 0
0 MSVVMIIMFLVAWSPYSIVCLWSSFGDPKKISPAMAIIAPLFAKSSTFYNPCIYVIANKK 2
1 FRRAILAMVRCQTRQEITINNALPMSVSQSALTSQNSSHLPA* 0

>PER_anoCar Anolis carolinensis (lizard)
0 MFLNDSANSSESDDEPHSAFSQAEHNIVAAYLITA 1
2 GVISLLSNIVVLGIFVKYKELRTATNAIIINLAFTDIGVSGIGYPMSAASDLHGSWKFGYTGCQ 0
0 IYAALNIFFGMASIGLLTVVAIDRYLTICKPHI 1
2 GSRLTATNYTTLILAAWINALFWASMPVVGWASYAPDPTGATCTVNWRKNDT 2
1 SFVSYTMSVIAVNFVIPLSVMFYCYYNVSKTMKYYMRNSCLENINIDWSDQVDVTK 0
0 MSVVMIIMFLLAWSPYSIVCLWSSFGDPKKISPAMAIVAPLFAKSSTFYNPCIYVIANKR 2
1 FRRAILAMIRCQTRQEITINNVLPMSVSQSTIA* 0

>PER_xenTro Xenopus tropicalis (frog)
0 METLAEVSTLLPAGTGTVNISDASSEVHSVFSQSEHNIVAAYLITA 1
2 GVISILSNIIVLGIFVKYKELRTATNAIIINLAFTDIGVSGIGYPMSAASDLHGSWKFGYVGCQ 0
0 IYAGLNIFFGMASIGLLTVVAIDRYLTICRPDI 1
2 GRRISGRHYTAMILAAWINAVFWSVMPVVGWSSYAPDPTGATCTINWRKNDV 2
1 SFVSYTMSVVAVNFVVPLMVMFYCYYNVSRTMKGYGSRSSLGGINADWSDQTDVTK 0
0 MSMVMIVMFLVAWSPYSIVCLWSSFGDPRKIPPAMAIIAPLFAKSSTFYNPCIYVIANKK 2
1 FRRAILSMVQCKSRQEVTLDNHFPMNVSQSTLTT* 0

Neuropsin (2+ marsupials)

Here Sarcophilus can be predicted to contain only NEUR1 because the ancient vertebrate genes NEUR2 and NEUR3 appear to terminate in sauropods and NEUR4 in platypus.

>NEUR1_homSap Homo sapiens (human) OPN5
0 MALNHTALPQDERLPHYLRDGDPFASKLSWEADLVAGFYLTII 1
2 GILSTFGNGYVLYMSSRRKKKLRPAEIMTINLAVCDLGIS 1
2 VVGKPFTIISCFCHRWVFGWIGCRWYGWAGFFFGCGSLITMTAVSLDRYLKICYLSY 1
2 GVWLKRKHAYICLAAIWAYASFWTTMPLVGLGDYVPEPFGTSCTLDWWLAQASVGGQVFILNILFFCLLLPTAVIVFSYVKIIAKVKSSSKEVAHFDSRIHSSHVLEMKLTK 0
0 VAMLICAGFLIAWIPYAVVSVWSAFGRPDSIPIQLSVVPTLLAKSAAMYNPIIYQVIDYKFACCQTGGLKATKKKSLEGFR 2
1 LHTVTTVRKSSAVLEIHEEV* 0

>NEUR1_dasNov
0 MALNHTALPQDDRLPHYLRDGDPFASKLSWEADLVAGFYLTII 1
2 gILSTFGNGYVLYMSSKRKKKLRPAEIMTINLAVCDLGIS 1
2 VVGKPFTIISCFCHRWVFGWIGCRWYGWAGFFFGCGSLITMTAVSLDRYLKICYLSY 1
2 GVWLKRKHAYICLAVIWAYASFWTTMPLVGLGDYVPEPFGTSCTLDWWLAQASVGGQVFILNILFFCLLLPTAVIVFSYVKIIAKVKSSSKEVAHFDSRIHSSHVLEMKLTK 0
0 VAMLICAGFLIAWIPYAVVSVWSAFGRPDSIPIQLSVVPTLLAKSAAMYNPIIYQVIDYKFACCQTGGLRATKKKSLEDFR 2
1 LHTVTTVRESSAVLEVHQEV* 0

>NEUR1_monDom
0 MALNHSVSPQDDYIPHYLRDGDPFASKLSWEADLVAGFYLTII 1
2 GVLSTLGNGYVIYMSSKRKKKLRPAEIMTVNLAVCDLGIS 1
2 VVGKPFTIISCFSHRWVFGWVGCRWYGWAGFFFGCGSLITMTAVSLDRYLKICHLSY 1
2 GTWLKRHHAFICLALIWAYATFWATVPFAGVGSYAPEPFGTSCTLDWWLAQASVAGQAFVLSILFFCLLFPTAVIVFSYVKIILKVKSSTKEVAHYDTRIQNSHILEMKLTK 0
0 VAMLICAGFLIAWIPYAVVSVWSAFGQPDSIPVQFSVVPTLLAKSAAMYNPIIYQVIDCKFACCQSGGQKAAKKESLRTYR 2
1 LHTVTTVRRSSAVLEIHQEv* 0

>NEUR1_macEug
0  1
2 GVLSTLGNGYVIYMSSKRKKKLRPAEIMTVNLAVCDLGIS 1
2 VVGKPFTIISCFCHRWVFGWVGCRWYGWAGFFFGCGSLITMTAVSLDRYLKICHLSy 1
2 GTWLKRHHAYICLVIIWAYATFWATMPLAGLGNYAPEPFGTSCTLDWWLAQASVTGQTFILNILFFCLLLPTAVIVFSYVKIIAKVKSSTKEVAHFDSRIQSSHVLEMKLTK 0
0  2
1 RHTVSTIRKSSSVSETYQEV* 0

>NEUR1_sarHar Sarcophilus harrisii (tasmanian_devil) 4 of 6 exons
0 1
2 GVLSTLGNGYVIYMSSKRKKKLRPAEIMTVNLAVCDLGIS 1
2 VVGKPFTIISCFSHRWVFGWVGCRWYGWAGFFFGCGSLITMTAVSLDRYLKICHLSY 1
2 GTWLKRHHAYICLVIIWAYATFWATMPLAGLGNYAPEPFGTSCTLDWWLAQASVTGQTFILNILFFCLLLPTAVIVFSYVKIIAKVKSSTKEVAHFDSRIQNSHSHVLEMKLTK 0
0 VAMLICAGFLIAWIPYAVVSVWSAFGQPDSIPVQFSVVPTLLAKSAAMYNPIIYQVIDCKFACCQSGGQKAAKKESLRDYR 2
1 * 0

>NEUR1_ornAna
0 MTNYSAPQLGDYLPHYLREGDPFVSKLSWEADLVAGVYLVII 1
2 GVLSTLGNGYVIYMSSRRKKKLRPAEIMTVNLAVCDLGIS 1
2 VVGKPFTIVSCFCHRWVFGWMGCRWYGWAGFFFGCGSLITMTAVSLDRYLKICHLSY 1
2 GTWLKRHHAYICLAIIWAYASFWATMPLVGLGNYAPEPFGTSCTLDWWLAQASVAGQAFILNILFFCLLLPTAVIVFSYVKIIAKVKSSTKEVAHFDSRIQNSHVLEMKLTK 0
0 VAMLICAGFLIAWIPYAVVSVWSAFGQPDSIPIQFSVVPTLLAKSAAMYNPIIYQVIDCRISCCRLGGPKTGKKESLKNSR 2
1 SHSMSTIRKPSAVSGPHQEV* 0

>NEUR1_galGal
0 MASDCNSSSQEEYLPHYMQQEDPFASKLSREADIIAGFYLTVI 1
2 GILSTLGNGYVIFMSSKRKKKLRPAEIMTVNLAVCDLGIS 1
2 VVGKPFSIISFFSHRWIFGWMGCRWYGWAGFFFGCGSLITMTAVSLDRYLKICHLAY 1
2 GTWLKRHHAFICLALIWAYATFWATVPFAGVGSYAPEPFGTSCTLDWWLAQASVAGQAFVLSILFFCLLFPTAVIVFSYVKIILKVKSSTKEVAHYDTRIQNSHILEMKLTK 0
0 VAMLICAGFLIAWIPYAVVSVWSAFGQPDSVPIQFSVVPTLLAKSAAMYNPIIYQVIDCKFACCRSGGPKTLQKKSSLKESR 2
1 MYTISSHRDSAALSGTQLEV* 0

>NEUR2_galGal Gallus gallus GenBank 5'UTR mistranslated as coding -B4GALT6 -NEUR2_galGal -KIAA1012
0 MDPSFANSTFQSKITEAADIVVGTCYMVF 1
2 GICSLCGNSILLYISYKKKHLLKPAEYFIINLAISDLAMTLTLYPLAVTSSLSHR 2
1 WLYGKHICLFYAFCGLFFGICSLSTLTLLSVVCCLKICFPAY 1
2 GNRFRRKHGQILIACAWTYAAIFACSPLAHWGEYGEEPYGTACCIDWQSTNVDVMSMSYTVVLFVLCFILPCGVIVTSYSLILVTVKESRKAVEQHVSGPTRINNVQTITAK 0
0 LSIAVCIGFFAAWSPYAIIAMWAAFGSIDKIPPLAFAIPAVFAKSSTLYNPIIHLLLKPNFRSNIAKDFTVIQQLCVRCCFCVKELQTYRSTFNTGLRTFKGKNESSCNALPIMEG
CSYFPSEKGSHTFECFKSYPNCFQERLSTMGCHLQDCESLENDLQVEVTQGSRNSMKVVEQEEKSTELDNLEITLEAVPVSCTFTDL* 0

>NEUR3_galGal Gallus gallus cOpn5L2 mRMA for Opsin 5-like 2 AB368183 chr3 XM_420056 CN231992 testis exon 2^3 rel NEUR1/2
0 MEEQYISKLHPVVDYGAGVFLLII 1
2 AILTILGNSAVLATAVKRSSLLKSPELLTVNLAVADIGMAISMYPLAIASAWNHAWLGGDASCIYYALMGFLFGVCSMMTLCAMAVIRFLVTNSSKSN 1
2 SNKISKNTVHILITFIWLYSLLWAILPLVGWGYYGPEPFGISCTIAWSKFHSSSNGFSFILSMFLLCTVLPALTIVACYLGIAWKVHKAYQEIQNINRIPHAAKLEKKLTL 0
0 MAVLISVGFLSAWTPYAAASFWSIFNSSDSLQPIVTLLPCLFAKSSTAYNPFIYYIFSKTFRHEIKQLQCCWGWRVHFFSADNSAENSVSMMWSGRDNIRLSPTAKVESQGAARH*

>NEUR4_ornAna Ornithorhynchus anatinus (platypus) XM_001508128  
0 MSLSHSLQVPWRNNLTFLNKEAQVSEQGETIIGIYLLAL 1
2 GWMSWFGNSMVIFILHRQRGILNPTDYLTFNLAVSDASVSVFGYSRGIIEIFNVFRDDGFLITSIWTCQ 0
0 VDGFLTLLFGLASINTLAMISVTRYIKGCHPHR 1
2 GHFINTANISVALILIWVSALFWSAGPVLGWGSYT 1
2 DRMYGTCEIDWAEANFSSICKSYIISIFFCCFFLPVSIMFFSYVSIIKMVKSSHTLAGADDPTDRQRRLDRDVTR 0
0 VSVVICTAFIVAWSPYAVISMWSAFGHSVPNLTSVLASLFAKSASFYNPIIYFGMNSKFRKDILVLLPCAKESKEPVKLKKFKNLRQKQGFTLQKPEKAHVLQVPDSGPMSLINTPPLGNRNSFDLACDNSDFECVRL* 0

Melanopsin (3+ marsupials)

Here Sarcophilus can be expected to have the main melanopsin but not the paralog MEL2 which terminates in sauropods

>MEL1_homSap Homo sapiens (human) Gq -GRID1 -WAPAL +LDB3 +BMPR1A 483 aa NM_033282 melanopsin OPN4   
0 MNPPSGPRVPPSPTQEPSCMATPAPPSWWDSSQSSISSLGRLPSISPT 0 
0 APGTWAAAWVPLPTVDVPDHAHYTLGTVILLVGLTGMLGNLTVIYTFCR 2
1 SRSLRTPANMFIINLAVSDFLMSFTQAPVFFTSSLYKQWLFGET 1
2 GCEFYAFCGALFGISSMITLTAIALDRYLVITRPLATFGVASKRRAAFVLLGVWLYALAWSLPPFFGW 1
2 SAYVPEGLLTSCSWDYMSFTPAVRAYTMLLCCFVFFLPLLIIIYCYIFIFRAIRETGR 2
1 ALQTFGACKGNGESLWQRQRLQSECKMAKIMLLVILLFVLSWAPYSAVALVAFAG 2
1 YAHVLTPYMSSVPAVIAKASAIHNPIIYAITHPKYR 2
1 VAIAQHLPCLGVLLGVSRRHSRPYPSYRSTHRSTLTSHTSNLSWISIRRRQESLGSESEV 0
0 GWTHMEAAAVWGAAQQANGRSLYGQGLEDLEAKAPPRPQGHEAETPGK 0
0 TKGLIPSQDPRM* 0

>MEL1_proCap
0 MNPPWGPRVPSRPAQEPSCMSTPASAGRWDSSQATASSLAELPPSSPT 0
0 EARTQTADWVPFPTVDVPDYAHYTLGTVILLVGLTGVLGNLMVIYIFFR 2
1 SRGLRTPANMFIINLAISDFLMSLTQAPVFFASSLYKRWLFGEA 1
2 GCEFYAFCGALFGITSMITLTAIALDRYLVITRPLATIGVVSKRRTALVLLGTWLYALAWSLPPFFGW 1
2 SAYVPDGLLTSCSWDYKSFMPSARTYTMLLCCFVFFLPLLVIIYCYVFIFKAIRETGR 2
1 ALQTFGACEGASETPRQWQRLQSEWKMAKIALLAILLYVLSWAPYSTVALVGFAG 2
1 YAHVLTPYMNSVPAVIAKASAIHNPIIYAITHPKYR 2
1 MAIAQHLPCLGVLLGVSDQHTRPYTSYRSTHHSTLSSQASDISWISGRRRQASLGSESEV 0
0 GWTDTEAAAAWEGAQQVSGRASCSQVLESMEANTPPRPQGWGPETPRK 0
0 VKGLPLLDPRA* 0

>MEL1_smiCra Sminthopsis crassicaudata (dunnart) DQ383281
0 MNPSPMLRHLSCPAQDSNCTKIMASISEWNNTEVDAYHLVDLPPITPT 0
0 AVVLPPYSQKVFPTADVPDYAHYTIGATILVVGFTGVLGNLLVIYTFCR 2
1 SRSLRTPANMFIINLAISDFFMSFTQAPVFFASSLYERWIFGEK 2
1 GCEFYAFCGALFGITSMITLMVIALDRYFVITRPLASIGMISKKKTGLILLGVWLYSLAWSLPPFFGW 1
2 SAYVPEGLLTSCSWDYTTFTPSVRAYTILLFCFVFFIPLTVIIYCYIFIFRAIKDTNK 2
1 AVQNIGSSEHTPSLRHFQRMKNEWKMAKIALVVILLFVLSWAPYSTVALVAFAG 2
1 YSHVLTPYMNSVPAIIAKASAIHNPIIYAISHPKYR 2
1 MAIAQNFPCLRAVLGIRHPRTQSFSSYRFTHRSTTASQASDISWQSRGRRQLSLGSESEA 0
0 GWNNIETGLTLRSLEGSCGMDEETMDTRELSASTKAKGQSWETLAKTLEE 0
0 MDDLSLLEAGTLLSSLDLQI* 0

>MEL1_sarHar Sarcophilus harrisii (tasmanian_devil)96% identity smiCra last exon missing FKUJDAX01C1KMN needed
0 MNPSPMLRHLSCSAQDTNCTKIMASISEWNNTEVDAYHLVDLPPITPT 0
0 AVVLPPYSQNVFPTADVPDYAHYTIGATILVVGFTGVLGNLLVIYTFCR 2
1 SRSLRTPANMFIINLAISDFFMSFTQAPVFFASSLYKRWIFGEK 2
1 GCEFYAFCGALFGITSMITLMVIALDRYFVITRPLASIGMISKKKTGLILLGVWLYSLAWSLPPFFGW 1
2 sAYVPEGLLTSCSWDYTTFTPSVRAYTILLFCFVFFIPLIVIIYCYIFIFRAIKDTNK 2
1 AVQNIGSRASTPSPRHFQRMKNEWKMAKIALVVILLFVLSWAPYSTVALVAFAG 2
1 YSHVLTPYMNSVPAIIAKASAIHNPIIYAISHPKYR 2
1 MAIAQNFPCLRAVLGIRHPRTQSFSSYRFTHRSTTASQASDISWQSRGRRQLSLGSESEA 0
0 GWNNIEAGIEGLTLRSLEGYCGMDEETMETREPSASAKAKGQ    0 
0 * 0

>MEL1_macEug Macropus eugenii frag
0 AVVLPPHSRNIFPTADVPDHAHYTVGAIILVVGFTGVLGNLLVIYTFCR 2
1 SRSLRTPANMFIINLAISDFFMSFTQAPVFFANSLYKRWIFGEK 2
2 GCEFYAFCGALFGITSMITLMVIALDRYFVITRPLASIGVVSKKKTGLILLGVWLYSLAWSLPPFFGW 1
2 AYVPEGLLTSCSWDYTTFTPSVRAYTMLLFCFVFFIPLIVIIYCYIFIFKAIQDTNK 2
1 ALQNIRSSESTASPRHFQRMKSEWKMAKIALVVILLFVLSWAPYSTVALVAFAG 2
1 SHILTPYMNSVPAIIAKASAIHNPIIYAISHPKYR 2

>MEL1_monDom Monodelphis domestica (opossum) Gq -GRID1 -WAPAL +LDB3 +BMPR1A
0 MNPSPMLRGLSCPAQDTNCTKIMASMSEWNNTEEDAYHLVDLPSIAPT 0
0 AVVLPPSSQNIFPTVDVPDHAHYTIGAIILAVGITGMLGNFLVIYTFCR 2
1 SHSLRTPANMFIINLAISDFFMSFTQAPVFFASSMYKRWIFGEK 1
2 ACEFYAFCGALFGITSMITLMAIALDRYFVITRPLASIGVISKKKTGFILLGVWLYSLAWSLPPFFGW 1
2 SAYVPEGLLTSCSWDYTTFTPSVRAYTMLLFCFVFFIPLIVIIYCYIFIFRAIQDTNK 2
1 AVHSIGSGESTASPRHCQRMKNEWKMAKIALVVILLYVLSWAPYSTVALVAFAG 2
1 YSHILTPYMNSVPAIIAKASAIHNPIIYAISHPKYR 2
1 MAIAQNFPCLRALLCVRHPRTRSFSSYRFTRRSTMTSQASDISWLPRGRRQLSLGSESEI 0
0 GWNNMEAGTTSLTSRNQQGSCRMDQETMETRELAAIAKAKGRSWETLEK 0
0 TLEEMDDSSLLEVSVDMEQ* 0

>MEL1_ornAna Ornithorhynchus anatinus (platypus) fragment
0 0
0   FPTADVPDHAHYTIGATILAVGFTGVLGNLLVIYTFCR 2
1 SRSLRTPANMFIINLSISDFFMSLTQAPVFFASSLHKRWIFGEK 1
2 GCQLYAFCGALFGITSMITLTVIALDRYFVITRPLASIGVISKKRALLILTGVWFYSLAWSLPPFFGW 1
2 sAYVPEGLLTSCSWDYMTFTPPVRAYTMLLFCFVFFIPLIMIIYCYFFIFRAIRGTNK 2
1 AVETIGSDDCRGSQRQCQRMKNEWKTAKIALMVILLYVISWCPYSVVALVAFAG
1 YSHLLTPYMNSVPAVIAKSSAIHNPIIYAITHPKYR 2
1 MAITKYIPCLGPLLRVSRQDSRSSSHYASSRRSTVTSQSLDGSWLPGRRRPLSSASDSES 0
0 0
0 * 0

>MEL1_anoCar Anolis carolinensis diverged frag
0 0
0 ERTMFNLPDPFPTVDVPTHAHYTIGAVILVVGITGTLGNLLVIYVFFR 2
1 IRGLRTPANMFVINLAVSDFL 1
2 GCELYAFCGALFGIASMITLTVIALDRYFVITRPLASIGAMSTKKALLILSGVWLYSLAWSLPPFFGW 1
2 sAYVPEGLLTSCSWDYITFTPSVRAYTMLLFCFVFFIPLIAIIYSYVFIFIAIKNSNR 2
1 AVQRTNSDNSKEGQKLYQKLKNEWKMAKVALIVILLVISWSPYSVVALVAFAG 2
1 YSHLLTPYMNSVPAVIAKASVIHNPIIYAIVHPKYR 2
1 MAIAKFLPCLGSLLRVPRKDSSYPSTRRPTVTSQSSDINGVPRGHRRLSSVSDSES 0
0 DWTDTEADISSQNSRVASGSISYRIYEDTTETIKVKSKMRSHDSGIFER 0
0 0
0 TGEDLNAFGWRREESYSGPSTSSQIPSIIVTFSNVQRTDLPLESSSGALCSRNSSYSWEKDSNS* 0

>MEL1_galGal Gallus gallus (chicken) Gq short exon 1 -GRID1 -WAPAL +LDB3 +BMPR1A 529 aa 16856781 AY88294 melanopsin OPN4m   
0 MDLPPRAPT 0
0 KMTVKDVRGAFPTVDVPDHAHYTIGTVILIVGITGTLGNFLVIYAFCR 2
1 SRTLQKPANIFIINLAVSDFLMSITQSPVFFTNSLHKRWIFGEK 1
2 GCELYAFCGALFGITSMITLMVIALDRYFVITKPLASVRVMSKKKALIILVGVWLYSLAWSLPPFFGW 1
2 SAYVPEGLLTSCSWDYMTFTPSVRAYTMLLFCFVFFIPLIAIIYSYVFIFEAIKKANK 2
1 SVQTFGCKHGNRELQKQYHRMKNEWKLAKIALIVILLYVISWSPYSVVALVAFAG 2
1 YSHVLTPFMNSVPAVIAKASAIHNPIIYAITHPKYR 2
1 TAIATYVPCLGFLLRVSPKESRSFSSYPSSRRTTITSQSSETSGLQKGKRRLSSISDSES 0
0 GCTDTETDITSMISRPASSQVSYEMGEDTTQTSDLGGKPKVKSHDSGIFRK 0
0 TVVDADEIPMVEINDTEHSATSTCKTSEKCNVEEIQ 0
0 RSESLSGIGLREGESRHRTSASQIPSIIITYSNVQGVELHSGYSAGFLHPKNKSHKQNKSSNS* 0

>MEL2_galGal Gallus gallus (chicken) Gq 0.0.1.2.2.1.1.1.0.0 indel +GRID2 +SMARCAD1 -PGDS -SEC24B +COL25A1 544 aa 000 nm 17977531 NM_204625 full
0 MGTQPHSVTKSEIPDHVLYTVGTCVLVIGSIGIIGNLLVLYAFYS 2
1 NKKLRTPQNFFIMNLAVSDFLMSASQAPICFVNSLHREWILGDI 1
2 GCDLYAFCGALFGITSMMTLLAISVDRYLVITKPLRSIQWTSKKRTIQIIAAVWLYSLGW 1
2 SVAPLLGWSSYVPEGLMISCTWDYVTYSPANRSYTMILCCCVFFIPLIIILHCYLFMFLAIRSTGR 2
1 DVQKLGSCSRKSFLSQSMKNEWKLAKIAFVVIIVYVLSWSPYACVTLIAWAG 2
1 RGNTLTPYSKSVPAVIAKASAIYNPIIYAIIHPRYR 2
1 KTIHNAVPCLRFLIRISKNDLLRGSINESSFRTSLSSHQSLAGRTKNTCVSSVSTGEA 0
0 NWSDVELDTVEPAHEKLQPRRSHSFSSSLRQKRDLLPDSYSCSEETEEK 0
0 VSLSSSYLEKVLGRSAFPSSPVALVTSSLRAASLPVGLNSSSASRGAGSDISQMKTEESHNNGGLDSIVSNTVPQIIIIPTSETNLFQEEPEEEETELFHFHDKKNNLLDLEGLSSSTEFLEAVEKFLS* 0

PRNP (3+ marsupials)

The Sarcophilus repeat region is of considerable interest -- the high GC content of this region makes it difficult to sequence and so provides a test of the 454 technology and Newbler assembler. This region consists in placentals a five octapeptide repeat, in marsupials and platypus a five nona- or decapeptide residue repeat that may resolve fine details of the marsupial phylogenetic tree, which in birds, lizards, turtles, frogs and fish is a hexapeptide repeat with trimeric internal substructure. Even though the single exon gene is clearly orthologous in all these species, the repeat regions within it are not directly comparable because they have expanded and contracted through replication slippage, plus experienced the odd repeat length change in marsupials and another in placentals.

The Sarcophilus prion gene has very high coverage that overcomes the occasional problem with frameshifts and allows the gene to be accurately tiled. However familiarity with the gene and reliable fiducial sequences are key to rapid assembly of the full length gene. No sequencing difficulties were observed in the high GC repeat region. The gene is very normal and has no indications whatsoever of abnormal numbers of repeats (4) or prion disease disposition.

Dasypus         MVRSRVGCWLLLLFVATWSELGLC KK.RPKPGGGWNTGG  SRYPGQ GSPGG NRYP     PQGGG  WGQ PHGGG  WGQ PHGGG  WGQ PHGGG  WGQ PHGGG  WGQ  GGAHGQ                
Trichosurus     MGKIQLGYWILVLFIVTWSDLGLC KKPKPRPGGGWNSGGS NRYPGQPGSPGG NRYPGWGH PQGGGTNWGQ PHPGGSNWGQ PHPGGSSWGQ PH GGSNWGQ             GG YN  
Sarcophilus     MGKIRLGYWILALFIVTWSDLGLC KKPKPRPGGGWNSGGS NRYPGQPGSAGG NRYPGWGH PQGGGTNWGQ PHPGGSSWGQ PHAGGSNWGQ PH.GGSNWGQ            SGSSYNQ
Monodelphis     MGKIHLGYWFLALFIMTWSDLTLC KKPKPRPGGGWNSGG  NRYPGQ    SG     GWGH PQGGGTNWGQ PHAGGSNWGQ PRPGGSNWGQ PHPGGSNWGQ PHPGGSNWGQ AGSSYNQ 
Macropus        MAKIQLGYWILALFIVTWSELGLC KKPKTRPGGGWNSGGS NRYPGQPGSPGG NRYPGWGH PQGGGTNWGQ PHPGGSSWGQ PHAGGSNWGQ PH.GGSNWGQ            GGGSYG
Ornithorhynchus ------------------------ -------GGGWNSG   NRYPGQPANPG      GWGH PQGGGASWGH PQGGGASWGH PQGGGSNWGH PQGGGASWGH PQ          GGGYS  

Dasypus         WNKPSKPKTNM KHVAGAAAAGAVVG LGGYLVGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRSVEQYSSEKNFVHD CV                         MERVVEQMCITQYQ 
Trichosurus     KWKPDKPKTNL KHVAGAAAAGAVVGGLGGYMLGSAMSRPVIHFGNEYEDRYYRENQYRYPNQVMYRPIDQYSSQNNFVHD CVNITVKQHTTTTTTKGENFTETDIKIMERVVEQMCITQYQN
Sarcophilus     KWKPDKPKTNM KHMAGAAAAGAVLGSLGGYVLGSAMSRPIMHFGNDYEDRYYRENQYRYPNQVMYRPIDQYSSQNNFVHD CVNITVKQHTTTTTTKGENFTETDIKIMERVVEQMCITQYQN
Monodelphis     KWKPDKPKTNM KHVAGAAAAGAVVGGLGGYMLGSAMSRPIMHFGNDYEDRYYRENQYRYPNQVMYRPIDQYNNQNNFVHD CVNITVKQHTTTTTTKGENFTETDIKIMERVVEQMCITQYQN
Macropus        KWKPDKPKTNL KHVAGAAAAGAVVGGLGGYMLGSAMSRPVMHFGNEYEDRYYRENQYRYPNQVMYRPIDQYGSQNSFVHD CVNITVKQHTTTTTTKGENFTETDIKIMERVVEQMCITQYQN
Ornithorhynchus KYKPDKPKTGM KHVAGAAAAGAVVGGLGGYMIGSAMSRPPMHFGNEFEDRYYRENQNRYPNQVYYRPVDHFCSQDGFVRD CVNITVTQHTVTTT.EGKNLNETDVKIMTRVLEQMC 

The signal region of Sarcophilus PRNP is expected to show the same length as the other 3 known marsupial sequences, which is confirmed by the sequence. Placentals exhibit a one residue deletion relative to this ancestral length.

MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Homo sapiens
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Pan troglodytes
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Gorilla gorilla
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Pongo pygmaeus
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Nomascus leucogenys
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Hylobates lar
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Symphalangus syndactylus
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Macaca arctoides
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Macaca fascicularis
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Macaca fuscata
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Macaca mulatta
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Macaca nemestrina
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Papio hamadryas
MA--NLGCWMLFLFVATWSDLGLCKK--RPKPG Callithrix jacchus
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Cebus apella
MA--NLGCWMLVVFVATWSDLGLCKK--RPKPG Cercopithecus aethiops
MA--NLGCWMLVVFVATWSDLGLCKK--RPKPG Cercopithecus dianae
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Colobus guereza
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Presbytis francoisi
MA--NLGCWMLVLFVATWSDLGLCKK--RPKPG Saimiri sciureus
MA--KLGYWLLVLFVATWSDVGLCKK--RPKPG Tarsius syrichta
MA--NLGCWMLVVFVATWSDVGLCKK--RPKPG Microcebus murinus
MA--RLGCWMLVLFVATWSDIGLCKK--RPKPG Otolemur garnettii
ME--NLGCWMLILFVATWSDIGLCKK--RPKPG Cynocephalus variegatus
MA--QLGCWLMVLFVATWSDVGLCKK--RPKPG Tupaia belangeri
MA--NLGYWLLALFVTMWTDVGLCKK--RPKPG Mus musculus
MA--NLGYWLLALFVTTCTDVGLCKK--RPKPG Rattus norvegicus
MA--NAGCWLLVLFVATWSDTGLCKK--RPKPG Cavia porcellus
MA--NLGCWLLVLFVATWSDLGLCKK--RTKPG Dipodomys ordii
MV--NPGCWLLVLFVATLSDVGLCKK--RPKPG Spermophilus tridecemlineatus
MA--HLGYWMLLLFVATWSDVGLCKK--RPKPG Oryctolagus cuniculus
MA--HLSYWLLVLFVAAWSDVGLCKK--RPKPG Ochotona princeps
MVKSHIGSWILVLFVAMWSDVGLCKK--RPKPG Bos taurus
MVKSHIGGWILVLFVAAWSDIGLCKK--RPKPG Sus scrofa
MVKSHMGSWILVLFVVTWSDMGLCKK--RPKPG Vicugna vicugna
MVKSHVGGWILVLFVATWSDVGLCKK--RPKPG Equus caballus
MVRSHVGGWILVLFVATWSDVGLCKK--RPKPG Diceros bicornis
MVKSLVGGWILLLFVATWSDVGLCKK--RPKPG Myotis lucifugus
MVKNYIGGWILVLFVATWSDVGLCKK--RPKPG Pteropus vampyrus
MVKSHIANWILVLFVATWSDMGFCKK--RPKPG Tursiops truncatus
MVKSHIGGWILLLFVATWSDVGLCKK--RPKPG Canis lupus familiaris
MVKSHIGSWILVLFVAMWSDVGLCKK--RPKPG Felis catus
MVKSHIGSWLLVLFVATWSDIGFCKK--RPKPG Mustela putorius
MVKSHIGSWLLVLFVATWSDIGFCKK--RPKPG Mustela vison
MVKSHIGSWILVLFVAMWSDVGLCKK--RPKPG Ailuropoda melanoleuca
MVKNHVGCWLLVLFVATWSEVGLCKK--RPKPG Erinaceus europaeus
MVTGHLGCWLLVLFMATWSDVGLCKK--RPKPG Sorex araneus
MVKSHLGCWIMVLFVATWSEVGLCKK--RPKPG Cyclopes didactylus
MVRSRVGCWLLLLFVATWSELGLCKK--RPKPG Dasypus novemcinctus
MVKGTVSCWLLVLVVAACSDMGLCKK--RPKPG Echinops telfairi
MVKSSLGCWILVLFVATWSDMGLCKK--RPKPG Loxodonta africana
MVKSSLGCWMLVLFVATWSDVGLCKK--RPKPG Procavia capensis
MAKIQLGYWILALFIVTWSELGLCKKP-KTRPG Macropus eugenii
MGKIHLGYWFLALFIMTWSDLTLCKKP-KPRPG Monodelphis domestica
MGKIRLGYWILALFIVTWSDLGLCKKP-KPRPG Sacophilus harrisii
MGKIQLGYWILVLFIVTWSDLGLCKKP-KPRPG Trichosurus vulpecular
MARLLTTCCLLALLLAACTDVALSKKG-KGKPS Gallus gallus
MAKLPGTSCLLLLLLLLGADLASCKKG-KGKPG Taeniopygia guttata
MARLLTTCCLLALLLAACTDVALSKKG-KGKPG Meleagris gallopavo
MGKHQMTCWLAIFLLLIQANVSLAKK--KPKPS Anolis carolinensis
MRRFLVTCWIAVFLILLQTDVSLSKKG-KNKPG Gekko gekkko
MGRYRLTCWIVVLLVVMWSDVSFSKKG-KGKGG Trachemys scripta (turtle)
MGRHLISCWIIVLFVAMWSDVSLAKKG-KGKTG Pelodiscus sinensis (turtle)
MPQSLWTCLVLISLICTLTVSSKKSGGGKSKTG Xenopus laevis
MLRSLWTSLVLISLVCALTVSSKKSGSGKSKTG Xenopus topicalis

>PRNP_sacHar Sarcophilus harrisii (tasmanian_devil) single exon gene YVLG like Dasypus
MGKIRLGYWILALFIVTWSDLGLCKKPKPRPGGGWNSGGSNRYPGQPGSAGGNRYPGWGHPQGGGTNWGQPHPGGSSWGQPHAGGSNWGQPHGGSNWGQ
SGSSYNQKWKPDKPKTNMKHMAGAAAAGAVLGGVGGYVLGSAMSRPIMHFGNDYEDRYYRENQYRYPNQVMYRPIDQYSSQNNFVHDCVNITVKQHTTTTTT
KGENFTETDIKIMERVVEQMCITQYQNEYRAAQYSYNMAFFSAPPVTLLLLGFLIFLIVS*

>PRNP_mdo Monodelphis domestica opossum, from frameshifted genomic
MGKIHLGYWFLALFIMTWSDLTLCKKPKPRPGGGWNSGGNRYPGQSGGWGHPQGGGTNWGQPHAGGSNWGQPRPGGSNWGQPHPGGSNWGQPHPGGSNWG
QAGSSYNQKWKPDKPKTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPIMHFGNDYEDRYYRENQYRYPNQVMYRPIDQYNNQNNFVHDCVNITVKQHTTT
TTTKGENFTETDIKIMERVVEQMCITQYQNEYRSAYSVAFFSAPPVTLLLLSFLIFLIVS*

>PRNP_tvu Trichosurus vulpecular brushtail opossum
MGKIQLGYWILVLFIVTWSDLGLCKKPKPRPGGGWNSGGSNRYPGQPGSPGGNRYPGWGHPQGGGTNWGQPHPGGSNWGQPHPGGSSWGQPHGGSNWGQGGY
NKWKPDKPKTNLKHVAGAAAAGAVVGGLGGYMLGSAMSRPVIHFGNEYEDRYYRENQYRYPNQVMYRPIDQYSSQNNFVHDCVNITVKQHTTTTTTKGENFTETDIKIMERVVEQM
CITQYQAEYEAAAQRAYNMAFFSAPPVTLLFLSFLIFLIVS*

>PRNP_meu Macropus eugenii (tammar wallaby)
MAKIQLGYWILALFIVTWSELGLCKKPKTRPGGGWNSGGSNRYPGQPGSPGGNRYPGWGHPQGGGTNWGQPHPGGSSWGQPHAGGSNWGQPHGGSNWGQ
GGGSYGKWKPDKPKTNLKHVAGAAAAGAVVGGLGGYMLGSAMSRPVMHFGNEYEDRYYRENQYRYPNQVMYRPIDQYGSQNSFVHDCVNITVKQHTTTTTT
KGENFTETDIKIMERVVEQMCITQYQNEYQAAQRYYNMAFFSAPPVTLLLLSFLIFLIVS*
 
>PRNP_oan  Ornithorhynchus anatinus platypus fragment
PHWGKSPVHHWIIDICVVHLERRCRGHLHPNPCPGGRCVQQQPNRYPGQPATPGGWGHPQGGGASWGHPQGGGSNWGHPQGGGASWGHPQGGGYSKYKPDKPKTG
MKHVAGAAAAGAVVGGLGGYMIGSAMSRPPMHFGNEFEDRYYRENQNRYSNQVYYRPVDQYGSQDGFVRDCVNITVTQHTVTTTEGKNLNETDVKIMTRVLEQMCVNLY

PRND (2+ marsupials)

Sarcophilus sequence for this intronless gene is a welcome addition to a limited existing set of early-diverging mammalian orthologs. With more data, the relative rates of divergence of PRND from its parental paralog PRNP could be compared in marsupial and placentals. It appears from the mere 75% identity between tasmanian devil and wallaby that doppels are diverging quite rapidly both from PRNP and from each other in the marsupial lineage, indicating some selectional pressure but not a hugely important function (that is, many residue positions have an increased reduced alphabet).

>PRND_hsa Homo sapiens (human) full
MRKHLSWWWLATVCMLLFSHLSAVQTRGIKHRIKWNRKALPSTAQITEAQVAENRPGAFIKQGRKLDIDFGAEGNRYYEANYWQFPDGIHYNGCSEANVTKEAFVTGCINATQAANQGEFQKPDNKLHQQVLWRLVQELCSLKHCEFWLERGAGLRVTMHQPVLLCLLALIWLTVK*

>PRND_dno Dasypus novemcinctus
MRKHLGGWRLAIVCVLLSGHLSMVKARGIKHRIKWNRKAAPGAAQVTEARVAEQRPGAFVRQGRRLDIDFGAEGNRYYEANYWQLPDGILYDGCAEANVTKEALVAGCVNATQLANQAELAHEGQDTLHRRVLGRLIRELCALKRCKFWPDRAAGPRLVRGAPVFGGLLLLIWLLVR*

>PRND_laf Loxodonta africana African elephant Afrotheria 176 aa revised/corrected
MRKHLGAWWLAIAFVLLLSHLSMVTARGIKHRIKWNRKALPNTGHVTAAQVTETRPGAFIRHGRKLDIDFGAEGNRYYEANYWQFPDGIHYDGCSEANVTKEMFVTSCINTTQAANQEEFSRKQDNKVYQRILWRLIRELCSVKHCDFWLDRGGGLRVSLDQPVMLCLLVFIWFMVK*  

>PRND_sacHar Sarcophilus harrisii (tasmanian_devil) single exon gene 77% macEug
MRTPLETWWIAIFFTLLFSDLSLVKAKGIRQRNKSNRKSLQTNRANPTREQPSKILQGTFIRKGRKLSINFGEEGNSYYEAHYKLFPDEIHYVGCAESSVTKDVFISNCVNVTHTANKLEPPEERNSSAIYSRVLEQLIKELCALKYCEFGMQIGAGFRLSLDQSMMVYLMILAFFIVK*

>PRND_mdo Monodelphis domestica doppel genomic revised +rassf2 -prnd -prnp
MRRHLGICWIAIFFALLFSDLSLVKAKTTRQRNKSNRKGLQTNRTNPTTVQPSEKLQGTFIRNGRKLVIDFGEEGNSYYATHYSLFPDEIHYAGCAESNVTKEVFISNCVNATRVINKLEPLEEQNISDIYSRILEQLIKELCALNYCEFRTGKGTGLRLSLDQYVMVYLVILTCLIVK*

>PRND_meu Macropus eugenii wallaby 
MRRHLGTWWTAIFFALLFSDLSLVKAKGTRQRNKSNRKSLQTNRVNPTTAQPSEILQGAFIRQGRKLSIDFGEEGNSYYETHYQLFPDEIHYVGCTESNVTKDIFISNCMNATHAVNNLETLEEKNASDIHSRVLEQLIKELCALKYCELETETGAGLKLSLDQSVMVYLVILTCLIVK*

>PRND_oan Ornithorhynchus anatinus  platypus 42% to opposum 187 aa 4 cys in register
MMTVRRRRRSGGARWLLVFLVLLSGDLSSLQARGPRPRNKAGRKPPPSNAGPDSPAPRPPAGARGTFIRRGGRLSVDFGPEGNGYYQANYPLLPDAIVYPDCPTANGTREAFFGDCVNATHEANRGELTAGGNASDVHVRVLLRLVEELCALRDCGPALPTGPAPRPGPPGPPAALALLTLVLLGAQ*

>PRND_aca Anolis carolinensis weak but real! scaffold_1221:78,884-117,121 syntenic, oriented like PRNP but no larger
MMQRPLVVAILLTALWSEVCLCRRVSGSANRRNKKTSTTTSAPKLQSSTTATTFQGNLCRGGQMIDNMDLEPNDKVYYKANLKIFPDGLYYPNCSLLLQPNTTKEELVGECVNFTIASNKLNLSKGKDLSNTKERVMWVLIHHLCANESCGQPCPLLQNSGNLHYIGQVLTVFVGLIGCSFLSAK*