PRDM11: giant missing exon
From genomewiki
Revision as of 08:19, 12 December 2011 by Tomemerald (talk | contribs) (→PRDM11 and amniote phylogeny)
Introduction: PRDM11
No vertebrate genome outside of mammals encodes a protein closely related to either PRDM7 or PRDM9. Since the latter are responsible for initiation of meiosis -- which arose very early in single-cell eukaryotes -- this raises questions about the meiotic process in the ancestral amniote, how that precedes without PRDM7/9 in contemporary birds and reptiles, and how PRDM7/9 arose and -- in mammals -- displaced the older mechanism.
A 2003 study reported that PRDM7 expression was strongly elevated in chicken auditory epithelia suggesting an auxiliary role outside meiosis. However bird genomes (and for that matter, those of all earlier vertebrates) don't contain a gene resembling PRDM7/9 in its details. Re-inspection of the human probes suggest that chicken PRDM11 expression was likely studied as this is the best overall Blast match at least to the zinc knuckle - PR(SET) domains.
These PRDM11 domains must share a close history of descent in the distant past with those of PRDM7/9 as the closest match among PRDM* genes still present in extant reptiles to the newly arisen chimeric mammalian PRDM7/9. Although PRDM11 lacks the KRAB domain and terminal zinc finger array and indeed has quite a different distal domain structure (a ZNF_TTF type zinc finger followed by a ubiquitous hATC dimerization Pfam motif), its comparative genomics and current functions are of considerable interest. PRDM11 is a much older gene than PRDM7/9, one that arose in early bony vertebrates and persisted in all descendent lineages including human. Its domain structure indicate a role in regulation of transcription; its methylation capability could mark up a histone for meiosis but it seems to lack any ability to recognize specific sequences in dna (in the manner of the zinc fingers of PRDM7/9).
The final exon of PRDM11 contains a very large open reading frame of 722 amino acids (2166 bp). This is an extreme outlier, given the size distribution of exons (averaging ~55 amino acids) in the human proteome. In fact, this exon (and a homolog) may be the second largest of all known exons, with only the gigantic first exon of the microtubule-associated protein MAP1A (2678 amino acids) being larger. It is not known how such large exons arise; in both cases here internal tandem duplication can be ruled out (though MAP1A has numerous small regions of low complexity). Another option is that these genes once had normal intron densities but these were lost by recombination with retroprocessed mature mRNA or came to be read through as coding (lost splicing capacity). This latter origin is not plausible in the case of PRMD11 because the last exon exhibits very strong conservation along its entire length (93% identical between human and alligator).
PRDM11 must also share a certain heritage with ZNF852. This protein is structured as a partial internal repeat of (KRAB ZNF_TTF)x2 + hATC dimerization domains. ZNF852 ends in a very large penultimate phase 2 exon weakly alignable with PRDM11 along most of its length (28% identity over positions 19-690). Neither protein contains C2H2-type zinc fingers. PRDM7/9 has a single KRAB domain but it is not readily alignable via Blastp with either KRAB domain of ZNF852. This implies a complex history of gene duplication coupled with domain shuffling -- PRDM7/9 shares a closely related PR(SET) domain with PRDM11 (but nothing else), which shares the large two-domain terminal exon (but nothing else) with ZNF852, which shares a KRAB domain intronated like that of PRDM7/9 (but nothing else).
Correcting the gene model
The curated NCBI reference gene model for human PRDM11 (NM_020229) is unsatisfactory given the human genome project has been out for 10 years. The sequence begins with a dubious first coding exon that has no phylogenetic support for translation even in placental mammals. This exon is more likely non-coding 5'UTR that happens (in human and a few primates) to contain an in-frame ATG codon for methionine (no statistical surprise). Initial methionines are very difficult to recognize as the Kozak sequence is too weak to provide a definitive signature. The best resolution would come from mass spectroscopy of in vivo protein production.
More seriously, the reference sequence terminates by reading through a splice junction to the first encountered stop codon, thereby omitting the gigantic terminal coding exon -- ironically one already identified as a standalone gene EAW68047 in the Ventner group paper. This exon is joined to the rest of the gene by the human transcript DR731303 which links it in the correct reading phase to the properly shortened preceding exon and by similar transcripts in dog, chicken, finch and frog (DN430942, BU271565, DC286485, DN081198/CK800288).
Although some transcripts skip it, this exon has no transcripts of its own to support standalone gene status. Its phase 2 splice junction has been conserved for many billions of years of branch length in bony vertebrates. It contains two well-established Pfam domains proving that it is not conserved-non-coding dna as concluded by some bioinformatic tools. A string of 2166 bp implausibly has an open reading frame of this length without a stop codon unless it encodes a protein.
Various gene prediction tools find this extending exon (Genscan, Geneid, N-Scan, SGP, UniGene, Exoniphy) while others fail to predict it (Ensembl, Encode, CCDS, MGC, Vega, and AceView). Oddly the predicted NCBI gene models in birds and lizards all correctly contain the exon (XM_421099 XM_003206406 XM_002199814 XM_003214639) but this information never got communication to the human genome annotation.
No further attention will be paid to the erroneous gene model on this site. It is impossible to understand protein function when 60% of the protein and two informative domains have been dropped.
Crystal structure of PRDM11
Here we are very fortunate to have a pre-publication entry at PDB (3RAY) that covers the zinc knuckle and PR(SET) domain of human PRDM11. The four zinc binding residues (3 cysteins and 1 histidine are clearly identified. Since this is the closest match PRDM7/9 have at PDB -- and PRDM11 is the closest match for the PR(SET) domain -- the setting for modelling PRDM7/9 is quite favorable. (to be continued shortly).
>PRDM11_homSap 3RAY zinc knuckle PR(SET) domains GDSSAMEVEPKKLKGKRDLIVPKSFQQVDFWFCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPQGMEVVKDT SGESDVRCVNEVIPKGHIFGPYEGQISTQDKSAGFFSWLIVDKNNRYKSIDGSDETKANWMRYVVISREEREQNLLAFQH SERIYFRACRDIRPGEWLRVWYSEDYMKRLHSMSQETIHRNLARGEKRLQREKSEQVLDNPEDLRGPIHLSVLRQGK
Curated PRDM11 reference sequences
The reference sequence for the human gene PRDM11 appears to be wrong in two respects: translating a segment of 5'UTR and running out into a stop codon rather than splicing to the large terminal exon. This gene model is not pursued further here for lack of comparative genomics and because the omitted exon contains two domains presumably vital to a role for PRDM11 in regulation of gene transcription.
>PRDM11_homSap Homo sapiens (human) original refSeq 511 aa model not supported PhosS 3RAY coverage knuckle SET 0 MLKMAEPIASLMIVECRACLRCSPLFLYQREK 0 0 DRMTENMKECLAQTNAAVGDMVTVVKTEVCSPLRDQEYGQPC 2 1 SRRPDSSAMEVEPKKLKGKRDLIVPKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPQGMEVVKDTSGESDVRCVNEVIPKGHIFGPYEGQISTQDKSAGFFSWL 0 0 IVDKNNRYKSIDGSDETKANWMR 2 1 YVVISREEREQNLLAFQHSERIYFRACRDIRPGEWLRVWYSEDYMKRLHSMSQETIHRNLAR 1 2 GEKRLQREKSEQVLDNPEDLRGPIHLSVLRQGKSPYKRGFDEGDVHPQAKKKKIDLIFKDVLEASLESAKVEAHQLALSTSLVIRKVPKYQDDAYSQCATTMTHGVQNIGQTQGEGDWKVPQGVSKEPGQLEDEEEEPSSFKADSPAEASLASDPHELPTTSFCPNCIRLKKKVRELQAELDMLKSGKLPEPPVLPPQVLELPEFSDPAGKLVWMRLLSEGRVRSGLCGG* 0
The sequences below use a gene model of human PRDM11 consistent with transcript data and vertebrate comparative genomics. The coding regions consists of seven exons and 1233 total amino acids, including the second largest exon in the entire proteome (722 amino acids). An early serine is post-translationally modified to phosphoserine (according to its UniProt entry Q9NQV5). There are four domains conserved in all species: an early zinc knuckle, a PR(SET) methylation domain, a ZNF_TTF transcription factor zinc finger and a distal hATC dimerization domain. All species containing the gene have these four domains and the same introns. While much older than PRDM7/9, PRDM11 cannot be traced back earlier than rayfinned fish and may have arisen in stem bony vertebrates though chondrichthyian data is admittedly meagre. Fish sequences are showing major signs of divergence in early exons and are also highly variable in the sixth exon. The PR(SET) domain of PRDM11 is the most closely related such domain found in non-mammalian amniotes (which lack and never had PRDM7/9).
>PRDM11_homSap Homo sapiens (human) corrected 511+722 aa PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization no early zinc finger or terminal array syn PFM8 related ZNF 862 0 MTENMKECLAQTNAAVGDMVTVVKTEVCSPLRDQEYGQPC 2 1 SRRPDSSAMEVEPKKLKGKRDLIVPKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPQGMEVVKDTSGESDVRCVNEVIPKGHIFGPYEGQISTQDKSAGFFSWL 0 0 IVDKNNRYKSIDGSDETKANWMR 2 1 YVVISREEREQNLLAFQHSERIYFRACRDIRPGEWLRVWYSEDYMKRLHSMSQETIHRNLAR 1 2 GEKRLQREKSEQVLDNPEDLRGPIHLSVLRQGKSPYKRGFDEGDVHPQAKKKKIDLIFKDVLEASLESAKVEAHQLALSTSLVIRKVPKYQDDAYSQCATTMTHGVQNIGQTQGEGDWKVPQGVSKEPGQLEDEEEEPSSFKADSPAEASLASDPHELPTTSFCPNCIRLKKKVRELQAELDMLKSGKLPEPPVLPPQVLELPEFSDPA 1 2 ASESMVSGPAIMEDDDQEVDSADESVSNDMMTATDEPSKMSSATGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYLDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPCLSVILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSSTESYLQALDRAF SALGIRLQDEKPTVGLGVDGANITASLRASMFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRSTAATLCEETEFLGDIRAVRWIIGEQN VLNALIKDYLEVVAHLKEVSSQTQRADASAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAYIFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGIAMKNLRVAE AKFQSIREKICQKTQVILAQRFDSRSRIFVKACQVFDLAAWPRSSEELMSYGKEDMVQIFDHLEAIPTFSRDVCREGLDPRGSLLMEWRELKADYYTKNGFKDLISHICKYKQRFPLLNK IIQVLKVLPTSTACCEKGRNALQRVRKNHRSRLTLEQLSDLLTIAVNGPPITNFDAKRALDSWFEEKSGNSYALSAEVLSRMSALEQKPALQTMDHGTEFYPDI* 0 >PRDM11_musMus Mus musculus (mouse) blat PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MTENMKECLAHTKAAVGDMVTVVKTEVCSPLRDQEYGQPC 2 1 SRRLEPSSMEVEPKKLKGKRDLIVTKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPQGMEVVKDAGGESDVRCINEVIPKGHIFGPYEGQISTQDKSAGFFSWL 0 0 IVDKNNRYKSIDGSDETKANWMR 2 1 YVVISREEREQNLLAFQHSERIYFRACRDIRPGERLRVWYSEDYMKRLHSMSQETIHRNLAR 1 2 GEKRLQREKAEQALENPEDLRGPTQFPVLKQGRSPYKRSFDEGDIHPQAKKKKIDLIFKDVLEASLESGNVEARQLALSTSLVIRKVPKYQDDDYGRAALTQGICRTPGEGDWKVPQRVAKELGPLEDEEEEPTSFKADSPAEASLASDPHELPTTSFCPNCIRLKKKVRELQAELDMLKSGKLPEPSLLPPQVLELPEFSDPA 1 2 ASESMVSGPAIMEDDDQEVDSADESVSNDVMTATDEPSKMSSATGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYLDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPCLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSSTESYLQALDRAF AALGIRLQDEKPTVGLGVDGANITASLRASMFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRSTASTLCEETEFLGDIRAVRWIIGEQN VLNALIKDYLEVVAHLKDVSSQTQRADASAIALALLQFLMDYQSMKLIYFLLDVIAVLSRLAYIFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGIAVKNLRVAE AKFQSIREKICQKTQVILAQRFDSRSRVFVKACQVFDLAAWPRNSEELLSFGKEDMVQIFDHLEAIPAFSRDVCREGTDPRGSLLMEWRDLKADYYTKNGFKDLLSHICKYKQRFPLLNK IIQVLKVLPTSTACCEKGRSALQRVRKNHRSRLTLEQLSDLLTIAVNGPPIANFDAKRALDSWFEEKSGNSYTLSAEVLSRMSALEQKPMLHVVDHGSEFYPDM* 0 >PRDM11_canFam Canis familiaris (dog) blat PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MTENMKECLAQTKAAVGDMVTVVKTEVYSPLRDQEYGQPC 2 1 SRRPDPSTMEVEPKKLKGKRELIMPKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPQGMEVVKEASGENDVRCINEVIPKGHIFGPYEGQISTQDKSAGFFSWL 0 0 IVDKNNRYKSIDGSDETKANWMR 2 1 YVVISREEREQNLLAFQHSERIYFRACRDIRPGERLRVWYSEDYMKRLHSMSQETIHHNLAR 1 2 GEKRLQREKSEQALDNPEDLRGPIQLPVLRQGKSPYKRGFDEGDAHPQAKKKKIDLIFKDVLEASLESAKVEAHQLALSTSLVIRKVPKYQDDAYSRCAMTMSHGVQNVSRTQGEGDWKIPQGASKEPGPLEDEEEEPSSFKADSPAEASLASDPHELPTTSFCPNCIRLKKKVRELQAELDMLKSGKLPEPPVLPAQVLELPEFSDPA 1 2 ASESMVSGPAIMEDDDQEVDSADESVSNDMLTAADEPSKMSSATGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYLDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPCLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSSTESYLQALDRAF SALGIRLQDEKPTVGLGIDGANVTASLRASMFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRSTASTLCEETEFLGDIRAVRWIIGEQN VLNALIKDYLEVVAHLKDVSSQTQRADASAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAYVFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGIAMKNLRVAE AKFQSVREKICQKTQVILAQRFDSRSRIFVKACQVFDLAAWPRSSEELMSYGKEDMVQIFDHLEAIPTFSRDVCREGLDPRGSLLMEWRELKADYYTKNGFKDLIGHICKYKQRFPLLNK IIQVLKVLPTSTACCEKGRNALQRVRKNHRSRLTLEQLSDLLTIAVNGPPIANFDAKRALDSWFEEKSGNSYALSAEVLSRMSALEQKPVLQTVDHGSEFYPDI* 0 >PRDM11_loxAfr Loxodonta africana (elephant) blat PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MTENMKECLAKTKAAVGDMVPVVKTEVCSPLHDQEYGQPC 2 1 SRRPDPSAMDVEPKKLKGKRDLIMPKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPQGMEVVKEASGENDVRCISEVIPKGHIFGPYEGQISTQDKSAGFFSWL 0 0 IVDKNNRYKSVDGSDETKANWMR 2 1 YVVISREEREQNLLAFQHSERIYFRVCRDIRPGERLRVWYSQDYMKRLHSMSQETIHRNLAR 1 2 GEKRLQREKSEQALDNPEDLRGSIQLPVLRQGKSPYKRGFDEGDLHPQAKKKKIDLIFKDVLEASLESAKVEAHQLALSTSLVIRKVPKYQDDTYSRCATTMSHGVQNVSRTQGEGDWKIPQGASKEPGPTEDEEEEPSSFKADSPAEASLASDPHELPTTSFCPNCIRLKKKVRELQAELDMLKSGKLPEPPVLPAQVLELPEFSDPA 1 2 ASESMVSGPAIMEDDDQEVDSADESVSNDIMTATDEPSKMSSATGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYLDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPCLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSGTESYLQALDRAF STLGIRLQDEKPTVGLGVDGANITASLRASMFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRSTASTLCEETEFLGDIRAVKWIIGEQN VLNALIKDYLEVVAHLKDISSQTQRADASAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAYVFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGIAMKNLRVAE AKFQSIREKICQKTQVILAQRFDSRSRIFVKACQVFDLAAWPRSSEELVSYGKEDMVQIFDHLEAIPTFSRDVCREGLDPRGSLLMEWRELKADYYTKNGFKDLISHVGKYKQRFPLLNK IIQILKVLPTSTVCCEKGRNALQRVRKNHRSRLTLEQLSDLLTIAVNGPPIANFDAKRALDSWFEEKSGHSYTLSAEVLSRMSALEQKPVLQAIDHGTEFYPDI* 0 >PRDM11_monDom Monodelphis domestica (opossum) blat PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MTENLKACLAHTQASMGEMVTVKTEVCSPRRDQEYGQPW 2 1 SGRPDPPSMEVEPKKPKGKRELIMTKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPMGIPDRAALTIPPGMEVVKEASGQSDVRCMNEVIPKGHIFGPYEGQISTQDKSAGFFSWL 0 0 IVDKNNHYKSIDGTDETKANWMR 2 1 YVVISREEREQNLMAFQHSEKIYFRVCRDIRPGERLRVWYSEDYMKRLHSMSQETIQRNLTR 1 2 GDKKLQREKPEKALDHQEDLRGPLQLTVLRHGKSAYKRGFDEVDAHPPPKKKKIDLIFKDVLEASLETSKIEEHPLAPGTPLVLRKAPKFHTEDVYDQCGMAISHGPQDLSRNQGEKEWKAPQGASYGPSKDTSLLEDEEEEPSSFKADSPAEASLASDLHELPTTSFCPNCIRLKKKIRELQAELDMLKSGKLPEPPLLPPQVPELPEFSDPT 1 2 ASESVVSVPTMLEDDDQEVDSADESVSNEMITATDEPSKMSSATGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYFDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDILADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRASMFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRLTASTLCEETEFLGDIRAVRWIIGEQN VLNALIKDYLEVVAHLKDVSGQTQRADASAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAYIFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGVAVKNLRVAE AKFQSIREKICQKTQVILAQRFDSRSRTFVKACQVFDLAAWPRSTEELMSYGKEDMIQIFDHLETIPSFSREICREGMDPRGSLLMEWRELKADYYTKNGFKDLISHICKYKQRFPLLNKI IQILKVLPTSTACCEKGRVALQRVRKNNRSRLTLEQLSDLLTIAVNGPPIANFDAKRALDSWFEEKSGNSYTLSAEVLSRMSALDQKPMLPTMDHGSEFYSDL* 0 >PRDM11_ornAna Ornithorhynchus anatinus (platypus) blat PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MTENLKDCLAQTQASMGEMVTV KTEVCSPHRDQEYGQPW 2 1 SGRPDPSSMEVEPKKLKGKRDLIMSKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPPGIEVVKEASGENDVRCMNEVIPKGHIFGPYEGQISTQDKSAGFFSWL 0 0 IVDKNNRYKSIDGTDETKANWMR 2 1 YIVISREEREQNLLAFQHSERIYFRVCRDIRPGERLRVWYSEDYMKRLHSMSQETIHRNLTR 1 2 GEKKLLREKTDKAPESQEDLRGPLQLTVLKQGKSPYKRSCDEGDAHPQTKKKKIDLIFKDVLEASLESAKIDEHQLATSTPLAFKKMPKFQAEDVFERCGAILPHGTQSFGRTHSEGDWKLGHGTPYGPSKEKGLLEEDQGEPSPIKVDSPTEASLTGDSQELPTTSFCPNCIRLKKKIRELQAELDMLKSGQLPEPPLVPPQVPELPEFSDPA 1 2 ASESLVSIPTILEDDDPEVDSADESVSNDMIAATDEPSKMSSATGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYLDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF AALGVRLQDEKPTVGLGVDGANVTASLRAGMFMTVRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRLTAATLCEETEFLGDIRAVRWIIGEQN VLNALIKDYLEVVAHLKDVSGQTQRADASAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAYVFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGVAVKNLRVAE AKFQSIREKICQKAQVILAQRFDSRSRTFVKACQVFDLAAWPRSSEELVSYGREDMVQILEHLEAIPSFSREVCREGADPRGALLTEWRELKADYYTKNGFKDLIGHVGKYKQRFPLLNK VIQILKVLPTSTACCEKGRSALQRVRKNHRSRLTLEQLSDLLTIAVNGPPIAHFDAKRALDSWFEEKSGNSYALSAEVLSRMSSLDQKPMLQSVDHGSEFYPDM* 0 >PRDM11_allMis Alligator mississippiensis (alligator) scaffold:58581 PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MSENLKDCLIQTQTSLGEMVTIKTEACSPHRDQEYGQPC 2 1 SGRPDPQSMEIEPKKLKGKRDLIMTKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRASLTIPPGMEVVKEPNGENDVRCMNEVIPKGHIFGPYEGQISSQDKSAGFFSWL 0 0 IVDKNNRYKSIDGTDETKANWMR 2 1 YVIISREEREQNLMAFQHSERIYFRTCRDIRPGERLRVWYSEDYMKRLHSMSQETINRNLTR 1 2 GDKKSQREKSEKNMENQEDMRGPLQLTTLKQGKSPYKRSCEEAESHPQTKKKKIDLIFKDVLEASLESAKLEEHQLTTSTPLSIRKASKYQTEDVFERCGTTIQHSSPNLSRNRSEGEWKVPHSSSFSTAKEMGLLEDEEEEPLSLKADSPTEPSLASTQGNSHEIPTTSFCPNCIRLKKKIRELQAELDMLRSGKLPEQPALAPQVPELQEFSDPT 1 2 ASESIISVPTIMEDDDQEVDSADESVSNDMIAATDEPSKMSSVTGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPKLMCELRVTAATLCEETEFLGDIRAVKWIIGEQN VLNALIKDYLEVVAHLKDVSGQTQRADASAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAYVFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGIAVKNLRVAE AKFQSIREKICQKTQVILAQRFDSRSRTFVKACQVFDLAAWPRSTEELMSYGKEDMVQIFEHLETVPSFSREVCREGMDIRGSLLMEWRELKVDYYTKNGFKDLLGHICKYKQRFPLLNK IVQILKVLPTSSACCEKGRNALQRVRKNNRSRLTLEQLSDLLTIAVNGPAIANFDCKRALDSWFEEKSGNSYALSAEMLSRMSSLDQKPMLQSMDHGSEFYPDI* 0 >PRDM11_galGal Gallus gallus XM_421099 PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MSENLKDCLNQTQASLGEMVTIKTEACSPHRDQEYGQPC 2 1 SGRLDPQSMDVEPKKLKGKRDLIMTKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPPGIEVVKEPSGENDVRCMNEVIPKGHIFGPYEGQISSQDKSAGFFSWL 0 0 IVDKNNRYKSIDGTDETKANWMR 2 1 YVIISREEREQNLMAFQHSERIYFRACRDIRPGEKLRVWYSEDYMKRLHSMSQETINRNLTT 1 2 GDKKLQKEKSEKNADNQEDTRAPLHFTTLKQGKSPYKRSYDEGESHPQTKKKKIDLIFKDVLEASLESAKFEEKQLATSTPLSTRATSKYQAEEIFERCSSAMQHGSLNLSRNRSEEEWKAPHGSSFSSAKEVGVLEDEEEEPLSLKADSPTELSLASAEGNSHEIPTTSFCPNCIRLKKKIRELQAELDMLRSGKLPEPPVLPPQVPELQEFSDPT 1 2 ASESIISVPTIMEDDDQEVDSADESVSNEMIAATDEPSKMSSATGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDVLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTASTLCEETEFLGDIRAVKWIIGEQN VLNALIKDYLEVVAHLKDVSGQTQRADASAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAYVFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGIAVKNLRVAE AKFQSIREKICQKTQVILAQRFDSRSRTFVKACQVFDLAAWPRSTDELMSYGKEDMVQIFEHLETVPSFSREVCREGMDTQGSLLMEWRELKVDYYTKNGFKDLLSHICKYKQRFPLLNK IVQILKVLPTSSACCEKGRNALQRVRKNNRSRLTLEQLSDLLTIAVNGPPIANFDCKRALDSWFEEKSGNSYALSAEMLSRMSSLDQKPMLQSVDHGSEFYPDI* 0 >PRDM11_melGal Meleagris gallopavo (turkey) blat/XM_003206406 PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MSENLKDCLNQTQASLGEMVTIKTEACSPHQDQEYGQPC 2 1 SGRPDPQSMDVEPKKLKGKRDLIMTKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPPGIEVVKEPSGENDVRCMNEVIPKGHIFGPYEGQISSQDKSAGFFSWL 0 0 IVDKNNRYKSIDGTDETKANWMR 2 1 YVIISREEREQNLMAFQHSERIYFRACRDIRPGEKLRVWYSEDYMKRLHSMSQETINRNLTT 1 2 GDKKLQKEKSEKNTDNQEDTRGPLQFTMLKQGKSPYKRSYDEGESHPQTKKKKIDLIFKDVLEASLESAKFEEKQLATSTPLSTRATSKYQAEEIFERCSGAMQHLSRNRSEEEWKAPHGSSLSSAKEVGVLEDEEEEPLSLKADSPTELSLASAEGNSHEIPTTSFCPNCIRLKKKIRELQAELDMLRSGKLPEPSVLPPQVPELQEFSDPT 1 2 ASESIISVPTIMEDDDQEVDSADESVSNEMIAATDEPSKMSSATGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDVLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTASTLCEETEFLGDIRAVKWIIGEQN VLNALIKDYLEVVAHLKDVSGQTQRADASAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAYVFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGIAVKNLRVAE AKFQSIREKICQKTQVILAQRFDSRSRTFVKACQVFDLAAWPRSTDELMSYGKEDMVQIFEHLETVPSFSREVCREGMDTQGSLLMEWRELKVDYYTKNGFKDLLSHICKYKQRFPLLNK IVQILKVLPTSSACCEKGRNALQRVRKNNRSrlTLEQLSDLLTIAVNGPPIANFDCKRALDSWFEEKSGNSYALSAEMLSRMSSLDQKPMLQSVDHGSEFYPDi* 0 >PRDM11_anaPla Anas platyrhynchos (duck) blast/HQ902403 PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MSENLKDCLNQTQASLGEMVTIKTEACSPHRDQEYGQPc 2 1 SGRPDPQSMDVEPKKLKGKRDLIVTKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPPGMEVVKEPSGENDVRCMNEVIPKGHIFGPYEGQISSQDKSAGFFSWL 0 0 IVDKNNRYKSIDGTDETKANWMR 2 1 YVIISREEREQNLMAFQHSERIYFRACRDIRPGEKLRVWYSEDYMKRLHSMSQETINRNLTR 1 2 GDKRLQREKSEKNVENQEDMRGPLQLTTLKQGKSPYKRSCDEGESHPQTKKKKIDLIFKDVLEASLESAKFEENQLATSTPLSIRTASKYQAEDIFERCGTAMQHGSLNLSRNRSEEEWKIPHGSSFSSAKEVGILDDDEEEPLSLKADSPTELSLASAQGNSHEIPTTSFCPNCIRLKKKIRELQAELDMLRSGKLPEPPELPPQVPELQEFSDPT 1 2 ASESIISVPTIMEDDDQEVDSADESVSNDMIAATDEPSKMSSATGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDVLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKWIIGEQN VLNALIKDYLEVVAHLKDVSGQTQRADASAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAYVFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGIAVKNLRVAE AKFQSIREKICQKTQVILAQRFDSRSRTFVKACQVFDLAAWPRSTDELMSYGKEDMVQIFEHLETVPSFSREVCREGMDTRGSLLMEWRELKVDYYTKNGFKDLLSHICKYKQRFPLLNK IVQILKVLPTSSACCEKGRNALQRVRKNNRSRLTLEQLSDLLTIAVNGPPIANFDCKRALDSWFEEKSGNSYALSAEMLSRMSSLDQKPMLQSMDHGSEFYPDI* 0 >PRDM11_taeGut Taeniopygia guttata (finch) XM_002199814 PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MSENLRDCLIQTQASLREMVTIKTEACSPHRDQEYGQPC 2 1 SGRPDPQSMEMEPKKLKGKRDVIMTKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPPGMEVVKEPSGENDVRCMNEVIPKGHIFGPYEGQISSQDRSAGFFSWL 0 0 IVDKNNRYKSIDGTDETKANWMR 2 1 YVIISREEREQNLMAFQHSERIYFRACRDIHPGEKLRVWYSEDYMKRLHSMSQETMNRSFTS 1 2 GDKMLQNENSEKNVENQEDARGALQFTTLKQGKSPYKRSCDEGESHPQTKKKKIDLIFKDVLEASLESAKFEENQLATSTPLSLRRASKYQAEDIFEQCGNAMQRSSLSLSRNQSESEWRVPHSSSFISAKEMSILEDEEEEPLSLKADSPTELSLASAQGNSHEIPSTSFCPNCIRLKKKIRELQAELDMLRSGKLPEAPVLPPQVPELQEFSDPT 1 2 ASESIISVPTIMEDDDQEVDSADESVSNDMIAATDEPSKMSSATGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKWIIGEQN VLNALIKDYLEVVAHLKDVSGQTQRADASAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAYVFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGIAVKNLRVAE AKFQSIREKICQKTQVILAQRFDSRSRTFVKACQVFDLAAWPRSTDELMSYGKEDMVQIFEHLETVPSFSREVCREGMDTRGSLLMEWRELKVDYYTKNGFKDLLSHICKYKQRFPLLNK IVQILKVLPTSSACCEKGRSALQRVRKNNRSRLTLEQLSDLLTIAVNGPPIANFDCKRALDSWFEEKSGNSYALSAEMLSRMSSLDQKPMLQSMDHGSEFYPDI* 0 >PRDM11_anoCar Anolis carolinensis (lizard) blat/XM_003214639 PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MSEKLNDCLGEMVTIKTEPCSPCREEEYGQLW 2 1 SSRKVDSQSVDVEPKKLKGKQDLIMSKSFQQVDFW 1 2 FCESCQEYFVDECPNHGPPMFLSDAPVPIGIPDRAALTVPPGMEVVKEANGERDVRCVGEIIPKGRIYGPYEGKLSSQDKSAGFFSWL 0 0 IVDKNNRYKSIDGTDETTSNWMR 2 1 YVAISREEREQNLMAFQHSERIYFRTCRDIRPGERLRVWYSEDYMKRLHSMSQETINRNLTR 1 2 GDKKSLRERSERNTENQMEMLYPLELTISKQGKSPYKRCSEEGVSQPQAKKKKIDLIFKDVLEASLESTKMEEHKVTRNSAPSTRKSSRFREQDASESCGTGMQHNSPTHSGSRN EDEWKVPHGPSFSVSKETGLLEDEGEEPLSFKLNSPTDLTLAPIDDEALGLPTTSLCPNCIRLKKKIRELQAELNMLRSGKLVEPPLLPPQVPEYQAFSYPT 1 2 ASETIMSVPTIMEDDDQEVDSADESVSNDMITATDEPSKMSAVTRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYRLRMHPEKTEEM CRNMTLLFNTAYHLAMEGRPYCDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERVRQSPFLSIILDGQSDDLLADTVAVYVQYISSDGPPATEFLSLQELGFSATDSYIQALDRAF SSLGIRLQDERPSVGLGIDGANITASLRANMYMTIRKTLPWLLCLPLMIHKPHLEVLDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKWIIGEQN VLNALIKDYLEVVAHLKDVSGQTQRADASAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAFIFQGEYLLVSQVDDKIEEAIQEISRLADSPGEYLQEFEENFRESFNGVAVKNLRVAE AKFQSIREKICQKTQVILAQRFEPRTRAFVKACQVFDLAMWPRSAEELMSYGREDMVQIFDHLEAVPTFSTDIIREGMDTRGSLLMEWRELKVDYYTKNGFKDLISHICKYRQRFPLLNK IIQILKVLPTSTACCEKGRNALQRVRKNNRSRLTLEQLSDLLTIAVNGPPIANFEAKRALDSWFEEKSSNSYALSAEMLSRMSSLDHKPMLQSMDHGSEFYPDI* 0 >PRDM11_xenTro Xenopus tropicalis (frog) blat/CF781198 PhosS 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 1 MSEISKECRVAFSPSLGDIVRVKREVGSPVEEQGYGHFR 2 1 SSVGPNSRCLDMEPKRLKEKRESTMSKSLQQVDFW 1 2 FCESCQEYFVDECPSHGPPILVPDTLVPIGMPERAALSVPCGIEVVKDSSGESEVRCVNEVIPKGHMFGPYEGQICSQDKSSGFFSWL 0 0 IVDNNNRYKSIDGTDEAYANWMR 2 1 YVVISREEREQNLMAFQHSEKIYFRTCRDIQPGEKLRVWYSEDYMKRLHSMSQETINRNLTQ 1 2 GDKRLLRENNERLLENQEDVKGTFPLATLKQGKSLYKRSCEEVDLHPQTKKKKIDLIFKDVLEASLETARIDEYHLVTSSPLSGQKKNPKYLYENHGDRCRMNRQCSSPQNQIRNMRDWKAKHVSASGLNRQASFPEDEVEDHSSVKAESPTESSAIGNVDEIPTTSFCPNCIRLKKKIRELQAELEMLRSEKMAETSQMTNQINEIPEFADAS 1 2 APEGVAIATTMIDDDEQEVDSADESVSNDMMAATDEPSKMSAGSGRRIRRFKQEWLKKFWFLRYSSTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLAMEGRPYYDFRPLAELLRKCELRVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSEDLLADTVAVYVQYTSSDGPPATEFLSLQELGLPTTESYLQGIDRAF SALGIRLQDERPTVGLGVDGANITAGLRANLYMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRLTAATLCEETEFLGDIRAVKWIIGEQN VLNALIKDYLEVVAHLKDVSGQTQRADTSAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAYVFQGEYLLVSQVDEKVEEAIQEISRLTDSPGEYLQEFEENFRESFNGIALKNLRVAE AKFQSIREKICQKTQVTLAQRFDSRSRMFVKACQVFDLSTWPRTTEELINYGEEDMLQIYELLETIPNFLHDLGREVADTRGNLLMEWRELKADYCTKNGFKDLIGHICKYKQRFLFLNK IVQILKVLPTSTACCEKGRNALQRLRKNNRSRLTLDQMSDLLAIAVNGAPIANFDAKRALDSWFEEKSGNSYSLSAEMLSKMSSLDQKPLLQPMEHGSEYYQDI* 0 >PRDM11_latCha Latimeria chalumnae (coelocanth) AFYH01005054 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 1 2 1 STGAAETPRIEGEPKRTKGKLETIMAKTLQQVDFW 1 2 FCEECQEHFVVECPTHGPPVFTMDTPVPVGMPERAALTAPPGIHIVKGSNGEIDVECVDEVVQKGRIFGPYEGQITTQDKSAGFFSWL 0 0 IVDKNNRYKSIDGTDETKANWMR 2 1 YVVISRDEREQNLLAFQHSEKIYFRASRNLHPGERLRVWYSDEYMKRLHSMSQETIDRNLTA 1 2 GNLKLQRENSEEGWDAQENLRGMLLKQGKSSYKRGNDEAESHQQPKRKKIDLIFKDVLEASLESSKLEGNSLATSSPLPLKKPIKFQLEDVLQKPEYYYKHVSQLLGRGEVEWKSHQKSGCSLPDNEDSDRIKEESPDEVPGNSTEEDPEDVPTTSFCPNCIRLKKKIRELQEELDRLRSGQPPASPQLPQVQELLEPPG 2 VQEAHPSVSLMEDDDQEVDSADESVSNDMIAASDETSKITVGASRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTVLFNTAYHLALEGRPYLDFRPLSDLLRKCELKVVDQYMNEGDCQILIHHIARALQEDLIERIRQSPFLSVILDGQTDDILADTVAVYIQYTTSDGPPATEFLSLQELGCVTTDSYVQAVDRAF AVFGLRLQDQRNVVGLGVDGTCLTAGLRANLFMTIRKTLPWLLCLPFMVHKPHLEVLDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKWIIGEQN VLNALIKDYLEVVAHLKDVSGQTQRADAAAIALALLQFLMDYQSIKLIYFLLDVIAVLSRLAFVFQGEYLLVCQVDDKIEEAIQEISRLSDSPGEYLMEFEENFRESFNGIALKNLRVAE AKFQSIREKICQKTQVILAQRFDNRSRPFIKACQMLDIATWPRSTDDLKNFGEEEIMVIYEQLELVPTFAREVCREGTDNRGSLVMEWRELKADFYSKNGFKDLIGHICKYRQRFPILNR VLQILKVLPSSAACCEKGRSALQRIRKNNRSRLTLDQLNDLLTIAINGPSIANFDAKRALDSWFEEKSGNSYALSAEVLNRMSADQKPMLQGMDFVSDFYPDI* 0 >PRDM11_danRef Danio rerio (zebrafish) blat/EB776339/EB946706/BX088562/XM_688756 3RAY coverage knuckle SET ZnF_TTF hATC_dimerization 0 MADSSTNPDHSSMEAEGECSTS 2 1 ASNEKSAEEPNKRLKVEHERYSSFW 1 2 FCEECKKYYLEDCPTHGPPVFVPDTPVVSGVPNRAALTAPSGIEVRRNGDKVDVYCMDEKIPKGALFGPYKGQIMASDKPSGPYSWM 0 0 IVDKDSKYKFIDGSDEATANWMR 2 1 FIHITSDESEQNLSAFQHGDQIYFRVCHRLKVGEKLGVWYSSEYMKRLQSVSRDSIDHNLDT 1 2 GVKSEDQEEPKGPVLRSAMHGRRTLSKHGSDEAENQPQAKKKKIDLIFKDVLEASLEANQSQNNPLNSTLSFPRARTNVCQVFCHPDAESKESVFTSGLVSMDHHEIGFDGKCIKMENTEEDEALTSEGPSTSFCPNCVRLKRRIRELEAELHRLRGQGHAEVKPVPASEMLAGEDHR 1 2 DTMTPIPAALEEDDQDVDSADESISADLLVAADESSKLSVGSGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMMTLLNAAYHLALEGRPFSDLRPLAELLKKCDLKVVDQYMNENDCQILIQHISRAFKEDLAEKIRLSPFLSIIMDGQNDDLLADMVAVYVQFTTTDGLPATEFLSLQRLCGGNVEGYLQAVDRAF GVLGLRLQDMLVVGLGIDGSNISSSLRANLYVAIRKTIPWVLCLPVMIHRPHLEVLDAISGKELSCLEDLENNLKQLLSFYRYSPRLMAELRSSAPTLSEETEFLGDIRAVRWIIGEPN VLNALIKDYLEVVAHLKTISNQTQRGDAAAIALSLLQFLLDYQSVKLIYFLLDVIAVFSRLAFIFQGDYLLVSQVDAKIEDAIHEIGQLVDSPGEYLQEFEDNFRESFNGVDLKNLRVAE SKFQSIREKICQQSQCILAQRFEPRSRTVVQACQVLDLASWPINRDDLGAYGEEEILVIFDHLETIPSSGRERSIERTDARGSLVVEWRDLKADYCSVNGFKEVVSHIFRYKQRYPLLN HILQIVRVLPTSTTCCDKGRGSLQKVRRNSRSRLTLDQINDLLTLAVNGPPIGSFDGKRALDSWFEEKSGNSISLSTEVLSRMSTTEQKSVLHNMDMNAEYYPDV* 0 >PRDM11_oreNil Oreochromis niloticus (tilapia) XM_003458287 first exons uncertain 0 MASENCRQIASCLQIEAEKAWRRSEPGRALC 1 2 fCEECQDCFHKECPSHGPPLFIQDTHAAPGTANRAALTVPSGLEVFSEEDEVDVRCVDAIYPKGALFGPYEGELVSKDRSSGFFSWI 0 0 IVDVNNTYQSIDGSDETKANWMR 2 1 YVRTSSEESDRNLTAFQHGKNIYFRVCRALVAGEKLRVWYSDDYIRRLHCVSQESIDRNLDT 1 2 GPGKDFKSRCLQSALQGKLSKQLSEESDGQPPAKRKKIDLIFKDVLEASLEESGKFRSRSGQPSEYKVPALVSRFDSSETGFGIPNLKVEEKEEEENQNTEKPSTSFCPNCVKLKRRILELEEELSRLRGEQRDAAASATSEQTQPQRDQAPPHPEQGPIEDFQ 1 2 GMEPLTPTQVVLDEDDQDVDSADESIAADLVISPEDSSKLSSGGGRRIRRFKQEWLKKFWFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CKNMMLLFNAAYHLALEGRPFSDLRSLAELLKKCELKVVDQYMNEGDCQILIHHIARAVKEDLAEKMRLSPFLSVIMDAQNDDLFSDMVAVYVQFVTNEGSPNTEFLSLQRLTVANVDGYLQVMDRAF GVLGLRFQDLLVVGLGVDGTNISSGMRANLYIAVQKTFPWILCLPIMIHRPHLEVLDAISGKELSCLEDLENNLKQLLSFYRYSPRMMAELRSTAPTLSEETEFLGDIRAIRWIIGEPN VLNALIKDYLEVVAHLKEISSQTQRADAAAIALTLLQFLMDYQSVKLIYFLLDIIAILSRLAFTFQGEYLLVSQVEAKIEEAIQEIGQLVDCPGEYLQEFEENFRESFNGVALKNLRVAE SKFQSIREKICNRSQSILSQRLDLQSRSFAKACKVLDLSTWPSNHEDLQAYGDEEIKIIFNHLESIPTAAQEGSQTEARGSLVVEWKDLKADYYSMNGFKEVIGHICRYKQRFPLLN RIVQVIRVLPSSTACCDKGRGSLQKMCKNNRSRLTLEQMNDLLTVAINGPPIANFDGKRALDSWFEEKSGSSYSLSAEVLNRMSAADQKCVLHSVDVNAEFYPDV* 0
PRDM11 fragmentary sequences from the unrecognized terminal exon were utilized in a Dec 2011 study by XX Shen et al of informative loci to determine the topology of the amniote tree, resolving the taxonomic position of turtles: outgroup to crocodillians + birds. (Note a microRNA-based analysis on the same date proposed outgroup to lizards.) Because that study sequenced species rarely represented at GenBank such as skink, salamander, caecilian and amphibia, translated sequences are reproduced here and supplemented with the appropriate region of the full length sequences PRDM11 above (which were not all used in the study). The fragment studied begins 16 residues within the ZNF_TTF zinc finger and terminates well before the end of the exon. The difference alignment shows a number of group synapomorphies consistent with turtle placement (though one gene alone does not suffice to reliably determine the species tree).
>PRDM11_homSap Homo sapiens (human) revised 511+722 aa WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYLDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPCLSVILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSSTESYLQALDRAF SALGIRLQDEKPTVGLGVDGANITASLRASMFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRSTAATLCEETEFLGDIRAVRW >PRDM11_musMus Mus musculus (mouse) blat WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYLDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPCLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSSTESYLQALDRAF AALGIRLQDEKPTVGLGVDGANITASLRASMFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRSTASTLCEETEFLGDIRAVRW >PRDM11_canFam Canis familiaris (dog) blat WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYLDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPCLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSSTESYLQALDRAF SALGIRLQDEKPTVGLGIDGANVTASLRASMFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRSTASTLCEETEFLGDIRAVRW >PRDM11_loxAfr Loxodonta africana (elephant) blat WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYLDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPCLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSGTESYLQALDRAF STLGIRLQDEKPTVGLGVDGANITASLRASMFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRSTASTLCEETEFLGDIRAVKW >PRDM11_monDom Monodelphis domestica (opossum) blat WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYFDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDILADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRASMFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRLTASTLCEETEFLGDIRAVR >PRDM11_ornAna Ornithorhynchus anatinus (platypus) blat WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYLDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF AALGVRLQDEKPTVGLGVDGANVTASLRAGMFMTVRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRLTAATLCEETEFLGDIRAVRW >PRDM11_galGal Gallus gallus XM_421099 WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDVLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTASTLCEETEFLGDIRAVKW >PRDM11_melGal Meleagris gallopavo (turkey) blat/XM_003206406 WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDVLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTASTLCEETEFLGDIRAVKW >PRDM11_anaPla Anas platyrhynchos (duck) blast/HQ902403 WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDVLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_taeGut Taeniopygia guttata (finch) XM_002199814 WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_strCam Struthio camelus (ostrich) HQ902400 frag ZnF_TTF WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_allMis Alligator mississippiensis (alligator) scaffold:58581 WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAF SSLGIRLQDEKPTIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPKLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_allSin Alligator sinensis (alligator) HQ902411 frag ZnF_TTF WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAFSSLGIRLQDEKPT IGLGVDGANITASLRADLFMTIRKALPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPKLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_croSia Crocodylus siamensis (crocodile) HQ902406 frag ZnF_TTF WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYYDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFSTTDSYLQALDRAFSSLGIRLQDEKP TIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPKLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_carIns Carettochelys insculpta (turtle) HQ902407 frag ZnF_TTF WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYFDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFCTTDSYLQALDRAFSSLGIRLQDEKPT IGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_podUni Podocnemis unifilis (turtle) HQ902402 frag ZnF_TTF WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYFDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFCTTDSYLQALDRAFSSLGIRLQDEKPT IGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_traScr Trachemys scripta (turtle) HQ902399 frag ZnF_TTF WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYFDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYTSSDGPPATEFLSLQELGFCTTDSYLQALDRAFSSLGIRLQDEKP TIGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_pelSin Pelodiscus sinensis (turtle) HQ902412 frag ZnF_TTF WFLQYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYFDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARSLREDLVERIRQSPFLSIILDGQSDDWLADTVAVYVQYTSSDGPPATEFLSLQELGFCTTDSYLQALDRAFSSLGIRLQDEKPT IGLGVDGANITASLRANLFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_anoCar Anolis carolinensis (lizard) blat/XM_003214639 WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYRLRMHPEKTEEM CRNMTLLFNTAYHLAMEGRPYCDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERVRQSPFLSIILDGQSDDLLADTVAVYVQYISSDGPPATEFLSLQELGFSATDSYIQALDRAF SSLGIRLQDERPSVGLGIDGANITASLRANMYMTIRKTLPWLLCLPLMIHKPHLEVLDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_hemBow Hemidactylus bowringii (gecko) HQ902409 frag ZnF_TTF WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYRLRMHPEKTEEM CRNMTLLFNTAYHLAMEGRPYCDFRSLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYISSDGPPATEFLSLQELGFSTADSYIQALDRAFSSLGIRLQDEKPS VGLGMDGANITASLRANMYMTIRKTLPWLLCLPLMVHKPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_sciRee Scincella reevesii (skink) HQ902404 frag ZnF_TTF WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYRLRMHPEKTEEM CRNMTLLFNTAYHLAMEGRPYCEFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERVRQSPFLSIILDGQSDDLLADTVAVYVQYISSDGPPATEFLSLQELGFSTTDSYIQALDRAFSSLGIRLQDEKPS VGLGIDGANITASLRANMYMTIRKTLPWLLCLPLMVHKPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_dibBou Dibamus bourreti (skink) HQ902405 frag ZnF_TTF WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYRLRMHPEKTEEM CRNMTLLFNTAYHLAMEGRPYCDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSDDLLADTVAVYVQYISSDGPPATEFLSLQELGFSATDSYIQALDRAFSSLGIRLQDEKPT VGLGVDGANITASLRASMYMTIRKTLPWLLCLPLMVHKPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAVKW >PRDM11_najAtr Naja atra (cobra) HQ902408 frag ZnF_TTF WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYRLRMHPEKTEEM CRNMTLLFNTAYHLAIEGRPYCDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALREDLIERVRQSPFLSIILDGQSDDLLADTVAVYVQYVSCDGPPATEFLSLQELGFSTTDSYVQALDRAFSSLGMRLQDEKPS VGLGIDGANITASLRANIYMTIRKTLPWLLCLPLMVHKPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRAIKW >PRDM11_batYen Batrachuperus yenyuanensis (salamander) HQ902410 frag ZnF_TTF WFLRYSSTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRSMTLLLNTAYHLAVEGRPYYDFRPLAELLRKCELRVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSEYLLADTVAVYVQYTSNDGPPATEFLSLQELGVPTTESYLQAIDRAFSALGIRLQDEKPT VGLGVDGFNITAGLRANMYMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRVTAATLCEETEFLGDIRGVRW >PRDM11_ichBan Ichthyophis bannanicus (caecilian amphibian) HQ902398 frag ZnF_TTF WFLRYSSTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLALEGRPYFDFRPLAELLRKCELRVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSEDLIADTVAVYVQYTSCDGPPATEFLSLQEIGLSTAESYLQGIDRAFSALGIRLQDEKPT VGLGIDGANITAGLRANMYMTIRKTLPWLLCLPFMVYRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRTTASTLCEETEFLGDIRAVRW >PRDM11_xenTro Xenopus tropicalis (frog) blat/CF781198 WFLRYSSTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLAMEGRPYYDFRPLAELLRKCELRVVDQYMNEGDCQILIHHIARALREDLVERIRQSPFLSIILDGQSEDLLADTVAVYVQYTSSDGPPATEFLSLQELGLPTTESYLQGIDRAF SALGIRLQDERPTVGLGVDGANITAGLRANLYMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRLTAATLCEETEFLGDIRAVKW >PRDM11_ranNig Rana nigromaculata (dark-spotted frog) HQ902401 frag ZnF_TTF WFLRYSSTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEM CRNMTLLFNTAYHLAMEGRPYYDFRPLAELLRKCELRVVDQYMNEGDCQILIHHIARALREDLIERIRQSPFLSIILDGQSEDLLADTVAVYVQYTSNDGPPATEFLSLQELALPTTESYLQGIDRAFSALGIRLQDERPS VGLGIDGVNITAGLRANLYMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRLTAATLCEETEFLGDIRAVKW
The structure of ZNF862 suggests a partial internal duplication at some point in its history. Its large penultimate exon of 702 amino acids is clearly related to that of PRDM11 both in terms of sequence identity and domain content. Its KRAB domain is also found in PRDM7/9 though percent identity is negligible.
>ZNF862_homSap Homo sapiens (human) refGene KRAB ZNF_TFF hATC dimerization dimerization 0 MEPRESGK 0 0 APVTFDDITVYLLQEEWVLLSQQQKELCGSNKLVAPL 1 2 GPTVANPELFRKFGRGPEPWLGSVQGQRSLLEHHP 1 2 GKKQMGYMGEMEVQGPTRESGQSLPPQKKAYLSHLSTGSGHIEGDWAGRNRKLLKPRSIQKSWFVQFPWLIMNEEQTALFCSACREYPSIRDKRSRLIEGYTGPFKVETLKYHAKSKAHMFCVNALAARDPIWAARFR SIRDPPGDVLASPEPLFTADCPIFYPPGPLGGFDSMAELLPSSRAELEDPGGDGAIPAMYLDCISDLRQKEITDGIHSSSDINILYNDAVESCIQ 0 0 DPSAEGLSEEVPVVFEELPVVFEDVAVYFTREEWGMLDKRQKELYRDVMRMNYELLASL 1 2 GPAAAKPDLISKLERRAAPWIKDPNGPKWGKGRPP 1 2 GNKKMVAVREADTQASAADSALLPGSPVEARASCCSSSICEEGDGPRRIKRTYRPRSIQRSWFGQFPWLVIDPKETKLFCSACIERPNLHDKSSRLVRGYTGPFKVETLKYHEVSKAHRLCVNTVEIKEDTPHTALV PEISSDLMANMEHFFNAAYSIAYHSRPLNDFEKILQLLQSTGTVILGKYRNRTACTQFIKYISETLKREILEDVRNSPCVSVLLDSSTDASEQACVGIYIRYFKQMEVKESYITLAPLYSETADGYFETIVSALDELDI PFRKPGWVVGLGTDGSAMLSCRGGLVEKFQEVIPQLLPVHCVAHRLHLAVVDACGSIDLVKKCDRHIRTVFKFYQSSNKRLNELQEGAAPLEQEIIRLKDLNAVRWVASRRRTLHALLVSWPALARHLQRVAEAGGQIG HRAKGMLKLMRGFHFVKFCHFLLDFLSIYRPLSEVCQKEIVLITEVNATLGRAYVALESLRHQAGPKEEEFNASFKDGRLHGICLDKLEVAEQRFQADRERTVLTGIEYLQQRFDADRPPQLKNMEVFDTMAWPSGIEL ASFGNDDILNLARYFECSLPTGYSEEALLEEWLGLKTIAQHLPFSMLCKNALAQHCRFPLLSKLMAVVVCVPISTSCCERGFKAMNRIRTDERTKLSNEVLNMLMMTAVNGVAVTEYDPQPAIQHWYLTSSGRRFSHVYTCAQVPARSPA 1 2 SARLRKEEMGALYVEEPRTQKPPILPSREAAEVLKDCIMEPPERLLYPHTSQEAPGMS* 0
PRDM11 and amniote phylogeny
A recent study searched through UCSC genomic multi-alignment files for the most informative regions for resolving the long-controversial phylogenetic relationships among amniotes. Among the most suitable coding regions was the distal region of the last exon of we now know to be PRDM11. This region was sequenced in various snakes, caecilians, turtles, birds and frogs that are poorly represented in sequence databases. That data is supplemented below with sequences from genome projects in the difference alignment (relative to human) to illustrate the evolution of this highly conserved region.
Note the three sites colored magenta associate turtles with birds + crocodilians to the exclusion of lizards in the overall tree topology: (amphibians,((lizards,(turtles,(birds,crocodilians))),(monotremes,(marsupials,placentals)))). This requires, as do all amniote topologies, various morphological convergences and reversals. The short explanation is that a 1903 choice of anatomical character (number of skull openings -- temporal fenestrae) was -- in retrospect -- a poor choice. This has left an unfortunate legacy of terms such as diapsid, anapsid, synapsid and indeed 'reptile' that do not correctly reflect the evolutionary history of amniotes.
Difference Alignment of Final Exon Region of PRDM11 Used in Establishing Amniote Phylogenetic Tree homSap WFLRYSPTLNEMWCHVCRQYTVQSSRTSAFIIGSKQFKIHTIKLHSQSNLHKKCLQLYKLRMHPEKTEEMCRNMTLLFNTAYHLALEGRPYLDFRPLAELLRKCELKVVDQYMNEGDCQILIHHIARALmagentaLVERIRQSPCLSVILDGQSDDLLA Homo sapiens (human) musMus ................................................................................................................................................I........... Mus musculus (mouse) canFam ................................................................................................................................................I........... Canis familiaris (dog) loxAfr ................................................................................................................................................I........... Loxodonta africana (elephant) monDom ...........................................................................................F.................................................F..I........I.. Monodelphis domestica (opossum) ornAna .............................................................................................................................................F..I........... Ornithorhynchus anatinus (platypus) galGal ...........................................................................................Y.................................................F..I........V.. Gallus gallus (chicken) melGal ...........................................................................................Y.................................................F..I........V.. Meleagris gallopavo (turkey) anaPla ...........................................................................................Y.................................................F..I........V.. Anas platyrhynchos (duck) taeGut ...........................................................................................Y.................................................F..I........... taeGut Taeniopygia guttata (finch) strCam ...........................................................................................Y.................................................F..I........... strCam Struthio camelus (ostrich) allMis ...........................................................................................Y.................................................F..I........... allMis Alligator mississippiensis (alligator) allSin ...........................................................................................Y.................................................F..I........... allSin Alligator sinensis (alligator) croSia ...........................................................................................Y.................................................F..I........... croSia Crocodylus siamensis (crocodile) carIns ...........................................................................................F.................................................F..I........... Carettochelys insculpta (turtle) podUni ...........................................................................................F.................................................F..I........... Podocnemis unifilis (turtle) traScr ...........................................................................................F.................................................F..I........... Trachemys scripta (turtle) pelSin ...Q.......................................................................................F...................................S.............F..I........W.. Pelodiscus sinensis (turtle) anoCar ..........................................................R..........................M.....C............................................V....F..I........... Anolis carolinensis (lizard) hemBow ..........................................................R..........................M.....C...S.............................................F..I........... Hemidactylus bowringii (gecko) sciRee ..........................................................R..........................M.....CE...........................................V....F..I........... Scincella reevesii (skink) dibBou ..........................................................R..........................M.....C.................................................F..I........... Dibamus bourreti (skink) najAtr ..........................................................R..........................I.....C.........................................I..V....F..I........... Naja atra (cobra) batYen ......S.................................................................S....L.......V.....Y..............R..................................F..I......EY... Batrachuperus yenyuanensis (salamander) ichBan ......S....................................................................................F..............R..................................F..I......E..I. Ichthyophis bannanicus (caecilian) xenTro ......S..............................................................................M.....Y..............R..................................F..I......E.... Xenopus tropicalis (frog) ranNig ......S..............................................................................M.....Y..............R..........................I.......F..I......E.... Rana nigromaculata (dark-spotted frog) homSap DTVAVYVQYTSSDGPPATEFLSLQELGFSSTESYLQALDRAFSALGIRLQDEKPTVGLGVDGANITASLRASMFMTIRKTLPWLLCLPFMVHRPHLEILDAISGKELPCLEELENNLKQLLSFYRYSPRLMCELRSTAATLCEETEFLGDIRAVRW Homo sapiens (human) musMus ..........................................A...............................................................................................S................. Mus musculus (mouse) canFam ...........................................................I....V.........................................................................S................. Canis familiaris (dog) loxAfr .............................G.............T..............................................................................................S...............K. Loxodonta africana (elephant) monDom .............................T.D...........S...........I...............................................................................L..S................. Monodelphis domestica (opossum) ornAna .............................T.D..........A...V.................V......G....V..........................................................L.................... Ornithorhynchus anatinus (platypus) galGal .............................T.D...........S...........I...............NL..............................................................V..S...............K. Gallus gallus (chicken) melGal .............................T.D...........S...........I...............NL..............................................................V..S...............K. Meleagris gallopavo (turkey) anaPla .............................T.D...........S...........I...............NL..............................................................V..................K. Anas platyrhynchos (duck) taeGut .............................T.D...........S...........I...............NL..............................................................V..................K. taeGut Taeniopygia guttata (finch) strCam .............................T.D...........S...........I...............NL..............................................................V..................K. strCam Struthio camelus (ostrich) allMis .............................T.D...........S...........I...............NL.......................................................K......V..................K. allMis Alligator mississippiensis (alligator) allSin .............................T.D...........S...........I...............DL......A................................................K......V..................K. allSin Alligator sinensis (alligator) croSia .............................T.D...........S...........I...............NL.......................................................K......V..................K. croSia Crocodylus siamensis (crocodile) carIns ............................CT.D...........S...........I...............NL..............................................................V..................K. Carettochelys insculpta (turtle) podUni ............................CT.D...........S...........I...............NL..............................................................V..................K. Podocnemis unifilis (turtle) traScr ............................CT.D...........S...........I...............NL..............................................................V..................K. Trachemys scripta (turtle) pelSin ............................CT.D...........S...........I...............NL..............................................................V..................K. Pelodiscus sinensis (turtle) anoCar .........I...................A.D..I........S........R.S....I...........N.Y..............L.I.K....V.....................................V..................K. Anolis carolinensis (lizard) hemBow .........I...................TAD..I........S..........S....M...........N.Y..............L...K..........................................V..................K. Hemidactylus bowringii (gecko) sciRee .........I...................T.D..I........S..........S....I...........N.Y..............L...K..........................................V..................K. Scincella reevesii (skink) dibBou .........I...................A.D..I........S.............................Y..............L...K..........................................V..................K. Dibamus bourreti (skink) najAtr .........V.C.................T.D..V........S..M.......S....I...........NIY..............L...K..........................................V.................IK. Naja atra (cobra) batYen ...........N...............VPT.......I........................F....G...N.Y.............................................................V................G... Batrachuperus yenyuanensis (salamander) ichBan ...........C.............I.L.TA.....GI.....................I.......G...N.Y.................Y...........................................T..S................. Ichthyophis bannanicus (caecilian) xenTro ...........................LPT......GI..............R..............G...NLY.............................................................L..................K. Xenopus tropicalis (frog) ranNig ...........N..............ALPT......GI..............R.S....I..V....G...NLY.............................................................L..................K. Rana nigromaculata (dark-spotted frog)
