Opsin evolution: Encephalopsin gene loss
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Revision as of 03:35, 7 April 2008 by Tomemerald (talk | contribs) (→Post-marsupial loss of TMT encephalopsin)
Introduction to Encephalopsin Evolution
Encephalopsin is a pivotal ciliary opsin, with basal evolutionary position to the imaging opsin gene expansion and well represented in early diverging deuterstomes, notably the cephalochordate Branchiostoma. Despite this, encephalopsin has been the subject of just one substantive publication dating to 1999. That article primarily emphasized its non-retinal distribution in mouse brain:
"Encephalopsin is highly expressed in the preoptic area and paraventricular nucleus of the hypothalamus ... in selected regions of the cerebral cortex, cerebellar Purkinje cells, a subset of striatal neurons, selected thalamic nuclei, and a subset of interneurons in the ventral horn of the spinal cord. Rostrocaudal gradients of encephalopsin expression are present in the cortex, cerebellum, and striatum. Radial stripes of encephalopsin expression are seen in the cerebellum."
The gene is well-represented in chondrichthyes and teleost fish with multiple independent copies, but single copies in amphibians, birds, lizard, marsupials, primates and rodents, with excellent amino acid conservation (over 60% between telost fish and human). Surprisingly, upon more intensive taxonomic sampling, functional encephalopsin turns out to completely absent in a variety of other mammalian clades. While interesting in its own right, this complicates the standard application of comparative genomics to the evolution of encephalopsin structure and function.
Massive encephalopsin gene loss in mammals
The table lists 10 species that today have unprocessed pseudogenes in place of a once-functional encephalopsin gene. The observed phylogenetic distribution of loss (which is irreversible) requires a minimum of 6 independent events, for example in some bats but not others. At the level of superordinal clades, no gene loss is observed in Euarchontoglires but Laurasiatheres (especially artiodactyls) are heavily affected as well as the Xenarthra within Atlantogenata and at least platypus within monotremes.
The odd feature of these pseudogenes is that they must all have arisen fairly recent on the mammalian time scale to remain observable today as decayed relics. However they survive at variable degrees of degeneration. This suggests that the losses are not coordinated with a single unifying global environmental event.
As the function of encephalopsin is obscure, the consequences of gene loss are even more so. Encephalopsin may have lost its supporting selected function; no increase in opsin gene number has compensated for this (from homology searches of complete genomes).
The clade-incoherent gene loss of encephalopsin is reminiscent of loss of GULO, the terminal enzyme for L-ascorbic acid biosynthesis, with relic gene fragments still detectable in guinea pigs (gene estimated lost 20 myr ago) and primates (lost on stem between lemurs and tarsier about 60 myr ago). At least 5 independent losses have been documented in some passerine birds, all tested species of bats, and teleost fish from zebrafish on (but not including sturgeon, chondrichthyes, or lamprey). A 2007 study of loss of GUCYD (GPCR signaling guanyl cyclase D) exemplifies modern pseudogene dating methods.
In the table, 'ok' indicates presence of a gene with conserved sequence characteristics appropriate to functioning opsins and appropriate to the ancestral encephalopsin class; ps indicates definite pseudogenization of the 4-exon gene (reading frame shifts, internal stop codons, loss of sequence conservation in expected regions); +- indicates partial gene recovery with some uncertainty (traces commonly have errors such as short indels and quality departure at their ends; repetitive base composition in exon 1 may have lead to trace read technical problems).
ok >ENCEPH_homSap Homo sapiens (human) NM_014322 OPN3 full ok >ENCEPH_panTro Pan troglodytes full ok >ENCEPH_gorGor Gorilla gorilla ok frag ok >ENCEPH_ponAbe Pongo abelii full ok >ENCEPH_nomLeu Nomascus leucogenys exon 1 ok frag ok >ENCEPH_macMul Macaca mulatta (rhesus) XP_001094239 full ok >ENCEPH_papHam Papio hamadryas 1st exon problematic 1x ok frag ok >ENCEPH_calJac Callithrix jacchus full ok >ENCEPH_tarSyr Tarsius syrichta ok >ENCEPH_micMur Microcebus murinus full ok >ENCEPH_otoGar Otolemur garnettii full +- >ENCEPH_tupBel Tupaia belangeri so-so frag ok >ENCEPH_musMus Mus musculus Opn3 Panopsin NM_010098 2aa del full ok >ENCEPH_ratNor Rattus norvegicus XP_573517 predicted 2aa del full ok >ENCEPH_speTri Spermophilus tridecemlineatus full ok >ENCEPH_dipOrd Dipodomys ordii full ok >ENCEPH_cavPor Cavia porcellus 3 aa del full ok >ENCEPH_oryCun Oryctolagus cuniculus full ok >ENCEPH_ochPri Ochotona princeps 5aa del ok frag ok >ENCEPH_canFam Canis familiaris (dog) XP_854433 full ok >ENCEPH_felCat Felis catus full ps >ENCEPH_bosTau pseudo frag ps >ENCEPH_turTru Tursiops truncatus pseudo frag ps >ENCEPH_susScro no coverage ps >ENCEPH_vicVic pseudo pseudo frag ps >ENCEPH_myoLuc Myotis lucifugus weak frag ok >ENCEPH_pteVam Pteropus vampyrus 86%=homSap full ok >ENCEPH_equCab Equus caballus full ps >ENCEPH_sorAra pseudo frag ps >ENCEPH_eriEur no coverage ok >ENCEPH_loxAfr Loxodonta africana 2 exons in browser, 1 2x full ps >ENCEPH_echTel Echinops telfairi no coverage ok >ENCEPH_proCap Procavia capensis ok frag ps >ENCEPH_dasNov Dasypus novemcinctus pseudo +- >ENCEPH_choHof Chololepis hoffmanni so-so frag ok >ENCEPH_monDom Monodelphis domestica (opossum) encephalopsin OPN3 75%=homSap full ok >ENCEPH_macEug Macropus eugenii ok frag ps >ENCEPH_ornAna Ornithorhynchus anatinus pseudo ok >ENCEPH_xenTro Xenopus tropicalis (frog) 45%=homSap full ok >ENCEPH_galGal Gallus gallus (chicken) 71%=homSap encephalopsin OPN3 full ok >ENCEPH_taeGut Taeniopygia guttata mrna CK301424 70%=homSap full ok >ENCEPH_anoCar Anolis carolinensis (lizard) 70%=homSap OPN3 full ok >ENCEPH_danRer Danio rerio (zebrafish) NM_001111164 mrna 61%=homSap full ok >ENCEPH_gasAcu Gasterosteus aculeatus (stickleback) 58%=homSap full ok >ENCEPH_oryLat Oryzias latipes 58%=homSap full ok >ENCEPH_takRub Takifugu rubripes (pufferfish) homSap=61% full
Post-marsupial loss of TMT encephalopsin
TMT (for teleost multiple tissue) is another fairly obscure opsin, again subject of but a single publication that established its expression in "a variety of neural and non-neural tissues, including a zebrafish embryonic cell line that exhibits a light entrainable clock" suggesting TMT regulates peripheral clocks in teleost fish.
We see below that orthologs are readily located in chondrichthyes, fish, frog, lizard, birds, and marsupials but once again the gene has been lost in all placental mammals even as it persists to the present day in other vertebrates, this time vanishing without a trace (suggesting by parsimony a single event on the ancestral common stem).
TMT is an encephalopsin-class opsin, clustering most closely with these opsins. Although found initially in fish, it is not the product of a whole genome duplication there because synteny is lacking, the two encephalopsins are quite diverged, and preceding and following species lacking the duplication also have both copies. Thus TMT likely arose in lamprey ancestor if not earlier. Indeed, the encephalopsins of cephalochordates more closely resemble TMT than they do encephalopsins. TMT might thus be the ancestral gene, with encephalopsin a derived form receiving more emphasis historically because it persisted into some placentals, notably human, unlike TMT.
Reference set of curated encephalopsins (including pseudogenes)
>ENCEPH_homSap Homo sapiens (human) NM_014322 OPN3 full
0 MYSGNRSGGHGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0
>ENCEPH_panTro Pan troglodytes full
0 MYSGNRSGGQGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0
>ENCEPH_gorGor Gorilla gorilla ok frag
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
>ENCEPH_ponAbe Pongo abelii full
0 MYSGNRSGGQGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLMVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVAIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGRLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0
>ENCEPH_nomLeu Nomascus leucogenys exon 1 ok frag
0 MYSGNRSGGQGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGN 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVLMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0
>ENCEPH_macMul Macaca mulatta (rhesus) XP_001094239 full
1 MYSGNRSGGQGYWDGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0
>ENCEPH_papHam Papio hamadryas 1st exon problematic 1x ok frag
0 MYSGNRSGGQGYWDGGGAAGTEGPALVGTLIPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLL LLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLFG 1
2 gIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0
>ENCEPH_calJac Callithrix jacchus full
0 MYSGNRSGGQGYWDGGEAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSNLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPLGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGHGHLVTPTISIVSYLFAKSNTVYNPVIYVFMIRK 0
0 FRRSLLQLLCLRMLRCQQPAKDLSAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTNGSKVDVIQVRPL* 0
>ENCEPH_tarSyr Tarsius syrichta weak full
0 MYSGNRSGGQGSWEGGGAAGAEGPAAAGIPAPIISRGTYERLALVLLGSIGLLGVGNNLLVLVLYYKFPRLRTPTHLLLANISLSDLLVSLFGVTFTFVSCLRNGWVWDTVDCMGYVLTIDLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDTSFVLFLFLGCLVVPMGVISYCYGHILYSIRe 0
0 LRCVEDLQTIQVIKILKYEKKVAKMCFFMIFTFLICWMPYIVICFLVVNSQGHLVTPTISVVSYLFAKSNTVYNPVIYIFMIRK 0
0 FRRSLLQFLCLRLLRCQQPAKDLPAAENEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDKTSGSKVDVIQVRPL* 0
>ENCEPH_otoGar Otolemur garnettii full
0 MYSGNRSGGQGFWEGGGAAGAEEPTPEGTLSPAPLFSPSAYERLALLLGSIGLLGVANNLLVLVLYYKFPRLRTPTHLFLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSGSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPVGVVAHCYGHILYSIRM 0
0 LRCVEDLQTTQVIKILKYEKKVAKMCFFMIFTFLVCWMPLIVICFLVVNGQGHLVTPTVSIVSYLLAKSNTVYNPVIYIFMLRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPAAESEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDNSDKTNGSKVDVIQVRPL* 0
>ENCEPH_micMur Microcebus murinus full
0 MYSGNRSGGQWFWEGGGAAGAEGPAPAGTLSPAPLFSPGTYERLALLLGSIGLLGVGNNLLVLVLYYKFPRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GIVSIATLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPVGVMVHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKILKYEKKLAKMCFLMIFTFLVCWMPYIVICFLVVNGQRHLVTPTVSIVSYLFAKSNTVYNPIIYIFMIRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPASESEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDNSDKTSGSKVDVIQVRPL* 0
>ENCEPH_tupBel Tupaia belangeri so-so frag
0 SGNRRGGQGLLEGGGAVGVEGLAPTGSQSPAPLFSRGTYERLALLLGSIGLLGVGHNLLVLVLYYKFPRLRTPTHLLLLNISLGDLLVSVFGVTFTFVTCLRNGWVWDTVSCAWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFPWAWRAITYIWLYSLAWAGAPLLGWNRYMLDVHGLGCTVDWKSK
0 MINILRYKKKVAKMCFLMILTFLICWMPYIVIRFLVVNGGYGHLITPTVSIVSFLFAKSSTVYNPVIYIFMIRK 0
0 FRRSLLQLLCFRLLRYQRPAKDLPAAGSEMQIRPIVMSQKDGDKPKKKVTFNSSSIIFIITSDESLSVDDSDKTSGSKVDVIQVRPL* 0
>ENCEPH_musMus Mus musculus Opn3 Panopsin NM_010098 2aa del full
0 MYSGNRSGDQGYWEDGAGAEGAAPAGTRSPAPLFSPTAYERLALLLGCLALLGVGGNLLVLLLYSKFPRLRTPTHLFLVNLSLGDLLVSLFGVTFTFASCLRNGWVWDAVGCAWDGFSGSLF 1
2 GFVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDIHGLGCTVDWRSKDANDSSFVLFLFLGCLVVPVGIIAHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKMLRYEKKVAKMCFLMAFVFLTCWMPYIVTRFLVVNGYGHLVTPTVSIVSYLFAKSSTVYNPVIYIFMNRK 0
0 FRRSLLQLLCFRLLRCQRPAKNLPAAESEMHIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVEDSDRSSASKVDVIQVRPL* 0
>ENCEPH_ratNor Rattus norvegicus XP_573517 predicted 2aa del full
0 MYSGNRSGGQGYWEDGAGAEGAAPAGTRSPAPLFSPTAYERLALLLGCLALLGVGGNLLVLLLYSKFPRLRTPTHLFLVNLSLGDLLVSLFGVTFTFASCLRNGWVWDAVGCAWDGFSGSLF 1
2 GFVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKSKDANDSSFVLFLFLGCLVVPMGIIAHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKMLRYEKKVAKMCFLMAFVFLTCWMPYVVTRFLVVNGYGHLVTPTVSIVSYLFAKSSTVYNPVIYIFMIRK 0
0 FRRSLLQLLCFRLLRCQRPAKNLPAAESEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVEDSDRSSASKVDVIQVRPL* 0
>ENCEPH_speTri Spermophilus tridecemlineatus full
0 MYSGNRSGSQGSWEGDGSAGAEGSAPEGTLSPTPLFSPGTNERLALLFRSVGLLGAGSNLLVLVLYYKFQGSAHPLTFFLVNISLGDLLMSLFGVTFTFVSCLRNRWVWDTVACVWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVEWKSKDANDSSFVLFLFLGCLVVPVGVIAHCYGHILYSIRM 0
0 LRCVEDLQIFQVIKILRYEKKLAKMCFVMVFTFLICWMPYIVVCFLVANGYGQRVTPTVSIVSNLFAKSSTVYNPVIYIFMIRK 0
0 FRRSLLQLLCSRLLRCQQPAKDLPAVGNEMQIRPIVISQKDGERPKKKVTFNSSSIVFIITSDESLSVDDSNRTSGSKADVIQVRPL* 0
>ENCEPH_dipOrd Dipodomys ordii full
0 MYSGNRSGGQEYWEDGGAAGSEGPAPAGTLSPAPLFSAGAYERLALLLGSAGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSRSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFTWAWRAITYIWLYSLAWAGAPLLGWNRYILDIHGLGCTVDWKAKDANDSSFVLFLFIGCLVVPVGIIAHCYGHILYSIRM 0
0 LRCVEDLQTIQIIKILQYEKKLAKMCFLMALTFLMCWMPYIVTCFLVVNSHGHLVTPTISIVSHLLAKSSTIYNPVIYIFMIRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPAAGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSVRSSGSKADVIQVRPL* 0
>ENCEPH_cavPor Cavia porcellus 3 aa del full
0 MYSGNRSSGQGYWEGGGPEDPAPAGTLSPAPLFSPGAYERLALLLGSLGLLGVGNNLLVLVLYYKFQRLRSPTHLFLANISLSDLLGSLFGVTFTFVSCLKNGWVWDAVGCVWDGFSRSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDIHGLSCTVDWKSKDANDSSFVLFLFLGCLVVPVGVIVHCYGHILYSIRM 0
0 LRGVEDLQTIQVMKILRSENKVAIMCFLMVFIFLVCWMPYIVICFLLVNGYRHRVTPTVSIVSYLFTKSSTVYNPVIYVLMIRK 0
0 FRRSLLQLHCLRLLRCQQPAKDLPAVEREMHIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVDDSDRTSGSKVDTIQVRPL* 0
>ENCEPH_oryCun Oryctolagus cuniculus full
0 MYSGNRSGEQGYWEGGGAAGAEGPGPAGTLSPAPLFSPSTYERLALLLGSIGLLGVGSNLLVLVLYYKFQRLRTPTLLFLVNISLSDLLVSVFGVTFTFVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDIHGLGCTVDWKSKNANDSSFVLFLFLGCLVVPVGVIAHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKILRYEKKVAKMCFFMVFTFLICWMPYVVICFLVVNGYGHLVTPTLSIVSYLFCKSSTAYNPIIYIFMIRK 0
0 FRRSLLQLLCFQPLRCQQPPKDLPTVGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIIASDESLAVDDNEKASGPKVDVIQVRPL* 0
>ENCEPH_ochPri Ochotona princeps 5aa del ok frag
0 MYSGNRSSGQGHWEDAEESEPAGTVSPAPLFSTNTYERLALLFGSLGLLGVGNNLLVLVLYYKFQRLRTPTHLFLVNLSLSDLLVSLFGVTFTLVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINYSWAWRAITYIWLYSLAWAGAPLLGWNRYMLDIHGLGCTVDWKSKNANDSSFVLFLFLGCLVVPVGVIAHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKILRYEKKVAKMCFFMIFTFLICWMPYIVIRFLVVNGYGRLVTPTISIVSYLFCKSSTVYNPVIYIFMIRK 0
>ENCEPH_canFam Canis familiaris (dog) XP_854433 full
0 MMRRVKLTLIPAAVLDIESQAPKDESLYFSICHFCPQKGFLEFQRLRTPTHLLLVNLSLSDLLVSLFGVTFTFVSCLRNGWVWDSVGCVWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWSGAPLLGWNRYILDVHGLGCTVDWKSKDANDSFFVLFLFLGCLVVPMGVIVHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILRYEKKVAKMCFLMIFIFLIFWMPYIVICFLVVNGYGHLVTPTVSIVSYLFAKSSTVYNPVIYIIMIRK 0
0 FRRSLLQLLCFRPLRCQRPAKDLPANGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESVSIDDSDKTSVSKVDVIQVRPL* 0
>ENCEPH_felCat Felis catus full
0 MYSRNRSGGQGHWEGGGAAGAERQGPAGTLSPAPLFSPGTYERLAMLLGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLLLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GTVSITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWSGAPLLGWNRYILDVHGLGCSVDWKSKDANDSSFVLFLFLGCLVVPVGVIAHCYGHILYSVRM 0
0 LRCVEDLQTIQVIKILRYEKKVAKMCFLMISTFLIFWMPYIVICFLVVNGYGHLVTPTVSIVSYLFAKSSTVYNPVIYIFMIRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPTNGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVEDSDKTSVSKVDVIQVRPL* 0
>ENCEPH_bosTau pseudo frag
0 P-----SASG---RRGG----A-----G*SSLTLPVSEGAYERVV-LLGSVGLPGVGSNLLVLVIYLKLPRLRSPARLLLLHVSLGDLLPSVLQAALAFAFPLRGSRVGGTTIGEWDGFSSSL* 1
2 GIVSIITLTRLAYECYICVIHARVINFPQAWRTIPCIWLSSTVWSGASLLGWNNHILDMHGPGCTGDWPSKDTSHSSFVLFLFLGCL GVIAHCHGHILFSIQ
0 F*RALLQLLCF*LLRCQIPAKDLSAVGREMRLTSSVKSQKDRDVTERQG-QAKEKRTFNSSSIIFIITNDESLSVGDSDRTNGSKVDVIQVHPL
>ENCEPH_turTru Tursiops truncatus pseudo frag
0 NCGGGGAGWEGG-----EGLWPGQPSLTQPV-SQGAYELLVLLLGSVGLLGVGSSLLVLVLYLKFPRLRSPSRLFLLHVGLGNLLPSVLRAALAFAFRPRGGVVGGATNCVWDGFSNSLW 1
2 GIFSIITLTTLACERYIGMIHNRVISFSWAWRAITYIWLYSLVRSGSPLLG*HRYILDVHVLGCAVDWKSKDTSDSSFVLFLFLDCMVVPVGVIAHCYGHILYSIRK 0
0 FRRALLQLLCFRLQRCQ*PAKDLPAVGSEMQIQLIVMPQKDRDRPKKKLTFNSSSIIFVITNDESLSVD-GERTSGS*VDVIQVCPL* 0
>ENCEPH_susScro no coverage
>ENCEPH_vicVic pseudo pseudo frag
2 GIVSIISLTVLAYECYIHVVHARMITFSWTWRAVTYIWLYTLVWSGVPLMG*NRYIL-FHGLGCAVDWKSKDANDFCFVLFLFLGSLVVPVGVIAHCYGHILYSIEL 0
0 RGVEDLQTIKVIRILRYENKLARMCFCMTFTFMILWMPYVVICFLMFSDGGHLVTLTVFIVS*PFTNSSTVYDAAFYIFMIRK 0
0 FQRALLHLLCFRLLRYQQPAKDLPTYQS*MQIRPIEMSQKVRDRPKKKVIFNSSPIIFIITHDGSLSVDDKD
>ENCEPH_myoLuc Myotis lucifugus weak frag
0 MFSGNRNG--GQFRGGQLGLGHRGVGASGTLGPRAFLKNIYFYSFERRR
>ENCEPH_pteVam Pteropus vampyrus 86%=homSap full
0 MHSGNRSGGLDSWEGGGAAGAEGPGLAGTLSPGSVFNPSTYERLALLLGSIGLLGVANNLLVLVFYYKFQQVRTPFYLFLVNISFSDLLVSFFGVTFTFVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GTVSMTTLTVLAYERYIRVVQARAIDFSWAWRTITYIWLYSLGWSGAPLLGWNRYILDVHGLGCAVDWKSKDANDSSFVLFLFLGCLVVPVVVIAHCYGHILYSVQM 0
0 LRCVEDLQTIQVIKILRYEKKMAKMCFLMIFTFLISWMPYIVICFLVVNGYGHLVTPTVSIVSYLFAKSSTVYNPVIYIFMIRK 0
0 FRRFVLQLLCFRPLRCRRPATDLPAGGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFVITSDESLSVDDSDKINGSKADGIQVRPL* 0
>ENCEPH_equCab Equus caballus full
0 MTAGTRAGGQGSWEGGGAAGAEGPGPAGPLSPAPLFSPGTYERLALLLGCLGLLGVGNNLLVLVLYSKFPRLRTPTHLLLVNISLSDLLVALFGVTFTFVSCLRNGWVWDAVGCAWDGFSSSLC 1
2 GIVSITTLTVLAYERYIRVVHARVINFSWAWRALTYIWLYSLAWSGAPLLGWNRYILDIHGLGCAVDWKSKDANDSTFVLFLFLGCLVVPMGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVMKILRYEKKLAKMCFFMIFTFLIFWMPYIVICFLVANGYGHLVTPTVSIVSYLFAKSSTIYNPIIYIFTIRK 0
0 FRRSLSQLLCFRLLRCQRPAKDQPPVGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVHDSDKINGSKVEVIQVRPL* 0
>ENCEPH_eriEur no coverage
>ENCEPH_sorAra pseudo frag
0 RSVHTSRRGLDAGDRGGAPGATEPGRADDAVLSAALLLGAGRGTLLVLILHQKCRRPLTSPLAQLGPVNVSRGKLLVSLFGITFVFFLRNCWVWETEGRGAFSCSVL
>ENCEPH_loxAfr Loxodonta africana 2 exons in browser, 1 2x full
0 MYSGNRSGGQDLWEGGGGSGGAGPAGTLSPAPVFRSGTYERLALLVGSIGLLGVGNNLLVLVLYYKFQRLRTPTHLFLVNISLSDLLVSLFGVTFTFVSCLRNGWVWDTVGCVWDGFSSSLF 1
2 GIASITTLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWSGAPLLGWNRYILDTHGLACTVDWKSNNSSDSSFVLFLFLGCLVVPVGVIAHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILRHEKKLAKMCLFMIFTFLICWMPYIVICFLVVNGYGHLVTPTISIVSYLFAKSSTVYNPVIYTFMIRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPVVGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVNNIDKTNGSKADVIQIRPL* 0
>ENCEPH_echTel Echinops telfairi no coverage
>ENCEPH_proCap Procavia capensis ok frag
2 GIASITSLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWSGAPLLGWNRYILDTHGLACTVDWKSNNTNDSSFVLFLFLGCLVVPVGVIVHCYGHILYSIRM 0
0 LRCVEDLQTIQVIKILRYEKKVAKMCLFMILTFLICWMPYIVICFLMVNDYGYLVTPTISIVSYLIAKSSTVYNPVIYTFMIRKV 0
0 FRRSLFQLLCFRLLRCQRPAKNKPEVGSEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVNDTDKINGSKADVIQVRPL* 0
>ENCEPH_dasNov Dasypus novemcinctus pseudo
0 MYSGNRSSGHES---GGPT--------GTLGSAAFFSPRTYERLALLAGAGGLLGAGGHLLVLALRCALPQLRSPPRRLLVTASLGDPLVSVFGVAFTCAACLRSG-VWDPAGCVGDGFGSGLC 1
2 GIVSTSSLTGLASEHSIRVVHASLISFSWAWAWLYSLAWSGVPLLGWDRYVLDVHRRGCTLNLRARDSSASSRVLFLFLGCVAVPVGVTVHCHGHILHSIRM 0
0 FLCVEGLQTVQVIKILKYEKKAATMCLVVVASFLMGWMPYIAIHFSVVNGYEHLVTPVVSTVSRLFAKSSPVYNPVIYIIMIRK 0
0 FHRSFL*LLFLQLLRCQRPAQDLPVVESEMQVRPTVMSQKDRHRPKKKVTFNSSSIIFIITSDESVSVNGSDKTNGSKFDVI * 0
>ENCEPH_choHof Chololepis hoffmanni so-so frag
0 MYSGNRSGGRDYWEGGGGAGAEGPGPTGTLSPALVFSPGTYERLAGLIGSIGLLGAGNNVLVLILYYKFQRLRTPTHLFLVNISFSDLLVSLFGVTFTFISCLRNGWVWDTVGCVWDGFSSSLF 1
2 GIVSITTLTVLAYERYIRVVHARVVNFSWTWRAITYIWLYSLACSGASLLGWNRYTLDIHGLACSVNWKSPDSSDSSFVLFLLLDCLTGPVAVIAHCY
0 LRCVEDLQTVQVIKILRYEKKVAKMCFVMIATFLMCWMPYIVICFLVVNGYGHLVTPTVSIVSHLFVKSSTVYNLVIYIFMLRK 0
0 FRRSLLQLLCFRLLRCQRPAKDLPVVGCEMQIRPIVMSQKEGHRPKKKVTFNSSSIIFIITSDESISVDGSDKTNGPKVDVIQVRPL* 0
>ENCEPH_monDom Monodelphis domestica (opossum) encephalopsin OPN3 75%=homSap full
0 MYSDNSSDDGGGGYWGSGRAGGASGTGVTGEPGPEGSPRQAPLFSPGTYELLALLIATIGLLGLCNNLLVLVLYYKFQRLRTPTHLFLVNISFNDLLVSLFGVTFTFVSCLRSGWVWDSVGCAWDGFSNTLF 1
2 GIVSIMTLTVLAYERYNRIVHAKVINFSWAWRAITYIWLYSLVWTGAPLLGWNRYTLEIHGLGCSVDWKSKDPNDSSFVIFLFFGCLMLPVGVMAYCYGHILYAIRM
0 LRCVEELQTIQVIKILRYEKKVAKMCFLMIAIFLFCWMPYAVICLLVANGYGSLVTPTVAIIASLFAKSSTAYNPIIYIFMSRK 0
0 FRRCLLQLLCFRLLKFQQPKKDRPVIRTEKQIRPIVMSQKVGDRPKKKVTFSSSSIIFIITSDETQMIDENDKNSGTKVNVIQVRPL* 0
>ENCEPH_macEug Macropus eugenii ok 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
>ENCEPH_taeGut Taeniopygia guttata mrna CK301424 70%=homSap full
0 MPAGNGTGTSGRPAPAAPEQEVPGERPLFSAGTYELLALLVATIGMLGLCNNLLVLVLYYKFKRLRTPTNLFLVNISLSDLLVSVFGVSLTFMSCLRSRWVWDAAGCVWDGFSSSLF 1
2 GIVSIMTLTALAYERYIRVVHAKVIDFSWSWRAITYIWLYSLAWTGAPLLGWNRYTLEIHGLGCSVDWKSKDPNDTSFVLLFFLGCLVAPVGIMAYCYGHILHAVRM 0
0 LRCVEDFQTVQVIKLLRYEKKVAKMCFLMISTFLICWMPYAVVSLLITYGYSNLVTPTVAIIPSFFAKSSTAYNPVIYIFMSRK 0
0 FRRCLLQLLCFRLMRFQRTMRETPATGSDKPIRPIVLSQKAGDRPKKKVTFSSSSVIFIITSDDAEQIEDSSKHNETKVNAIQVKPL* 0
>ENCEPH_anoCar Anolis carolinensis (lizard) 70%=homSap OPN3 full
0 MFSANGTRSGAGSDLEPGPGQQQQQREASEEEERGAGLSPFSAGTYELLALLVAAIGLLGLCNNLLVLVLYAKFKRLRTPTHLFLVNISLSDLLVSLFGVSFTFGSCLRHRWVWDAAGCVWDGFSNSLF 1
2 GIVSIMTLTVLAYERYIRVVHARVIDFSWSWRAITYIWLYSLAWTGAPLLGWNHYTLEIHGLGCSVDWQSKEPSDSSFVLFFFLGCLAAPVGIMAYCYGHILHAIRM 0
0 LRCVEDLQSIQVIKILRYEKKVAKMCFLMVTTFLICWMPYAVVSLLIAYGYGHLITPTVAIIPSFFAKSSTAYNPVIYIFMSRK 0
0 FRRCLVQLFCVQFLRFKRTLKEQPAIESNKPIRPIVMSQKVGDRPKKKVTFSSSSIIFIITSDDTEQIDVSTKCSDTKINVIQVKPL* 0
>ENCEPH_xenTro Xenopus tropicalis (frog) 45%=homSap full
0 MPVTNGSHNNSISWLHSKDMFTEDTYHFLALIVATVGFLGLVNNLLVLILYCKFKRLQTPTNLLFFNTSLCHFVFSLLAITFTFMSCVRGSWAFSVEMCVFHGFSKNLL 1
2 GIVSFGTLTVVAYERYARVVYGKYVNSSWSKRSITFVWVYSLAWTGFPLIGWNLYTFETHKLDCSFEWTATDPKDTAFVLLFFLACITLPLSIMAYCYGYILYEIQK 0
0 LRSVKNIQNFQEITILDYEIKMAKMCLLMMLTFLIGWMPYTILSLLVTSGYSKFITPTITVMPSLLAIASAAYNPVIHIFTIKK 0
0 FRQCLVQLLPPINFHPPINPPINNFWRLLKNLNGRLAMKKVKPVLGKGRSHNRPEKKVPPINFSSSDFFTRTTSDTGTHGITESTKGKRTNVRLIQVHPL* 0
>ENCEPH_danRer Danio rerio (zebrafish) NM_001111164 mrna 61%=homSap full
0 MNSFNETPTEAHLENYNYIFADETYKLLTFTIGSIGVLGFCNNIIVIILYSRYKRLRTPTNLLIVNISVSDLLVSLTGVNFTFVSCVKRRWVFNSATCVWDGFSNSLF 1
2 GIVSIMTLSGLAYERYIRVVHAKVVDFPWAWRAITHIWLYSLAWTGAPLLGWNRYTLEVHQLGCSLDWASKDPNDASFILFFLLGCFFVPVGVMVYCYGNILYTVKM 0
0 LRSIQDLQTVQTIKILRYEKKVAVMFLMMISCFLVCWTPYAVVSMLEAFGKKSVVSPTVAIIPSLFAKSSTAYNPVIYAFMSRK 0
0 FRRCMLQMLCSRLTSLQHTIKDRPLSRIEHPIRPIVMSQSRTDRPKKRVTFSSSSIVFIIASHDTHPLDITSKCNDEPDINVIQVRPL* 0
>ENCEPH_takRub Takifugu rubripes (pufferfish) homSap=61% full
0 MNPANGSRSERSAEQLLFSGDTYRVLAFTIGTIGAFGFCNNFVVLALYCRFKRLRTPTNLLLVNISLSDLLVSLFGINFTFAACVQGRWTWTQATCVWDGFSNSLF 1
2 GIVSIMTLAALAYERYIRVVHAQVVDFPWAWRAIGHIWLYALAWTGAPLLGWNRYTLEIHRLGCSLDWASKDPNDASFILLFLLACFFVPVGIMIYCYGNILYAVQM 0
0 IRSIQDLQTVQIIKILRYEKKVSVMFFLMISCFLLCWTPYAVVSMMVAFGRRSMVSPTMAIIPSFFAKSSTAYNPLIYVFMSRK 0
0 FRHCLLQLLCSRLSWLQRSLKERPLAPVQRPIRPIVMSRPCGKGNRPKKKVTFSSSSIVFIITSDDFGQLDVTSKSGDSADVNAIQVRPL* 0
>ENCEPH_gasAcu Gasterosteus aculeatus (stickleback) 58%=homSap full
0 MNPDNGTREERSTDHSIFAVGTYKLLAFAIGTIGVFGFCNNVVVIVLYCKFKRLRTPTNLLVVNISLSDLLVSVIGINFTFVSCIRGGWTWSRATCIWDGFSNSLF 1
2 GIVSIMTLASLAYERYIRVVHAQVVDFPWAWRAIGHIWLYSLVWTGAPLLGWNRYTLEIHRLGCSLDWASKDPNDASFILLFLLACFFVPVGIMIYCYGNILYAVQM 0
0 LRSIQDLQTVQIIKILRYEKKVAVMFLLMISCFLLCWTPYAVVSMMEAFGRKNMVSPTVAIIPSFFAKSSTAYNPLICVFMSRK 0
0 FRRCLMQLLCSRVTCLQCNLKERPLAPVQRPIRPIVVSAACGGGRVRPKKRVTFSSSSIVFIITRNDIRHTDVTSNTRESSEANVFQVRPL* 0
>ENCEPH_oryLat Oryzias latipes 58%=homSap full
0 MNPANESRAGRHEERSVFAVGTYKLLTVIIGTIGVFGFCNNLLVILLYCKFKRLRTPTSLLLVNISLSDLLVSVVGINFTLASCVKGRWMWSQATCVWDGFSNSLF 1
2 GIVSIMTLAALAYERYIRVVHAQVVDFPWAWRAIGHIWLYSLAWTGAPLLGWNRYTLEIHQLGCSLDWASKDPNDAAFILLFLLGCFFVPVGIMIYCYGNILYAVRM 0
0 LRSIEDLQTVQIIKILRYEKKVAAMFLLMISCFLVCWTPYAVVSMMEAFGKKSMVSPTVAIVPSFFAKSSTAYNPLIYVFMNRK 0
0 FRRCFLQLLGSRLCSKISWLQCTLKEHPLTPVERPIRPIVASTSCGSRHRPKKRVTFNSSSIVFMITGDEFQQLDVTSKSRNSSEANVFHVRPL* 0
>ENCEPH_calMil Callorhinchus milii (elephantfish) wgs frag
0 MNPTNSTEPQEEHLFSPNTYKLLAVIIGTIGIVGFCNNILVLLLYYKFKRLRTPTNLLLVNISVSDLLVSVFGLSFTFVSCTQGRWGWDSAACVWDGSHSLF 1
2 GTVSIVTLTVLAYERYIRVVNAKATNFPWAWRAITYTWFYSLAWSGAPLV
0 0
0 YRRCLSQLFCSHLMSLQWSIKDPSSKARNDMPVKPIVLSQKGDRPKKRVTFSSSSIVFIITSDDTQELGSIAGSNATQISIVQVQPL* 0
>ENCEPH_squAca Squalus acanthias (dogfish) Gt 0...2...0.0 indel x x x x 202 aa 000 nm no_ref genome fragment
0 MNAANSTDTREESLFSPGTYQVLAVIIGTIGVVGFCNNLLMLVLYCKFKRLRTPTNLFLVNISISDLLLSVFGVIFTFVSCVKGRWVWDSAACVWDGFSNCLF 1
2 GISSIMSLTVLAYERYIRVVNATAIDFSWAWRAITYIWLYSLAWTGAPLIGWNSYTLELHRLGCSVNWDSRNPSDTSFVLFLFLGCLLCPIGVIAYCYG
>ENCEPH_petMar Petromyzon marinus (lamprey) no_ref genome fragment
0 MQSPKQDSLHYAGDTGAKAAPDSAQGNASALGSNFLLHGGDLGEGSTAFSAATFRLLAGVVGTIGVAGFLNNLLLVALFVGFKRLQTPTNLLLVNISLSDLLVSVFGNTLTLVSCVRRRWVWGNGGCVWDGFSNSLF 1
2 GIVSISTLTALSYERYARLIKAQVLDFSWAWRAVTYTWLYSAAWTGAPLLGWSRYVLEKHGLGCSIDWASSNPPDAAFVLFFFLGCLAAPLLVMGFCFGRIALAITQ 0
0 CWSPYAVASLFVASGFEHLVSPPVSIVPSLLAKSNAVCNPLLFLLMSGN 0
>ENCEPH4_braFlo Branchiostoma floridae (amphioxus) 12435605 AB050608 encephalopsin Amphiop4 new exon 12 and 34 + perfect fit
0 MALYNNTSSPSQDLLWDAPYSQGHIWDNSSASNSSEDVMDQGKVELQDFSDAGYTAIATCLALI 1
2 GFVGFTNNFVVILLIGCHRQLRTPFNLLLLNMSVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANSLF 1
2 GIVSLVTLSALAFERYCVVVRSSDMLTYKSSLVVITFIWLYSLLWTSLPLLGWSSYQFEGHN 0
0 VGCSVNWVQHNPDNVSYIVTLMVTCFFVPMVVVCWSYAWIWRTVRM 0
0 SSEAKPECGNSQNAGRLVTTMVVVMIICFLVCWTPYAVMALIVTFGADHLVTPTASVIPSLVAKSSTAYNPIIYVLMNNQ 0
0 FREFLLARLQRVCCRQQAVPRVTPMDDNVHVRLGGEGPSQSQQFLPAGENVENVDMLEYVQENCKPKADSLSTISE* 0
>ENCEPH4_braBel Branchiostoma belcheri (amphioxus) no_ref genome encephalopsin Amphiop4 introns from braFlo
0 MPLYNTSSGPTQGLPWDTPYSQDPIWNDSSPSNSSEDAVVDQGRGELQDFSDAGYTAIATGLALI 1
2 GLVGSMNNFVVILLIGCHRQLRTPFNLLLLNVSVADLLVSVCGNTLSFASAVQHRWLWGRPGCVWYGFANSLF 1
2 GIVSLVTLSALAFERYCVVVRSSEMLTYKSSLGMIAFIWMYSLLWTSLPLLGWSSYQFEGHS 0
0 VGCSVNWVKHNVNNVSYIITLMVTCFFVPMVVVCWSYACIWRTVRM 0
0 SAEMKSEFGNPQNTGRLVTTMVVVMIVCFLVCWTPYTVMALIVTFGADHLVTPTASVIPSLVAKSSTAYNPIIYVLMNNQ 0
0 FREFLLARLRTFCCRQPRMLRVTPMDDNAHARLVGEGPSHAQQVIPSEENGENVEMRKVQGNQLKADSLSTISE* 0
>ENCEPH5_braFlo Branchiostoma floridae (amphioxus) no_ref genome encephalopsin extra 0 intron
0 MLGMHNVMNATDYDNNNATFAAWNFQRNGTTEEEVEFSGFDTVAVVIAAIGIAGFLSNGAVVLLFLKFRQLRTPFNMLLLNMSVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANHLF 1
2 GLVSLISLAVISYERYRMVVKPKGPGSSYLTYNKVGLAIIFIYLYCLLWTTLPIVGWSSYQLE 0
0 GPKISCSVAWEEHSLSNTSYIVAIFIMCLLLPLLIIIYSYCRLWYKVKK 0
0 GSQNLPPAIRKSSQKEQKIARMVVVMITCFLVCWLPYGAMALVVSFGGESLISPTAAVVPSLLAKSSTCYNPLVYFAMNNQ 0
0 FRRYFQDLLCCGRRLFDASASVNTCNTSAMPRHSPVFQKPDSDQYNGIQKSREPQMRTTGQNAPYRQWIEMQTIAVVVKADEVNNKFGEVKT* 0
>ENCEPH5_braBel Branchiostoma belcheri (amphioxus) AB050609 encephalopsin Amphiop5 extra Nfrag in mrna
0 MLGIYNVVNATEYGNNTTFAAWDFKRNGTGGEEEVEFFGYDAVAGVIAIIGVVGFVSNGAVVVLFLKFPQLRTPFNLLLLNMAVADLLVSVCGNTLSFASAVRHRWLWGRPGCVWYGFANHLF 1
2 GLVSLISLAVISFLRYRMVVKPKGPGSSYLTYTKVGLAILFIYLYCLLWTTLPIAGWSSYQLE 0
0 GPKIGCSVAWEEHSWSNTSYIVVLFITCLFAPLLIIVYSYYRLWHKVKQ 0
0 GSRNLPAAMRKSSQKEQKIAMMVIVMITCFMVCWLPYGAMALVVTFGGERLISHTAAVVPSLLAKSSTCYNPVVYFAMNSQ 0
0 FRRYFQDLLCCGRRLFDVSQSVVTGNTAMPRNNSQGFRKDDSDQKQDNGLPKQSEGPMCDHSSNESQMEGSRHNTAASQQWIEMQTIAVVVKAVEVDTSAANEP* 0
>ENCEPH6_braFlo browser duplicated frag
0 VAAILALIGVLGIVNNSTTLYLVGRYKQLRTPFNILMVNLSVSDLLMCVLGTPFSFVSSLHGRWMFGHSGCEWYGFICNF 1
2 GIVSLITLTVISYERYLLMKRLPNERILSYRAVALAVVFIWCYSLLWTAPPLVGWSSYGPEGYGISCSVNWESRTANDTSYIVAYFVGCLVFPVAIIVISYTRLLILYMRQ 0
0 APSAPMQMLVRREKRVTKMVVVMIMGFTICWTPYTIVALIVTCGGEGIITPAAATVPALFAKSSVVYNAAIYVAMNNQ 0
0 FRKCFLRSLNCRSQPRDPSSQQYTLKTNQVGMSTSGSQAARTADRIKTVHVATANPQDHRSSSGQAVEDNGGFRKSLTHSLPLNSISTLLEAEK* 0
>ENCEPH_strPur Stronglyocentrotus purpuratus GLEAN3_03451 modified terminal exon by extending penultimate to stop codon
0 MSLATKKHFIRNAVEEGGHLLEKWDKGG 2
1 YAFIMTFLGLNSLMSHAVIAVDRYLVITKPHF 1
2 GIVVTYPKAFLMISIPWVFSFAWAVFPLAGWGEFTYEGTGAWCSVRWDSDQPQIMSYVLAMMFLTFISSIVIMMYCYICIFLTTRRMPRWATSNSIKTHERNRRRR 2
1 EQKLLKTLIAIAIAFLVAWSPYAITSMIVVFGGSELLSLTATTLPSLFAKSSVMINPIIYAVTSRVFRKSLKK 0
0 MLTSFFPGCMTYIMTDKSPPSSSRPIQLGLCKYHFLY* 0
Reference set of 14 TMT encephalopsins from elephantshark to marsupial
>ENCTMT_monDom Monodelphis domestica TMT opsin XM_001372110 MSR full 0 MSNNLTTNLSLEALLSASEDKQRNGLSRTGHTIVAVFLGIILIFGSISNFIVLVLFCKFKVLRNPVNMLLLNISISDMLVCLSGTTLSFASSIQGRWIGGKHGCRWYGFANSCF 1 2 GIVSLISLAILSYERYRTLTLCPGQGADYQKALLAVAGSWLYSLVWTVPPLIGWSSYGTEGAGTSCSVHWTSKSVESVSYIMCLFIFCLVIPILVMVYFYGRLLYAVKQ 0 0 VGKIRKTAARKREYHVLFMVVTAVICYLICWVPYGMIALLATFGPPGVVSPVANVVPSILAKSSTVCNPIIYVLMNKQ 0 0 IKGEKTLDRAAGLKVKKTRELGDHMLRVSRSVQITD* 0 >ENCTMT_macEug Macropus eugenii frag 0 MSINLTANLSFGTLLPDSEEKQRSGLSRTGHTVTAVFLGLILILGVINNFIVLVLFCKFKVLRNPVNMLLLNISISDMLVCLTGTTLSFASSIRGRWIAGYHGCRWYGFANSCF 1 2 GIVSLISLAVLSYERYRTLTLCPRQGTDYHKALLAVAGSWLYSLIWTVPPLIGWSSYGTEGAGTSCSVHWTSKSVESVSYIMCLFIFCLVIPILFMVYFYGRLLYTVKQ 0 0 VGKIRKSAARKREYHVLFMVVTAVICYLICWVPYGMIALLATFGPPGVVSPVANVVPSILAKSSTVCNPIIYILMNKQ 0 0 * 0 >ENCTMT_ornAna Ornithorhynchus anatinus frag 0 GLSRTGHTMVAVFLGIILVFGFMNNLIVLILFCKFKALRNPVNMIMLNISASDMLVCVSGTTLSFASNISGRWIGGDPGCRWYGFVNSCL 1 2 GIVSLISLAVLSYERYRTLTLHPKQSTDYQKAVLAVGASWIYSLIWTIPPLLGWSSYGTEGAGTSCSVHWSSKSPVSVSYIVCLFIFCLVIPVLVMIYCYGRLLYAVKQ 0 0 IGKARKTAARKREYHVLFMVITTVICYLVCWMPYGVTALLATFGQPGTVSPEASVIPSILAKSSTVCNPIIYILMNKQ 0 0 * 0 >ENCTMT_galGal Gallus gallus XM_001234388 mRNA multiple tissue opsin full 0 MNHTWTYNLSFGAPTDPVEPRAGLSRNGHTVVAVFLGFILFFGFLNNLIVLILFCKFKTLRNPVNMLLLNISISDMLVCISGTTLSFASNIHGKWIGGEHGCRWYGFVNSCF 1 2 GIVSLISLAVLSYERYSTLTLCNKRSDDYRKALLAVGGSWVYSLLWTVPPLLGWSSYGIEGAGTSCSVRWSSETAESTSYIICLFIFCLVIPVMVMMYCYGRLLYAVKQ 0 0 VGKIHKNTARKREYHVLFMVITTVICYLVCWIPYGVIALLATFGKPGVVTPVASIIPSILAKSSTVCNPIIYILMNKQ 0 0 FLTLKLNEGRSGSFENVFCSKKFEKYALLMLSY* 0 >ENCTMT_taeGut Taeniopygia guttata last exon questionable full 0 MNHTWMYNLSFGAPAHPVEPRAGLSRSGHTVVAVFLGLILFFGFLNNLIVLILFCKFKTLRNPVNMLLLNISVSDMLVCISGTTLSFASNIRGKWIGGDHACRWYGFVNSCF 1 2 GVVSLISLAVLSYERYNTLTLCHKRSDDFRKALLAVAGSWIYSLVWTVPPLLGWSSYGVEGAGTSCSVRWSSESAESTSYIICLFVFCLVVPVMVMMYCYGRLLYAVKQ 0 0 VGKIHKNAARKREYHVLFMVIPTVICYLVCWIPYGVIALLATFGKPGAVTPITSIIPSILAKSSTVCNPIIYILMNKQ 0 0 ILTLKFDNGRSGNFESVFCGRKSAKYA* 0 >ENCTMT_anoCar full 0 MSELSSNLTFNMSTSIEEPGSGLSRMGHNIVAVFLGLILVFGFLNNLVVLILFCKFKTLRNPVNMLLLNISASDMLVCISGTTLSFVSNIYGRWIGGEHGCRWYGFVNSCF 1 2 GIVSLISLAILSYERYSTLTQTNKRGSDYQKALLGVGGSWLYSLIWTVPPLIGWSSYGLEGAGTSCSVRWTSETLESVTYIICLFIFCLAIPVLVMIYCYARLFYAVKQ 0 0 VGKLRKTSARKREFHVLFMIITTIICYLICWMPYGVIALLATFGRPGLVSPVASVIPSILAKSSTVFNPIIYILMNKQ 0 0 FQFYKCFLMLLHCQPSSVADGETICQSKVMAIHQNQKAQGGVILKSQVVPQMDEKAICLLSPESSLDPVLESTPQLSKENSFL* 0 >ENCTMT_xenTro full 0 MSTIKNWTTNISVENSMSYIENDLSLPTEAVLSRTGHTVVAIFLGFILIFGFLNNFVVLILFCKFKTLRTPVNMMLLNISASDMLVCVSGTTLSFTSSIKGKWIGGEYGCQWYGFVNSCF 1 2 GIVSLISLAILSYERYSTLTLYNKGGPNFKKALLAVASSWLYSLVWTVPPLLGWSSYGREGAGTSCSVRWTSESVESVSYIICLFIFCLALPVFVMLYCYGRLLYAVKQ 0 0 VGKIRKIAARKREYHVLFMVITTVICYLLCWLPYGVVALLATFGRPGVISPVASVVPSILAKSSTVFNPIIYILMNKQ 0 0 FYKCFLILFHCHPTSSADGKSICQSNYTVIQLNQKLNNIVAIPGQTQIPESVDKMPCIHRQNNESPSDQMPQSTTEHLISGT* 0 >ENCTMT_danRer Danio rerio NM_001118899 full 0 MIVSNLSVLSCRRNSALCLGAVEGHLEASSSYRTLSPTGHILVAVSLGFIGTFGFLNNLLVLVLFGRYKVLRSPINFLLVNICLSDLLVCVLGTPFSFAASTQGRWLIGDTGCVWYGFANSLL 1 2 GIVSLISLAVLSYERYCTMMGSTEADATNYKKVIGGVLMSWIYSLIWTLPPLFGWSRYGPEGPGTTCSVDWTTKTANNISYIICLFIFCLIVPFLVIIFCYGKLLHAIKQV 0 0 SSVNTSVSRKREHRVLLMVITMVVFYLLCWLPYGIMALLATFGAPGLVTAEASIVPSILAKSSTVINPVIYIFMNKQ 0 0 FYRCFRALLNCDKPQRGSSLKSSSKTKPFRPGRRTDNFTFMVASVGPNQTNPVEDGPPSADNTKPAVLSLVAHYNG* 0 >ENCTMT_takRub Takifugu rubripes (teleost) -CALD1 +TNK2 -RAB18 +ABI1 12670711 AF402774 encephalopsin TMT multiple tissue full 0 MIVSNVSLSGCAGVNGAVCAAEGHQAGGSDRSTLTPTGNLVVSVFLGFIGTFGLVNNLLVLVLFCRYKMLRSPINLLLMNISISDLLVCVLGTPFSFAASTQGRWLIGEAGCVWYGFANSLF 1 2 GVVSLISLAVLSFERYSTMMTPTEADPSNYCKVCLGITLSWVYSLVWTVPPLFGWSSYGPEGPGTTCSVNWTAKTTNSISYIICLFVFCLIVPFLVIVFCYGKLLCAIRQ 0 0 VSGINASTSRKREQRVLCMVVIMVICYLLCWLPYGVVALLATFGPPDLVTPEASIIPSVLAKSSTVINPIIYVFMNKQ 0 0 FYRCFLALLCCQDPRSGSSMKSSSKVATKAKGVTPTGQRRTDFLYMVASLGRPAATIPQLGPSFDATNDFTKPPSSDTIKPVVVSLAAHCDG* >ENCTMT_tetNig Tetraodon nigroviridis full 0 MIASNASVSGCAGVHGAACAADAPPAGGSHRSSSSLTPTGNLVVSVFLGLIGTSGLVSNLLVLVLFCRFKVLRSPINLLLVNISVSDLLVCVLGTPFSFAASTQGRWLIGAAGCVWYGFVNSLFG 1 2 GIVSLISLAVLSFERYSTMMTPTEADSSNYCKVCLGIGLSWVYSLLWTVPPLLGWSSYGPEGPGTTCSVNWTAKTANSVSYIICLFVFCLILPFLVIVFCYGKLLCAIRQ 0 0 VSGVNASMSRRREQRVLFMVVVMVICYLLCWLPYGVVALLATFGPPGLVTPAASIIPSILAKSSTVINPVIYVFMNKQ 0 0 FSRCFLSLLCCEDPRSSTSLRSSSRVTTKAVRGGTLTGQRRTNHLLYMVAALGRPVATAMPQLGPSFDATYDITKAPSSDNHQPVVVSLEAHG* 0 >ENCTMT_gasAcu Gasterosteus aculeatus (stickleback) genome +TNK2 +ENC full 0 MIVSNLSLSGCAGVSSALCAAAGEGHLSGGSHRNTLTPTGHLVVAVCLGFIGTLGLMNNLLVLVLFCRYKMLRSPINLLLINISISDLLVCVLGTPFSFAASTQGRWLIGEGGCVWYGFANSLFG 1 2 GIVSLISLAVLSYERYSTMVAPTEADSSNYHKISLGITLSWVYSLIWTAPPLFGWSHYGPEGPGTTCSVDWTARTANSISYIICLFVFCLIVPFLVIVFCYGKLLCAIRQV 0 0 VSGINASLSRKREQRVLFMVVIMVVCYLLCWLPYGIMALMATFGPPGLITPVASIIPSVLAKTSTVINPVIYVFMNKQ 0 0 FYRCFKALLRCEAPRPSSSLKSSSKVPTKAMRGAAVTGPRHTNNFLFVVASLGRPVATIPQLGPSVEPTIDVTGGPSSDNNKPVIVSLVAQCDG* 0 >ENCTMT_oryLat Oryzias latipes (medaka) genome SLC12A3 two frags 0 MLVSNVSLGGCAEFNSALCAGAGEEHLGGGSYRTTLTPTGHLIVAVCLGFIGTFGLVNNLLVLVLFCRYKILRSPINLLLINISISDLLVCVLGTPFSFAASTQGRWLIGEGGCVWYGFANSLCG 1 2 GIVSLISLAVLSYERYSTMMTPAEADSSNYRKISLGIILSWGYSLLWTLPPLFGWSHYGPEGPGTTCSVDWTAKTANNISYIICLFVFCLIVPFMVIVFCYGKLLYAIKQV 0 0 VSGINVSVSRKREQRVLFMVVIMVICYLLCWLPYGIMALLATFGPPDLVTPEASIIPSVLAKTSTAINPVIYVFMNKQ 0 0 * 0 >ENCTMT_pimPro Pimephales promelas frag GHLVVAVCLGFIGTGFLNNTLVLILFCRYKVLRSPMNYLLVSIAVSDLLVCVLGTPFSFAASTQGRWLIGRAGCVWYGFINSCL 1 2 GVVSLISLAVLSYERYCTMMGATQADSTNYKKVAMGIAFSWIYSMVWTLPPLFGWSCYGPEGPGTTCSVNWAARTANNVSYIICLFFFCLILPFIVIVYSYGRLLQAITQ 0 0 VSRINTVVSRKREQRVLFMVITMVVCYLLCWLPYGIMALLAAFGRPGLVTPAASIVPSVLAKTSTVINPIIYIFMNKQ 0 0 FCRCFHALIMCTTPQRGSSFKNSSKVTKTLRTVRRANGQNVTFAVASAGHPTICAPH >ENCTMT_calMil Callorhinchus milii (elephantfish) wgs frag 0 MLNSSPNSSPSLPLSQVGWTGLSRTGLTVVAVCLGIIMVLGFLNNLLVLVLFCKYKVLRSPMNMLLLNISVSDMLVCICGTPFSFAASVQGRWLVGEQGCKWYGFANSLF 1 2 GIVSLMSLTILSYDRYITITGTTEADITNYNKTIVGIALSWIYSLMWTLPPLFGWSNYGPEGPGTTCSVNWQSKEVSSKSYIICLFIFCLLMPFLVIVYCYGKLVLAVRK 0 0 AQTREHRILLMVISMVTFYLLCWLPYGTVALIGTFGNADLITPTCSVIPSILAKSSTVINPVIYVIMNKQ 0
