RetrogeneDB ID: | retro_csav_8 | ||
Retrocopy location | Organism: | Pacific transparent sea squirt (Ciona savignyi) | |
| Coordinates: | reftig_77:2569098..2570280(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCSAVG00000007085 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CSA.10126 | ||
| Ensembl ID: | ENSCSAVG00000008457 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_csav_8
ATATTTTTTATTTTCGCCATGAAAGTAGCTTTCGTTTTGCTGTCTGTCCTTCTGGCTTTCGCAGCTGGCAAGGTAATCAA
GCTAAAAAAGATGAGATCTATCCGTCAGGACATGCGTGACAAGAATACCGACCTTTCCGCCATTATCCCGCCCCGTTACG
TCCGTTTTATCGCAAGAAACGGTGCCCCGGAACCCCTCACAAACTACTTGGACGCACAGTACTACGGTGATATCACGATA
GGGACCCCGCCCCAAACCTTCACTGTGGTGTTTGATACCGGGTCCTCGAACCTTTGGGTCCCCTCTGTAAAATGCTCTAT
TACAGATGTTGCATGTTTGATCCATGATAAGTACAAGTCTGGCTCTTCGTCAACATACATCGCAAATGGCACGACCTTCG
CGATCCAGTATGGCAGTGGAAGCCTTTCGGGCTTTGTAAGTAGCGACACGGTCATAATTGGTGGAATCGTAAGCAAAAAT
CAGTTGTTCGCCGAAGCTACAAAGGAACCAGGTCTGACGTTTGTTGCAGCTAAATTCGACGGCATTTTAGGAATGGGTTA
CCCAGAGATCTCCGTCAATGGAATTCTTCCTGTTTTCAATCAAATGTTCAAACAAGGAGCTGTGGCTAAGAATCAGTTCT
CATTCTACTTGAACCGAGACCCAAATGCGGCTAGTGGCGGTGAGCTTTTCCTTGGAGGAGTGGACACGGCACGCTTCACT
GGGAATTTCTCCTACCATCCAGTGACAGTAAAGGGCTACTGGCAGATACAGATGGACAGTGTTAACGTGGGAAGTGCGCA
AAGTGCATGTGTAGGAGGGTGCAAGGCGATCGTCGATTCCGGTACATCTCTGCTTGCGGGACCTTCTACCGAAATCGCCA
AAATCAACAAACTAATCGGAGCTACATCATTCCTGCATGGAGAGTATGTCGTTCCGTGCAGTTCCATTCCAACCCTCCCG
GATATCACTTTCATGCTCAGCGGGAAGAAGTACGTCCTCACGGCCAAGGATTATGTGATGCAGGAGTCCGCTGGAGGCGA
GAGCATTTGCATCTCCGGCTTCATGGGTCTCGACATCCCCGCCCCAAGAGGCCCGTTGTGGATCTTGGGTGACATCTTTA
TGGGGAAGTTCTACACCACGTTCGATTTCGCCAACAACCGGGTCGGATTCGCCACTTTGAGA
ORF - retro_csav_8 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.24 % |
| Parental protein coverage: | 92.97 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KYTPSFGRSTSNEPLTNYLDAQYFGEIAIGTPEQKFTVIFDTGSSNLWIPSATCPSNNYACLLHNKYDST |
| .Y.....R....EPLTNYLDAQY.G.I.IGTP.Q.FTV.FDTGSSNLW.PS..C.....ACL.H.KY.S. | |
| Retrocopy | RYVRFIARNGAPEPLTNYLDAQYYGDITIGTPPQTFTVVFDTGSSNLWVPSVKCSITDVACLIHDKYKSG |
| Parental | ASSTYVADGDNFAIQYGTGSMVGFESVDTVKIAGIPSTNQVFAEATEEPGITFVAAKFDGILGMGYPTIS |
| .SSTY.A.G..FAIQYG.GS..GF.S.DTV.I.GI.S.NQ.FAEAT.EPG.TFVAAKFDGILGMGYP.IS | |
| Retrocopy | SSSTYIANGTTFAIQYGSGSLSGFVSSDTVIIGGIVSKNQLFAEATKEPGLTFVAAKFDGILGMGYPEIS |
| Parental | VNGIKPVFNQMYEQGAVDKNQFAFYLNRDPTGEEGGEICLGGVNEARYTGEFNYHSVTRKGYWQLKMDSV |
| VNGI.PVFNQM..QGAV.KNQF.FYLNRDP....GGE..LGGV..AR.TG.F.YH.VT.KGYWQ..MDSV | |
| Retrocopy | VNGILPVFNQMFKQGAVAKNQFSFYLNRDPNAASGGELFLGGVDTARFTGNFSYHPVTVKGYWQIQMDSV |
| Parental | AVADADATAACVGGCQIIVDSGTSLITGPTVDTDAINHAIGAIRFVQGEYLVICRNIPNMPDITFVLDGI |
| .V..A....ACVGGC..IVDSGTSL..GP......IN..IGA..F..GEY.V.C..IP..PDITF.L.G. | |
| Retrocopy | NVGSAQ--SACVGGCKAIVDSGTSLLAGPSTEIAKINKLIGATSFLHGEYVVPCSSIPTLPDITFMLSGK |
| Parental | EYVLTPDDYVLKITQDGVTQCLSAFMGMDIPEPTGPLWILGDAFMGKYYTSFDFDTDQVGFAKL |
| .YVLT..DYV......G...C.S.FMG.DIP.P.GPLWILGD.FMGK.YT.FDF....VGFA.L | |
| Retrocopy | KYVLTAKDYVMQESAGGESICISGFMGLDIPAPRGPLWILGDIFMGKFYTTFDFANNRVGFATL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ciona savignyi was not studied using RNA-Seq expression data.
Ciona savignyi was not studied using ChIP-Seq data.
10 EST(s) were mapped to retro_csav_8 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| BW521085 | 2569372 | 2569595 | 95.6 | 213 | 10 | 203 |
| BW539145 | 2569217 | 2569578 | 100 | 359 | 0 | 359 |
| BW576307 | 2569063 | 2569598 | 96.9 | 517 | 17 | 499 |
| BW577139 | 2569106 | 2569562 | 96.1 | 437 | 18 | 419 |
| BW578178 | 2569069 | 2569600 | 96.8 | 513 | 17 | 495 |
| BW578438 | 2569062 | 2569503 | 95.5 | 420 | 20 | 399 |
| BW579610 | 2569257 | 2569553 | 96.3 | 284 | 11 | 273 |
| BW580007 | 2569087 | 2569595 | 96.4 | 484 | 14 | 463 |
| BW589136 | 2569078 | 2569551 | 95.2 | 447 | 23 | 423 |
| BW590160 | 2569285 | 2569758 | 95.8 | 452 | 20 | 432 |
Ciona savignyi was not studied using FANTOM5 data.
retro_csav_8 was not experimentally validated.
Retrocopy orthology:
Ciona savignyi does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000010157 | 1 retrocopy | |
| Ciona intestinalis | ENSCING00000005258 | 1 retrocopy | |
| Ciona savignyi | ENSCSAVG00000008457 | 1 retrocopy |
retro_csav_8 ,
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