RetrogeneDB ID: | retro_csav_35 | ||
Retrocopy location | Organism: | Pacific transparent sea squirt (Ciona savignyi) | |
| Coordinates: | reftig_83:352166..353313(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCSAVG00000001602 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCSAVG00000003934 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_csav_35
AAACCCAACATTGTATTCATCCTGGCCGACGACTTTGGCTTCAACGACATCGGGTACCATGCAGTGGAGCACCATTCTGA
TATGAAGACTCCATTTCTGGATTCCCTGGCAATGTCCGGAGTAAGGTTGGAGAATTATTACATTCAGCCGATTTGCTCTC
CATCTAGAAGTGTCTTAATGAGCGGAAGGTATCAGATCCACACTGGTTTGCAACATTACGTTATATCTCCCCAACAGAGG
AACGGGCTGCCTTTGGAAAACATTATACTGCCGGAGCAGTTGCATAAATGTGGCTACGATACTCACATGGTTGGGAAATG
GCATCTGGGATTCTACAAGGAAGACTTCACCCCTTGGAAACGTGGGTTCAATTCCTACTTTGGATATTTGACAGGTGGTG
GAAGATTATTACACAAAATGGAGATGTGATGGAAAATTGTGTGGTTACGATATGTCTTCAGAAAAGGGTCCAACTAATGA
GACTTATGGGAAGTATTCTGCTAACTTATTTGTTGACAAAGCGAAAGAGGCTATAGACAAAAGAAATACGAACCAACCTT
TATTTTTATACGTCGCTTTTCAGTCAGTTCATTCTCCAATGGAAGTTCCTGCATCTTATGAAAAACCGTTTGCTTATATT
AAAGATAACAACCGAAGAGCGTATGGTGGTATGGTGGCAGCCATGGATGAAGCTGTTAAAAACATCACACTTCACTTGCA
AGCTGCTGGAATATGGAACAACACACTTTTAATATTTTCAGCAGATAACGGTGGCCAGACACTGTCCGGTGGAAATAATT
ATCCTCTTAGAGGAAGGAAGCTTACACTTTGGGAAGGTGGGATCAAAGGTGTTGGATTCGTGCATGGGGAAATGCTTAAT
GTCCCAAACCCAAATGTTATAGTTAATAATGAAATGATGCATATTTCCGATTGGTTTCCCACAATAATGGCTGCAAGTCA
ATGCCCCTATGTAGAAGGCACACAAAAGCTTGACGGTGTTAATCAATGGGATACCATTCTTGGAAACGCTGTCTCACCCA
GAAAAGAAATTCTTCTAAACATAGACCCACTGTTCACGCCAATGTATTATAACCAAACTCCACGGAAATCTGTCAAAATG
GACTTTGATACGTCAGTTCACGCAGGA
ORF - retro_csav_35 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.44 % |
| Parental protein coverage: | 75.05 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RPHIVFVLADDFGYNDIGYHAREHCSQMYTPFLDSLAAKGVKLENYYVQPICSPTRGQLLTGRYQIHTGL |
| .P.IVF.LADDFG.NDIGYHA.EH.S.M.TPFLDSLA..GV.LENYY.QPICSP.R..L..GRYQIHTGL | |
| Retrocopy | KPNIVFILADDFGFNDIGYHAVEHHSDMKTPFLDSLAMSGVRLENYYIQPICSPSRSVLMSGRYQIHTGL |
| Parental | AHGIIKAAQPYGLPLDNILLSQQLRKCGYKTNMVGKWHLGFFREEYLPWNRGFQNFFGFLNGG-VNHYTR |
| .H..I...Q..GLPL.NI.L..QL.KCGY.T.MVGKWHLGF..E...PW.RGF...FG.L.GG....YT. | |
| Retrocopy | QHYVISPQQRNGLPLENIILPEQLHKCGYDTHMVGKWHLGFYKEDFTPWKRGFNSYFGYLTGG>EDYYTK |
| Parental | YHCEPKKTRRFCGYDMIDSRHGPINSTYGEYSTNLFVRKAKEMIDRHNKAKPMFLYLSLQAVHGPLQVPN |
| ..C..K.....CGYDM..S..GP.N.TYG.YS.NLFV.KAKE.ID..N...P.FLY...Q.VH.P..VP. | |
| Retrocopy | WRCDGK----LCGYDM-SSEKGPTNETYGKYSANLFVDKAKEAIDKRNTNQPLFLYVAFQSVHSPMEVPA |
| Parental | QYLKRFKHIKDRNRKIYAGMVYAMDRGIRQLVKHLKRVRMWKDTIFIFSTDNGGQTTRGGNNWPLRGKKG |
| .Y.K.F..IKD.NR..Y.GMV.AMD........HL.....W..T..IFS.DNGGQT..GGNN.PLRG.K. | |
| Retrocopy | SYEKPFAYIKDNNRRAYGGMVAAMDEAVKNITLHLQAAGIWNNTLLIFSADNGGQTLSGGNNYPLRGRKL |
| Parental | TLWEGGIRAVGFVHGKPLQLNGP--MVNHELLHVSDWYPTIMSATQCPLMVGTQNVDGYDQWDTIRKNKI |
| TLWEGGI..VGFVHG..L....P...VN.E..H.SDW.PTIM.A.QCP...GTQ..DG..QWDTI..N.. | |
| Retrocopy | TLWEGGIKGVGFVHGEMLNVPNPNVIVNNEMMHISDWFPTIMAASQCPYVEGTQKLDGVNQWDTILGNAV |
| Parental | SKRTEILHNIDPLHKKLTIGSEYREGFDVSVRAAIRSG |
| S.R.EIL.NIDPL..........R.............G | |
| Retrocopy | SPRKEILLNIDPLFTPMYYNQTPRKSVKMDFDTSVHAG |
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.
No EST(s) were mapped for retro_csav_35 retrocopy.
Ciona savignyi was not studied using FANTOM5 data.
retro_csav_35 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ciona savignyi | ENSCSAVG00000003934 | 1 retrocopy |
retro_csav_35 ,
|