RetrogeneDB ID: | retro_itri_1267 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393419.1:192340..194069(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSTOG00000025133 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | WWC1 | ||
| Ensembl ID: | ENSSTOG00000015095 | ||
| Aliases: | None | ||
| Description: | WW and C2 domain containing 1 [Source:HGNC Symbol;Acc:29435] |
Retrocopy-Parental alignment summary:
>retro_itri_1267
AAGGTGGAGCTTCTGCTCCTGGAAGGCACCACGGGCTTCCGGCCCTCGGGTTGCATCACCACTATCCAGGAGGACGAGGT
GGCCAAGACCCAGAAGGCAGAGGGAGGTGGCCGCTTGCCGGCCCTGCGCTCCCTGTCTGGCACCCCAAAGTCCATGACTT
CCCTGTCCCCACTTTCTTCCCTCTCCTCCCCGTCCCCGCCCTGCTCCCCTCTCATTGCTGACCCCCTTCTGACTGGAGAT
ACCTTTCTGAGCCCAGTGGAGTTTGAAGACCCAGAGCTAAGTGCCACTCTGTGTGAGCTGAGCCTCAGGAGCGGCACCCC
GGAGAGATACCGGCTGGAAGAACCAGGAGCAGAGGGCAAGCCTTTGGGCCAAGCTGTGAATGCAGCCCAAGGGTGCGGCC
TCAAAGTGGCCTGTGTCTCAGCCACAGTGTCAGACGAGTCAGTGGCTGGGGACAGTGGTGTGTACCAGGCTTCTGTGCAG
AGACTGGGTGCTTCAGAAGCCACTGCTGCATTCGACAGTGATGAATCAGAAGCAGCAGGTGCCACTCGGATTCAGATTGC
CCTGAAGTATGATGAGAAGAATAAACAATTTGCAATATTAATCATCCAACTGAGTAACCTTTCTGCTCTTTCCCTGCTGC
AAGATCAGAGAGTGAACATCCTCGTGGCTATCCTCCCTTGCTCTGAAAGCACCACCTGCCTATTCAGGACCCGGTTCCTG
GACGCCTCGGACACCCTCTTGTTCAACGAGATGTTCTGGGTGTCGGTGTCCTACCAAGCCCTTCACCAGAAGACCTTAAG
AGTCGATGTCTGCACCACTGACAGGAGCCACGTGGAAGAGTGCCTGAGAGGTGCCCAGATCAGACTGGCAGAGGTGTGCT
GCTCTGGGGAGAGGTCGACTCGCTGGTACAACCTCTTGAGCTACAAATACTTGAAGAAGCAGAGCAGCGGTCCCAAGGCA
GCTGGAGTTGCGGGCCCCAGCCCAGGGCCTGAACGCATGGACGCTGTGTCTGCCCTGCTGGAGCAGATGGCAGTGGAGCT
AGAGAAGAGGCAGGAGAGCAGGAGCAGCCCACAGGTGCTAGAAGACAGCTGGAGGTACGAGGAGGAGACCTGCGAGAATG
AGGCTGTGGCTGAGGAGGAGGAGGACGAAGAGGGGGAGGAAGCGGAGGGAGAAGATTTTTTTTTTGCAGAGAAAGCCTCC
CCAGATGATCACCCGGCATTGAAGGCATTGAAGGTGGATAAAGAGACCAACACAGACACAGTGGCCCCATCCCCCACAGT
GGTGCGGCTCAAGGACCGGCGTGTGGGCACCCCATCGCCAGGGCCATTTCTTCAGGGGGAGCACCATCATCCGCTCCAAG
ACCTTCTCCCCAGGGCCCCAGAGCCAGTACGTGTGCCGGCTGAATCGGAGCAACAGTGATAGCTCCACTCTCTCCAAAAA
GCCACCTTTTGTGCGAAACTCCCTGGAGCAGCGCAGCGTCAGGATGAAGCGGCCTTCCTCTGTGAAATCCCTGTGCACCG
GGCGCCTGATCCGCACCTCGCTGGACCTTGAGCTGGACCTGCAGGCAACGCGAACCTGGCACAGCCAACTGACTCAGGAG
ACTTCGGTGCTGCGGGAGCTCAAGGAGCGGCTGGAGCAAGCCAAGAGCCACAGGGAGAAGGAGCTGCCACAGTGGCTGCG
CGAGGATGAGCGCATCCACCTGCTGCTGAGGATGCTAGAGAAGAGGATG
ORF - retro_itri_1267 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.39 % |
| Parental protein coverage: | 54.47 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KVELLLLEGTTGFRPSGCITTIHEDEVAKTQKAEGGGRLQALRSLSGTPKSMTSLSPRSSLSSPSPPCSP |
| KVELLLLEGTTGFRPSGCITTI.EDEVAKTQKAEGGGRL.ALRSLSGTPKSMTSLSP.SSLSSPSPPCSP | |
| Retrocopy | KVELLLLEGTTGFRPSGCITTIQEDEVAKTQKAEGGGRLPALRSLSGTPKSMTSLSPLSSLSSPSPPCSP |
| Parental | LIADPLLTGDAFLSPLEFEDPELSATLCELSLGSGTRERYRLEEPGAEGKPLGQAVNAAQGCGLKVACVS |
| LIADPLLTGD.FLSP.EFEDPELSATLCELSL.SGT.ERYRLEEPGAEGKPLGQAVNAAQGCGLKVACVS | |
| Retrocopy | LIADPLLTGDTFLSPVEFEDPELSATLCELSLRSGTPERYRLEEPGAEGKPLGQAVNAAQGCGLKVACVS |
| Parental | AAVSDESVAGDSGVYEASVQRLGASEATAAFDSDESEAAGATRIQIALKYDEKNKQFAILIIQLSNLSAL |
| A.VSDESVAGDSGVY.ASVQRLGASEATAAFDSDESEAAGATRIQIALKYDEKNKQFAILIIQLSNLSAL | |
| Retrocopy | ATVSDESVAGDSGVYQASVQRLGASEATAAFDSDESEAAGATRIQIALKYDEKNKQFAILIIQLSNLSAL |
| Parental | SLLQDQRVNIRVAILPCSESTTCLFRTRPLDASDTLLFNEMFWVSASYQALHQKTLRVDVCTTDRSHVEE |
| SLLQDQRVNI.VAILPCSESTTCLFRTR.LDASDTLLFNEMFWVS.SYQALHQKTLRVDVCTTDRSHVEE | |
| Retrocopy | SLLQDQRVNILVAILPCSESTTCLFRTRFLDASDTLLFNEMFWVSVSYQALHQKTLRVDVCTTDRSHVEE |
| Parental | CLGGAQISLAEVCRSGERSTRWYNLLSYKYLKKQSSGPKAAGAAGPSPGPEHTDAVSALLEQTAVELEKR |
| CL.GAQI.LAEVC.SGERSTRWYNLLSYKYLKKQSSGPKAAG.AGPSPGPE..DAVSALLEQ.AVELEKR | |
| Retrocopy | CLRGAQIRLAEVCCSGERSTRWYNLLSYKYLKKQSSGPKAAGVAGPSPGPERMDAVSALLEQMAVELEKR |
| Parental | QESRSSSQVLEDSWRYEEETCENEAVAEEEEDEEGEEVEGEEDFFAEKASPDDH-PALKVDKETNTDTVA |
| QESRSS.QVLEDSWRYEEETCENEAVA.............E....AEKASPDDH...........T.T.. | |
| Retrocopy | QESRSSPQVLEDSWRYEEETCENEAVAXXXXXXXXXXXXXEXXXXAEKASPDDHXXXXXXXXDKETNTDT |
| Parental | PSP--TVVRPKDRRVGIPSPGPFL-RGSTIIRSKTFSPGPQSQYVCRLNRSDSDSSTLSKKPPFVRNSLE |
| ..P..TVVR.KDRRVG.PSPGPFL.RGSTIIRSKTFSPGPQSQYVCRLNRS.SDSSTLSKKPPFVRNSLE | |
| Retrocopy | VAPSPTVVRLKDRRVGTPSPGPFL>RGSTIIRSKTFSPGPQSQYVCRLNRSNSDSSTLSKKPPFVRNSLE |
| Parental | RRSVRMKRPSSVKSLRTERLIRTSLDLELDLQATRTWHSQLTQEISVLRELKERLEQAKSHGEKELPQWL |
| .RSVRMKRPSSVKSL.T.RLIRTSLDLELDLQATRTWHSQLTQE.SVLRELKERLEQAKSH.EKELPQWL | |
| Retrocopy | QRSVRMKRPSSVKSLCTGRLIRTSLDLELDLQATRTWHSQLTQETSVLRELKERLEQAKSHREKELPQWL |
| Parental | REDERFRLLLRMLEKRV |
| REDER..LLLRMLEKR. | |
| Retrocopy | REDERIHLLLRMLEKRM |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_1267 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1267 was not experimentally validated.
Retrocopy orthology:
Ictidomys tridecemlineatus 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 | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000015095 | 1 retrocopy |
retro_itri_1267 ,
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