RetrogeneDB ID: | retro_sscr_200 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 1:274710778..274711418(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARIH1 | ||
| Ensembl ID: | ENSSSCG00000001922 | ||
| Aliases: | None | ||
| Description: | ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila) [Source:HGNC Symbol;Acc:689] |
Retrocopy-Parental alignment summary:
>retro_sscr_200
TATTTCACTGGCCTTGAATGTGGACATAAGTTTTGTATGTAGTGGTGGAGCAAATATTTAACTACCAAAATAATGGAAGA
AGGAATGGGACAGACTATTTCGTGTCCTGCTCATGGTTGTGATATTTTAGTGGATGACAATACAGTTAAGCAACTGATCA
CTGATTCAGAAGTTGAATTAAAGCATTTAGCATTTAATAACAAACAGCTTTGTAGAGTGCAATCAACTGTTAAAGTGGTG
TCCTGCCCCAGATTGCCATCATGTTGTGAAAGTTCAATATTCTGATGCTAAACATGATCGCTGAAAATGTGGGTGCCAGT
TTTGCTTTAAGTATGGAGAAAATTGGCATGACCCTGTTAAGTGTAAATGGTTGAATAAGTGGATTAAAAAGTGTGATGAT
GACAGTGAAACTTCTAATTGGATTGCAGCTAACACAAAGGAATGTCCCAAATGCCACGTCACAATTGAGAAAGATGGCAG
TTGTAATCACATGATCTGTAGTAACCAGAACTGTAAAGCAAAGTTTTGCTGGTTGTATCTTGGTCCTTGAGAACCACATC
GATCTGCTTGGTACAACTGTAACTGCTATAATGAGGATGATGCAAAGGCAGCAAGAGACAAAGGCAGCAAGGATGATGCA
ORF - retro_sscr_200 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.11 % |
| Parental protein coverage: | 62.1 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | YFTGLECGHKFCMQCWSEYLTTKIMEEGMGQTISCPAHGCDILVDDNTVMRLITDSKVKLKYQ-HLITNS |
| YFTGLECGHKFCM..WS.YLTTKIMEEGMGQTISCPAHGCDILVDDNTV..LITDS.V.LK...HLITNS | |
| Retrocopy | YFTGLECGHKFCM*WWSKYLTTKIMEEGMGQTISCPAHGCDILVDDNTVKQLITDSEVELKHL>HLITNS |
| Parental | FVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCGRQFCFNCGENWHDPVKCKWLKKWIKKCDDDSETSN |
| FVECN.LLKWCPAPDCHHVVKVQY.DAK..R.KCG.QFCF..GENWHDPVKCKWL.KWIKKCDDDSETSN | |
| Retrocopy | FVECNQLLKWCPAPDCHHVVKVQYSDAKHDR*KCGCQFCFKYGENWHDPVKCKWLNKWIKKCDDDSETSN |
| Parental | WIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNEDDAKAARDAQE |
| WIAANTKECPKCHVTIEKDG.CNHM.C.NQNCKA.FCW..LGP.EPH.SAWYNCN.YNEDDAKAARD... | |
| Retrocopy | WIAANTKECPKCHVTIEKDGSCNHMICSNQNCKAKFCWLYLGP*EPHRSAWYNCNCYNEDDAKAARDKGS |
| Parental | RSRA |
| ...A | |
| Retrocopy | KDDA |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 10 .35 RPM |
| SRP014902_testis | 0 .00 RPM | 19 .80 RPM |
| SRP018288_heart | 0 .00 RPM | 30 .52 RPM |
| SRP018288_kidney | 0 .00 RPM | 19 .01 RPM |
| SRP018288_liver | 0 .00 RPM | 15 .83 RPM |
| SRP018288_lung | 0 .00 RPM | 13 .95 RPM |
| SRP018856_adipose | 0 .00 RPM | 27 .31 RPM |
| SRP035408_brain | 0 .00 RPM | 14 .13 RPM |
| SRP035408_liver | 0 .00 RPM | 15 .24 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_200 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_200 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_200 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Otolemur garnettii | ENSOGAG00000012095 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000001922 | 2 retrocopies |
retro_sscr_142, retro_sscr_200 ,
|
| Drosophila melanogaster | FBgn0017418 | 1 retrocopy |