RetrogeneDB ID: | retro_sscr_530 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 16:75345230..75345807(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ADAL | ||
| Ensembl ID: | ENSSSCG00000004710 | ||
| Aliases: | None | ||
| Description: | adenosine deaminase-like [Source:HGNC Symbol;Acc:31853] |
Retrocopy-Parental alignment summary:
>retro_sscr_530
CAGGAGAACAAGAGCCAGAGGTCAATCTTTTACTTGGAATTATCTAAAGTGGAACTTCATACCCAGGTGAATGGATCGAT
CAGTTCTAATACTGTGAAAAAATGAAAAGCCAAAAAGCCAGGTCTTAAAATCCATGATCAGATGACTGATTAACAAAGGG
GAAAAAAAAGGACTTTAGAAGAATGTTTCCAGATATTTCAAATTATTTATAAGCTTTGCATTAGCCCTGAAGATATTTTA
ATGGACACAAAAGATGTCATTAAAGAATTCATAGATAATGATGTCAATACCTAAAGTAAGGAACACACACAGAAGAGAAA
ATGCTACAAGAATGACTAAAAAGACTTACAACGGAATCTGTGCTTGAGAAGATAAAACCATCTGAAAAAGGAACATAGAC
ATTGATGTTAGATATCGGATAGCAGTCGACAGAAGAGGTGACACTTCTGTTGCCAAGGAGACTATTAGACTTGCTAAAGA
GTTCTTCCTTTCTACTGAGGACGAAGTTCTTGGGCTCAACCTGGGTGGAGACCCTACTGTAGGAGAAGCAAAATTTCTTG
GAACATTTTTAGAAGCT
ORF - retro_sscr_530 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.13 % |
| Parental protein coverage: | 54.65 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | EEQQSWKTTFYSKLPKVELHAHLNGSISSNTIKKLITKKPGLKIHDQMTMIDKGKKRTLEECFQMFPIIH |
| .E..S....FY..L.KVELH...NGSISSNT.KK...KKPGLKIHDQMT........TLEECFQ.F.II. | |
| Retrocopy | QENKSQRSIFYLELSKVELHTQVNGSISSNTVKK*KAKKPGLKIHDQMTD*QRXXXXTLEECFQIFQIIY |
| Parental | QLTTSPEDILMVTKDVIKEFADDGV-KYL-ELRSTPRGENATGMTKKTY-VESVLEGIKQSK-QENVDID |
| .L..SPEDILM.TKDVIKEF.D..V..YL...R.T.R.ENAT.MTKKTY..ESVLE.IK.S....N.DID | |
| Retrocopy | KLCISPEDILMDTKDVIKEFIDNDV<QYL<KVRNTHRRENATRMTKKTY>TESVLEKIKPSE<KRNIDID |
| Parental | VRYLISIDRRGGPSAAKENVKLAEEFFLSTEGIVLGLDLSGDPTAGQAKDFLEPLLEA |
| VRY.I..DRRG..S.AKE...LA.EFFLSTE..VLGL.L.GDPT.G.AK.FL...LEA | |
| Retrocopy | VRYRIAVDRRGDTSVAKETIRLAKEFFLSTEDEVLGLNLGGDPTVGEAK-FLGTFLEA |
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 | 2 .12 RPM |
| SRP014902_testis | 0 .00 RPM | 4 .95 RPM |
| SRP018288_heart | 0 .00 RPM | 11 .58 RPM |
| SRP018288_kidney | 0 .00 RPM | 7 .88 RPM |
| SRP018288_liver | 0 .00 RPM | 4 .48 RPM |
| SRP018288_lung | 0 .00 RPM | 15 .07 RPM |
| SRP018856_adipose | 0 .00 RPM | 3 .94 RPM |
| SRP035408_brain | 0 .00 RPM | 6 .57 RPM |
| SRP035408_liver | 0 .00 RPM | 2 .52 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_530 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_530 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_530 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Bos taurus | retro_btau_1539 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000014476 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000002337 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000024818 | 2 retrocopies | |
| Sus scrofa | ENSSSCG00000004710 | 1 retrocopy |
retro_sscr_530 ,
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