RetrogeneDB ID: | retro_sscr_317 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 13:39529148..39529468(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSSSCG00000011725 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sscr_317
AATACTTAGCATAAGCCTAGTTTTGAGGTCCACAACATCCTCAGAGAGTCTGGGTGTACTTGGGAAATCAGCCAGATGCC
AGTGATTTTGAAATCATTACATTTTGGTGGAGACCCATTTCAGAAACAGCCCTCATTCCAGAGATCTTGGTTATTTGAAT
CTTTCCTACTAGTAATCTCATGCCTGGTTTACCTGTAGCACCTGGCAGTGAGATCCATGTAGCAGTGGTGTCAAAGATGG
TCACTGAGGTTAAGAGGATTCTTGGCATTTCATGAATTATGGATGACTAAACATCAAAGCTCCTACGAACTATTGTGTGG
ORF - retro_sscr_317 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.19 % |
| Parental protein coverage: | 54.87 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | STLRQADFEAHNILRESGYAGKISQMPVILTPLHFDRDPLQKQPSCQRS-VVIRTFITSDFMTGIPATPG |
| .T.....FE.HNILRESG....ISQMPVIL..LHF..DP.QKQPS.QRS..VI..F.TS..M.G.P..PG | |
| Retrocopy | NT*HKPSFEVHNILRESGCTWEISQMPVILKSLHFGGDPFQKQPSFQRS<LVI*IFPTSNLMPGLPVAPG |
| Parental | NEIPVEVVLKMVTEIKKIPGISRIMYDLTSKPPGTTEW |
| .EI.V.VV.KMVTE.K.I.GIS.IM.D.TSK...T..W | |
| Retrocopy | SEIHVAVVSKMVTEVKRILGIS*IMDD*TSKLLRTIVW |
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 .62 RPM |
| SRP014902_testis | 0 .00 RPM | 25 .60 RPM |
| SRP018288_heart | 0 .00 RPM | 11 .53 RPM |
| SRP018288_kidney | 0 .00 RPM | 14 .97 RPM |
| SRP018288_liver | 0 .00 RPM | 11 .03 RPM |
| SRP018288_lung | 0 .00 RPM | 17 .21 RPM |
| SRP018856_adipose | 0 .00 RPM | 11 .17 RPM |
| SRP035408_brain | 0 .00 RPM | 16 .13 RPM |
| SRP035408_liver | 0 .00 RPM | 13 .36 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_317 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_317 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_317 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000011725 | 2 retrocopies |
retro_sscr_317 , retro_sscr_942,
|