RetrogeneDB ID: | retro_cjac_2410 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:13718588..13718946(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | VAMP7 | ||
| Ensembl ID: | ENSCJAG00000016289 | ||
| Aliases: | None | ||
| Description: | vesicle-associated membrane protein 7 [Source:HGNC Symbol;Acc:11486] |
Retrocopy-Parental alignment summary:
>retro_cjac_2410
ATGAATAGTGAGTTCTCGAGTGTCTTGGCTGCACAGCTGAAGCCTCACTCCGAGAATAAGGGCCTAGACAAAGTGATGGA
GACTCAAGCCCAAGTGGATGAAATGAAAGGAATTATGGTCAGAAACATAGATCTGGTAGCTCAGTGAGAAGAAAGATTGG
AATTATTGATTTACAAAACAGAAAAATCTCCTGGATTCTTCTGTCACCTTCAAAACTACTAGCAGAAATCTTGCCCGAGC
CACGTGTATGAAGAACCTCAAGCTCACTATCATCATTATCATCATATTAATTGTGTTCATCTATGTCATTGTCTCACCTC
TCTGTGGTGGATTTACATGGCCAAGCTACGCAAAGAAA
ORF - retro_cjac_2410 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.17 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MNSEFSSVLAAQLKHHSENKGLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTE-NLVDSSVT |
| MNSEFSSVLAAQLK.HSENKGLDKVMETQAQVDE.KGIMVRNIDLVAQ..ERLELLI.KTE.NL.DSSVT | |
| Retrocopy | MNSEFSSVLAAQLKPHSENKGLDKVMETQAQVDEMKGIMVRNIDLVAQ*EERLELLIYKTE>NLLDSSVT |
| Parental | FKTTSRNLARAMCMKNLKLTIIIIVISIVFIYIIVSPLCGGFTWPSCVKK |
| FKTTSRNLARA.CMKNLKLTIIII.I.IVFIY.IVSPLCGGFTWPS..KK | |
| Retrocopy | FKTTSRNLARATCMKNLKLTIIIIIILIVFIYVIVSPLCGGFTWPSYAKK |
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 |
|---|---|---|
| SRP051959_colon | 0 .00 RPM | 18 .33 RPM |
| SRP051959_heart | 0 .00 RPM | 18 .22 RPM |
| SRP051959_kidney | 0 .02 RPM | 33 .10 RPM |
| SRP051959_liver | 0 .02 RPM | 23 .87 RPM |
| SRP051959_lung | 0 .00 RPM | 23 .86 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 17 .67 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 13 .87 RPM |
| SRP051959_spleen | 0 .00 RPM | 26 .41 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2410 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2410 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2410 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016289 | 2 retrocopies |
retro_cjac_1958, retro_cjac_2410 ,
|
| Cavia porcellus | ENSCPOG00000024405 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000051412 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000001270 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000025036 | 1 retrocopy |