RetrogeneDB ID: | retro_cjac_1958 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:130853102..130853435(-) | ||
| 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_1958
TTCCTGGAGGTGACAGAGCATATTCTGGCTAAGATACCTTCTGAAAATAACAAACTAAGGTACTCACATGGCAATTATTT
GTTTCATTACATCTGCCAAGACAGGATTGTATATCTTTGTATCACGGATGATGATTTTGAATGTTCCCGAGACTTTAATT
TTCTGAATGAGATAAAGAAGAGGTTCCAGACTGCTTATGGTTCAAGAGCACGGACAGCACTTCCATATGCCAAGGAAAGT
GAGTTCTCAAGTGTCTTGGCTGCACAGCTGAAGCATCACTCTGAGAATAAGGGCCTAGACAAAGTGATGGAGACTCAACC
CCAAGTGGATGAA
ORF - retro_cjac_1958 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.89 % |
| Parental protein coverage: | 77.08 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | FLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITDDDFERSRAFNFLNEIKKRFQTTYGSRA |
| FLEVTE.ILAKIPSENNKL.YSHGNYLFHYICQDRIVYLCITDDDFE.SR.FNFLNEIKKRFQT.YGSRA | |
| Retrocopy | FLEVTEHILAKIPSENNKLRYSHGNYLFHYICQDRIVYLCITDDDFECSRDFNFLNEIKKRFQTAYGSRA |
| Parental | QTALPYAMNSEFSSVLAAQLKHHSENKGLDKVMETQAQVDE |
| .TALPYA..SEFSSVLAAQLKHHSENKGLDKVMETQ.QVDE | |
| Retrocopy | RTALPYAKESEFSSVLAAQLKHHSENKGLDKVMETQPQVDE |
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 .02 RPM | 18 .33 RPM |
| SRP051959_heart | 0 .00 RPM | 18 .22 RPM |
| SRP051959_kidney | 0 .00 RPM | 33 .10 RPM |
| SRP051959_liver | 0 .00 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_1958 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1958 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1958 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 |