RetrogeneDB ID: | retro_cjac_1102 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 13:58763856..58764198(+) | ||
| Located in intron of: | ENSCJAG00000020517 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000020524 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000003568 | ||
| Aliases: | None | ||
| Description: | SH3 domain-binding glutamic acid-rich-like protein [Source:UniProtKB/TrEMBL;Acc:F7GVV1] |
Retrocopy-Parental alignment summary:
>retro_cjac_1102
ATGGTGATCCGTGTATATATCGCATCTTCCTCTGGCTCTACGGCGATTAAGAAGAAACAGCAGGATGTGCTTGGTTTCCT
AGAAGCCAACAAAATAGGATTTGAAGAAAAAGATATTGCAGCCAATGAAGAGAATCGGAAGTGGATGAGAGAAAATGTAC
CTGAAAATAGTCGACCAGCCACAGGGTACCCCCTGCCACCTCAGATTTTCAATGAAAGCCAGTATCGAGGGGACTATGAT
GCTTTCTTTGAAGCCAGAGAAAATAATGCAGTGTATGCCTTCTTAGGCATGACAGCCCCTCCTGGTTCAAAGGAAGCAGA
AGTGCAAGCAAAGCAGCAAGCA
ORF - retro_cjac_1102 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.46 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MVIRVYIASSSGSTAIKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGYPLPPQIF |
| MVIRVYIASSSGSTAIKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGYPLPPQIF | |
| Retrocopy | MVIRVYIASSSGSTAIKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGYPLPPQIF |
| Parental | NESQYRGDYDAFFEARENNAVYAFLGLTAPPGSKEAEVQAKQQA |
| NESQYRGDYDA....................GSKEAEVQAKQQA | |
| Retrocopy | NESQYRGDYDAXXXXXXXXXXXXXXXXXXXXGSKEAEVQAKQQA |
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 | 1 .33 RPM | 4 .37 RPM |
| SRP051959_heart | 1 .79 RPM | 5 .95 RPM |
| SRP051959_kidney | 0 .80 RPM | 3 .19 RPM |
| SRP051959_liver | 0 .52 RPM | 1 .58 RPM |
| SRP051959_lung | 1 .32 RPM | 5 .34 RPM |
| SRP051959_lymph_node | 1 .16 RPM | 3 .31 RPM |
| SRP051959_skeletal_muscle | 0 .26 RPM | 0 .63 RPM |
| SRP051959_spleen | 2 .33 RPM | 6 .89 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1102 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1102 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1102 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 10 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000004130 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000003568 | 2 retrocopies |
retro_cjac_1102 , retro_cjac_140,
|
| Cavia porcellus | ENSCPOG00000012267 | 3 retrocopies | |
| Dipodomys ordii | ENSDORG00000011106 | 2 retrocopies | |
| Equus caballus | ENSECAG00000012612 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000013216 | 1 retrocopy |