RetrogeneDB ID: | retro_cjac_1494 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 16:3347995..3348400(-) | ||
| Located in intron of: | ENSCJAG00000015678 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAB8A | ||
| Ensembl ID: | ENSCJAG00000014120 | ||
| Aliases: | None | ||
| Description: | RAB8A, member RAS oncogene family [Source:HGNC Symbol;Acc:7007] |
Retrocopy-Parental alignment summary:
>retro_cjac_1494
CTGCCGAAGACCTGCGATTACGTGTTCAAGCTGCTGCTGATCGGGGACTCGGGGGTGGGGAAGACCTGCGTCCTGTTCCG
CTTCTCCGAGGACGCCTTCAACTCCACGTTTATCTCCACCATAGGAATGGACTTTAAAATTAGGACCATAGAGCTCGACG
GCAAGAGAATGAAGCGGCAGATACGGGACACAGCCGGTCAGGGGCGGTTTCGGACGATCCGGACAGCCTACCGCAGGGGT
GCGATGGGCATCATGCTGGTTTATGACGTCACCGACGAGAAGTCCTTCCACAACACCCGGAACTGGATTCGGAACATTGA
GGAGCATGGCTCTGCATATGTTGAAACGATGATGCTCGGGAACACGTGTGATGAGAACCACAAGAGACAGGTTTCCAAGG
AACGG
ORF - retro_cjac_1494 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.7 % |
| Parental protein coverage: | 65.22 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAKTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERF |
| ..KT.DY.FKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIG.DFKIRTIELDGKR.K.QI.DTAGQ.RF | |
| Retrocopy | LPKTCDYVFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGMDFKIRTIELDGKRMKRQIRDTAGQGRF |
| Parental | RTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKER |
| RTI.TAY.RGAMGIMLVYD.T.EKSF.N.RNWIRNIEEH.SA.VE.M.LGN.CD.N.KRQVSKER | |
| Retrocopy | RTIRTAYRRGAMGIMLVYDVTDEKSFHNTRNWIRNIEEHGSAYVETMMLGNTCDENHKRQVSKER |
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 | 14 .27 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .79 RPM |
| SRP051959_kidney | 0 .02 RPM | 11 .85 RPM |
| SRP051959_liver | 0 .00 RPM | 9 .44 RPM |
| SRP051959_lung | 0 .00 RPM | 11 .66 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 14 .02 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .16 RPM |
| SRP051959_spleen | 0 .00 RPM | 17 .12 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1494 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1494 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1494 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000001599 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000014120 | 1 retrocopy |
retro_cjac_1494 ,
|
| Otolemur garnettii | ENSOGAG00000013894 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000009756 | 1 retrocopy |