RetrogeneDB ID: | retro_cjac_1356 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 15:80209238..80209695(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000010339 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1356
GGAAGGAAGGAAGGACAGAATAAAGGAGGGAGGGAGGGAGGAAGGAAGCAAGGAGGGAAGGGAGGGAGGGAGGAGGGGAA
ACAGGAAAGAAGGAAAAAGAGAGAAGGAGAAAAAAAGGAGGGAGGGAGGCAGGAAAGAAGGAAGGAAGAAGAGAGGGAGA
GAGGAAGGAAGGAGGAAGGGAGCAAGAGAAGAAGGAAGGAAGGAAAGAAGATAGAGAGGCAGGGAGGGAGGGAAGGGGGA
AGGAGAGAGGGAAGGAAGGGGGAAGGAAAGAGGGAAGGAGGGAGGGAGTGAGGGAAGAAGGAAGAAAGGAAAGAAGGAAG
GAGAGAGGCAGGGAGGGAAGGGGGAAGGAAAGAGGGAAGAAGGAAAGAAGAAAGGACAGGGAGGGAAGGAGGGAGGGAAA
AGGAAGGAGGGAGGGAGGGAAGGAAGGAAGGAAAGAAAGAAAGAAGGTAGGAAAGAA
GGAAGGAAGGAAGGACAGAATAAAGGAGGGAGGGAGGGAGGAAGGAAGCAAGGAGGGAAGGGAGGGAGGGAGGAGGGGAA
ACAGGAAAGAAGGAAAAAGAGAGAAGGAGAAAAAAAGGAGGGAGGGAGGCAGGAAAGAAGGAAGGAAGAAGAGAGGGAGA
GAGGAAGGAAGGAGGAAGGGAGCAAGAGAAGAAGGAAGGAAGGAAAGAAGATAGAGAGGCAGGGAGGGAGGGAAGGGGGA
AGGAGAGAGGGAAGGAAGGGGGAAGGAAAGAGGGAAGGAGGGAGGGAGTGAGGGAAGAAGGAAGAAAGGAAAGAAGGAAG
GAGAGAGGCAGGGAGGGAAGGGGGAAGGAAAGAGGGAAGAAGGAAAGAAGAAAGGACAGGGAGGGAAGGAGGGAGGGAAA
AGGAAGGAGGGAGGGAGGGAAGGAAGGAAGGAAAGAAAGAAAGAAGGTAGGAAAGAA
ORF - retro_cjac_1356 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.53 % |
| Parental protein coverage: | 90.3 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | GREGGRNEGAREREGEEGKREGKGGRE-GGKEGRKGRERGRKEGGREREGEEGKREG-RREGGKEGRKKE |
| GR..G.N.G...REG...K..GKGGRE.GG..G.K..ER.RK.GGRE....EG.REG.R.EGG.E..KKE | |
| Retrocopy | GRKEGQNKGG--REGGR-KQGGKGGRE<GGETGKKEKERRRKKGGREAGKKEGRREGERKEGGREQEKKE |
| Parental | -RKREREREKE-REREREREREREERKE-RKRKKERKRKEGRKEGKRE-RERERKEGRKEGRFEEE---R |
| .RK..RE...E.R..ER..E..R.E....R...K...RKEGR.E..RE..E..R.EG.K.G....E...R | |
| Retrocopy | GRKEDREAGREGRGKERGKEGGRKEGRR>RE*GKKEERKEGRREAGRE>GEGKREEGKKKGQGGKEGGKR |
| Parental | KEGRKEGRKEGRKEGRKE |
| KEG..EGRKE..KEGRKE | |
| Retrocopy | KEGGREGRKERKKEGRKE |
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 | 0 .00 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .00 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1356 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1356 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1356 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000010339 | 9 retrocopies |
retro_cjac_1356 , retro_cjac_2297, retro_cjac_2882, retro_cjac_3255, retro_cjac_3637, retro_cjac_3700, retro_cjac_3728, retro_cjac_386, retro_cjac_420,
|