RetrogeneDB ID: | retro_cjac_386 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:20423185..20423538(+) | ||
| 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_386
GGGAAGGAAGGAAGGAAGGAAGGAAGGACAAAAAGAAGGAAGGAAGGAAATAAGGGAGAGAGGGAAGAAGAAAGGAAGAG
AGGGAGGGAGGAAGGAAGGAGAAAGAGAGAGGGAGGGAGGGAATGAGGGAGAGAGGAGGAAGGAAGGAGAAAGAGAAAGA
GAAGGAGAGAAGTATGGAGGGATGAAGGGAGGGAATGTGGGAGACAGGAAGAAGGAAGGAAGGAAAGAAGGAAGGAAGGA
GAAATAGAGAAAGAGAGAAGGAGGGAAGGATGGAGGGAGGGAATGAGGGAGAGAGTATGGAGGGAGGGAGGGAGGGAGGG
AGGAAGGAAGGAAGGAAGGAGGGAAGGAAGGAA
GGGAAGGAAGGAAGGAAGGAAGGAAGGACAAAAAGAAGGAAGGAAGGAAATAAGGGAGAGAGGGAAGAAGAAAGGAAGAG
AGGGAGGGAGGAAGGAAGGAGAAAGAGAGAGGGAGGGAGGGAATGAGGGAGAGAGGAGGAAGGAAGGAGAAAGAGAAAGA
GAAGGAGAGAAGTATGGAGGGATGAAGGGAGGGAATGTGGGAGACAGGAAGAAGGAAGGAAGGAAAGAAGGAAGGAAGGA
GAAATAGAGAAAGAGAGAAGGAGGGAAGGATGGAGGGAGGGAATGAGGGAGAGAGTATGGAGGGAGGGAGGGAGGGAGGG
AGGAAGGAAGGAAGGAAGGAGGGAAGGAAGGAA
ORF - retro_cjac_386 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.83 % |
| Parental protein coverage: | 70.91 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | GKEGRK-GRERGRKEGG-REREGEEGKREGRREGGKE-GRKKERKREREREKEREREREREREREERKER |
| GKEGRK.GR...RKEG..RER....G...GR.EG..E.GR...R.R....EKE.E.ER..E..RE...E. | |
| Retrocopy | GKEGRKEGRTKRRKEGN>RERGKKKGREGGRKEGERE>GREGMRERGGRKEKEKEKERSMEG*REGMWET |
| Parental | KRKKERKRKEGRKEGKRERERERKEGRKEGRFEEERKEGRKEGRKEGRKE |
| .R.KE.K.KEGR....RE.E.....G......E..R..GRKEGRKEGRKE | |
| Retrocopy | GRRKEGK-KEGRRNREREKEGRMEGGNEGESMEGGREGGRKEGRKEGRKE |
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 | 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_386 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_386 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_386 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,
|