RetrogeneDB ID: | retro_cjac_3970 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286451.1:150790..151030(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000005286 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3970
GAGAAATGTATCTTGTGTGCAAAGCATGTAGCTGATAAGTATGTACAGCTTTTGTCCCAGTTTATTTCTCCATTTCCTGG
ATACATTTGGGGAAGGCACATCACAGGTCTTTGTGGGAAGAAATAGAAAGAAATCACAAAAGCAATTAAGAGAGCTCAAA
TAATGGGGTTTATGCCAGTTATATACAGGGATCCTGAATATCTCAAGGACCCTAAAGTTTGTAATATCAGATATCAGGAA
GAGAAATGTATCTTGTGTGCAAAGCATGTAGCTGATAAGTATGTACAGCTTTTGTCCCAGTTTATTTCTCCATTTCCTGG
ATACATTTGGGGAAGGCACATCACAGGTCTTTGTGGGAAGAAATAGAAAGAAATCACAAAAGCAATTAAGAGAGCTCAAA
TAATGGGGTTTATGCCAGTTATATACAGGGATCCTGAATATCTCAAGGACCCTAAAGTTTGTAATATCAGATATCAGGAA
ORF - retro_cjac_3970 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80. % |
| Parental protein coverage: | 55.56 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KKCILCGKRVDYKNVQLLSQFVSPFTGCIYGRHITGLCGKKQKEITKAIKRAQILGFMPVTYKDPAYLKD |
| .KCILC.K.V..K.VQLLSQF.SPF.G.I.GRHITGLCGKK.KEITKAIKRAQI.GFMPV.Y.DP.YLKD | |
| Retrocopy | EKCILCAKHVADKYVQLLSQFISPFPGYIWGRHITGLCGKK*KEITKAIKRAQIMGFMPVIYRDPEYLKD |
| Parental | PKVCNIRYRE |
| PKVCNIRY.E | |
| Retrocopy | PKVCNIRYQE |
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 | 5 .88 RPM |
| SRP051959_heart | 0 .00 RPM | 9 .65 RPM |
| SRP051959_kidney | 0 .00 RPM | 10 .49 RPM |
| SRP051959_liver | 0 .00 RPM | 13 .10 RPM |
| SRP051959_lung | 0 .02 RPM | 6 .95 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 7 .90 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 10 .44 RPM |
| SRP051959_spleen | 0 .00 RPM | 9 .43 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3970 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3970 was not experimentally validated.