RetrogeneDB ID: | retro_cjac_2570 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:133110088..133110385(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | PRAP1 | ||
| Ensembl ID: | ENSCJAG00000005205 | ||
| Aliases: | None | ||
| Description: | proline-rich acidic protein 1 [Source:HGNC Symbol;Acc:23304] |
Retrocopy-Parental alignment summary:
>retro_cjac_2570
CTTCTCATGGTCACCAGCCTTTTGGCTGTGCTGTTGTCGGGGGCCGGTGTGACCCCAGCACCCAAGGTCCCTGTCAAGGT
CCAAGTCAAACACCAGCCCTCGGAGCAGGATGCAGCAAAGGCCTAGGGTGCCCGTCTGATGGAGCCAACAGAGAAGGACA
GCCAGCTGGTGGGGGTGCTCCCCATCCAGAAGCCGAAGCTCTTGACTGCTGAGGAGAAGCCACCAGGCACCAAGGCCTGG
GTGGAGACCAAGGACATCCTGGGCCATGTCCTGAGCCCCCAGCAGGGTCCTGAGCCC
CTTCTCATGGTCACCAGCCTTTTGGCTGTGCTGTTGTCGGGGGCCGGTGTGACCCCAGCACCCAAGGTCCCTGTCAAGGT
CCAAGTCAAACACCAGCCCTCGGAGCAGGATGCAGCAAAGGCCTAGGGTGCCCGTCTGATGGAGCCAACAGAGAAGGACA
GCCAGCTGGTGGGGGTGCTCCCCATCCAGAAGCCGAAGCTCTTGACTGCTGAGGAGAAGCCACCAGGCACCAAGGCCTGG
GTGGAGACCAAGGACATCCTGGGCCATGTCCTGAGCCCCCAGCAGGGTCCTGAGCCC
ORF - retro_cjac_2570 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.8 % |
| Parental protein coverage: | 69.23 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LLVVTSLLAVLLWEAGAGPAPKVPDKVQAKHWPSEQDTEKAQGAREVEPPEKDDQLVGLFPVQKPKLLTA |
| LL.VTSLLAVLL..AG..PAPKVP.KVQ.KH.PSEQD..KA.GAR..EP.EKD.QLVG..P.QKPKLLTA | |
| Retrocopy | LLMVTSLLAVLLSGAGVTPAPKVPVKVQVKHQPSEQDAAKA*GARLMEPTEKDSQLVGVLPIQKPKLLTA |
| Parental | EEKPLGTKAWVETQDILGHVLSPQQGPEP |
| EEKP.GTKAWVET.DILGHVLSPQQGPEP | |
| Retrocopy | EEKPPGTKAWVETKDILGHVLSPQQGPEP |
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 .33 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .02 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .49 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .09 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .02 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .04 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .11 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2570 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2570 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2570 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000005205 | 1 retrocopy |
retro_cjac_2570 ,
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