RetrogeneDB ID: | retro_cjac_1952 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:122627358..122627758(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UBE2V1 | ||
| Ensembl ID: | ENSCJAG00000036984 | ||
| Aliases: | None | ||
| Description: | ubiquitin-conjugating enzyme E2 variant 1 [Source:RefSeq peptide;Acc:NP_001192018] |
Retrocopy-Parental alignment summary:
>retro_cjac_1952
AATTTCCAACTTTTGGAAGAACTTGAAGAAGGTTAGAAAGGAGTAGAAGATGGCACAGTTAGCTAGGGTCTTGAAGATGA
TGAAGACATGACACTTATAAGATGGACAGGGATGATAATTGGGCCTCCAAGAATAACTTATGAAAACTGAATATACAACC
TTAAAATAGAACATGAACCCAAATACCCAGAAGCACCCCCCTTTGTAAGATCAATAACAAAAAATTAATATGAATGGAGT
TTATGGTTCTAATGGAGTGGTGGACCCCAAAACCATATGTGCTGGCAAAATGGCAGAATTCAAATCATCAAAGTTATCCT
GCAAGAGCTTTGGTGCTTACTGAATGTCTAAAGAAAATATGAAACTCCCTCAGCCACCTGAAGGACAGTGTTACAACAAT
ORF - retro_cjac_1952 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.11 % |
| Parental protein coverage: | 91.16 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | NFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTIYENRIYSLKIECGPKYPEAPPFVR |
| NF.LLEELEEG.KGV.DGTVS.GLEDDEDMTL.RWTGMIIGPPR..YEN.IY.LKIE..PKYPEAPPFVR | |
| Retrocopy | NFQLLEELEEG*KGVEDGTVS*GLEDDEDMTLIRWTGMIIGPPRITYEN*IYNLKIEHEPKYPEAPPFVR |
| Parental | FVT-KINMNGVNSSNGVVDPRAISVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQCYSN |
| ..T.KINMNGV..SNGVVDP..I....K.....S.K..........MSKENMKLPQPPEGQCY.N | |
| Retrocopy | SIT>KINMNGVYGSNGVVDPKTICA-GKMAEFKSSKLSCKSFGAY*MSKENMKLPQPPEGQCYNN |
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 .24 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .47 RPM |
| SRP051959_kidney | 0 .00 RPM | 7 .65 RPM |
| SRP051959_liver | 0 .00 RPM | 5 .65 RPM |
| SRP051959_lung | 0 .00 RPM | 7 .40 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 7 .72 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 6 .97 RPM |
| SRP051959_spleen | 0 .00 RPM | 7 .18 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1952 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1952 was not experimentally validated.