RetrogeneDB ID: | retro_cjac_2868 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:25983847..25984210(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CHMP5 | ||
| Ensembl ID: | ENSCJAG00000008104 | ||
| Aliases: | None | ||
| Description: | charged multivesicular body protein 5 [Source:HGNC Symbol;Acc:26942] |
Retrocopy-Parental alignment summary:
>retro_cjac_2868
ATGAACTGATTCTTTGGGAAAGTGAAACCCAAGCCTCCGCCACCTGGCCTGACTGACTGCACTGGCGTGGTGAACAGCAG
GGCAGAGTCCATTGACAAGAAGATTTCTGGATTGGATGCTGAGCTAGTGAAGGATAATGATCAGATCAAGAAGATGAGAG
AGGATCCTGCAAAGAATGTGGTCAAGCAGAAAGCCTTGCAAGTTTTAAAGCCAAAGCAGATGTATGAGCAGTAGCGGGAC
AATCTCGTCCTACAGTCATTCAACATGGAACAAGCCAATTGTACCATCCAGTCATTGAAAGACACCAGGACCATGGCTGG
TGCTATGAAGCTGGAAGTAAAGGAAATCAAGACGACAAGCAAG
ORF - retro_cjac_2868 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.86 % |
| Parental protein coverage: | 55.25 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MNRFFGKAKPKAPPPSLTDCIGTVDSRAESIDKKISRLDAELVKYKDQIKKMREGPAKNMVKQKALRVLK |
| MN.FFGK.KPK.PPP.LTDC.G.V.SRAESIDKKIS.LDAELVK..DQIKKMRE.PAKN.VKQKAL.VLK | |
| Retrocopy | MN*FFGKVKPKPPPPGLTDCTGVVNSRAESIDKKISGLDAELVKDNDQIKKMREDPAKNVVKQKALQVLK |
| Parental | QKRMYEQQRDNLAQQSFNMEQANYTIQSLKDTKTTVDAMKLGVKEMKKAYK |
| .K.MYEQ.RDNL..QSFNMEQAN.TIQSLKDT.T...AMKL.VKE.K...K | |
| Retrocopy | PKQMYEQ*RDNLVLQSFNMEQANCTIQSLKDTRTMAGAMKLEVKEIKTTSK |
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 | 22 .72 RPM |
| SRP051959_heart | 0 .00 RPM | 20 .33 RPM |
| SRP051959_kidney | 0 .00 RPM | 33 .10 RPM |
| SRP051959_liver | 0 .00 RPM | 20 .99 RPM |
| SRP051959_lung | 0 .00 RPM | 25 .08 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 13 .70 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 16 .68 RPM |
| SRP051959_spleen | 0 .00 RPM | 25 .21 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2868 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2868 was not experimentally validated.