RetrogeneDB ID: | retro_cjac_3478 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01181319.1:4154..4444(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000015697 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3478
TCCTCGGCATCCCTCTGTCCCAGCCACAGCTCAGGACACCCCTCTGCAGGAACAAGCCTGGTGGGCTGCCTGGAACCTGG
ACCCGTCTAGCGGCCGCCCTGCTGCTGCTGGCTGTGGGCTGCTTCCTGGCCATGTGGCAGCTCCAGCATCAAGGCAGCCC
GACAGGAAGACTGGGCTCCATGGCCCCTCCACCCAGCGGACACTCCCATGGCCCTGGCATTTAACATCACGGTGCCATCA
TCAACCCTGCAGGTCAATCATGCTGGCAGCGGCTCGGGGGAGGGAGGGTC
ORF - retro_cjac_3478 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.43 % |
| Parental protein coverage: | 68.31 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | TSEALVPNPWRPQDSSG-NKAGGLPGTWARLVAALLLLAMGCFLAMWQLQHQGSPTGGLGSMAPPPSGHS |
| .S..L.P.......S.G.NK.GGLPGTW.RL.AALLLLA.GCFLAMWQLQHQGSPTG.LGSMAPPPSGHS | |
| Retrocopy | SSASLCPSHSSGHPSAG<NKPGGLPGTWTRLAAALLLLAVGCFLAMWQLQHQGSPTGRLGSMAPPPSGHS |
| Parental | HGPGVYHHGAIISPAGQAWSCLLPGGNV |
| HGPG..HHGAII.PAGQ.....L.GG.V | |
| Retrocopy | HGPGI*HHGAIINPAGQSCWQRLGGGRV |
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 .04 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_3478 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3478 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3478 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 | ENSCJAG00000015697 | 1 retrocopy |
retro_cjac_3478 ,
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