RetrogeneDB ID: | retro_cjac_2302 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:187504803..187505062(-) | ||
| Located in intron of: | ENSCJAG00000014023 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000001349 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2302
AGTTGGCGAGGAAGATCAGCATATAGGCTTAGACCTAGAGGTCGGTCTCTGCAGCCTCCTGAGCTGCCTGGGCCTGTGCT
CGAGCCAGTGATGAACAGCCTCAGCAAGAGGCACCGCTGCCGGAAAGACAGGGCCCCGCCCCCGGCCAGGAGAGAGAGAA
GGACCCGGTGCTGCTGAGAGGCTCACGCTTGACTGGGAAGCGGATCTCGGGAGCCACCTCCAAGACTGGGATGAATGCAG
AGGAGGTCCTGGTGTCCGG
ORF - retro_cjac_2302 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.75 % |
| Parental protein coverage: | 79.09 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | SWRGRSTYR--PRPRSLQPPELTGTMLEP-SVEEPEEEKPPTESRDPTPDQKREDD-QGVAEIQVPDLEA |
| SWRGRS.YR..PR.RSLQPPEL.G..LEP.S.E.P..E.P..E...P.P.Q.RE.D..G.AE....D.EA | |
| Retrocopy | SWRGRSAYRLRPRGRSLQPPELPGPVLEP<SDEQPQQEAPLPERQGPAPGQEREKD<PGAAERLTLDWEA |
| Parental | DLQELCQSKTGGECGDGPDVK |
| DL....Q.....EC..GP.V. | |
| Retrocopy | DLGSHLQD--WDECRGGPGVR |
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 .00 RPM |
| SRP051959_heart | 0 .09 RPM | 0 .00 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .04 RPM |
| SRP051959_lung | 0 .03 RPM | 0 .15 RPM |
| SRP051959_lymph_node | 0 .05 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .04 RPM | 0 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2302 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2302 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2302 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Pongo abelii | retro_pabe_2422 |
Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000001349 | 1 retrocopy |
retro_cjac_2302 ,
|
| Nomascus leucogenys | ENSNLEG00000008241 | 1 retrocopy |