RetrogeneDB ID: | retro_cjac_3421 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01178985.1:11195..11440(+) | ||
| 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: | ENSCJAG00000037406 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3421
CAGGCTGGAGTGAAGTGGCATAATCTCAGCTCATTGCAACCCCTGCCTTCCATGTTTCAGCAATTTTTTTGCCTCTGCCT
ACCAAGTAGCTCTGACTACAGACATGTACAACCATGCATGGCTAATTTTTGTATTTTTAGTAAGATAGGGTTTCCTCATG
TTGGTCAGGCTGGTCTCAAACTGCTGACCTCAGATGATCCACCCACCTCGACCTCCCTAAGTGCTGGGATTACAGGCATA
AGCCA
ORF - retro_cjac_3421 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.47 % |
| Parental protein coverage: | 82.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | QAGVQWRDLGSLQPPPPGFKQFCCLSLPSSWDYRRAPPRPANFCIFSK-DRVSSCWPGWSRSLDLRISGF |
| QAGV.W..L.SLQP.P..F.QF.CL.LPSS.DYR...P..ANFCIFSK.DRVSSCW.GWS...DLR.S.. | |
| Retrocopy | QAGVKWHNLSSLQPLPSMFQQFFCLCLPSSSDYRHVQPCMANFCIFSK<DRVSSCWSGWSQTADLR*STH |
| Parental | LSLPKCWDYRREP |
| L.LPKCWDYR..P | |
| Retrocopy | LDLPKCWDYRHKP |
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 .09 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .58 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .09 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .21 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .11 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .11 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_3421 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3421 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3421 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 10 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000037406 | 10 retrocopies |
retro_cjac_3399, retro_cjac_3402, retro_cjac_3421 , retro_cjac_3540, retro_cjac_3565, retro_cjac_3590, retro_cjac_3621, retro_cjac_3687, retro_cjac_3718, retro_cjac_3798,
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