RetrogeneDB ID: | retro_cjac_3399 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01177997.1:10460..10744(+) | ||
| 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_3399
TTTGAGATGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACGACCTCGGCTCACTGCAACCTCCGCCTCCTGG
ATTCAAGCGATTCCCCTGCTTGAGCCTCCTTGGTAGCTGTAATTACAGGCGCACAAAACCAGACCTGGCTAATATTTTTG
TATTTTTAGTAGATATGGGCTTTCATCATGTTGGCCAGACTGTTCTTGAACTCCGGATCTCAGATGACCCACCCTCCTTG
GCCTCCCAAAGTGCTGGAATTACAAGCGTGAGTCACCATGCCCA
ORF - retro_cjac_3399 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.58 % |
| Parental protein coverage: | 94.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | FETGSHSVTQAGVQWRDLGSLQPPPPGFKQFCCLSLPSSWDYRRAPP-RPA-NFCIFSKDRVSSCWPGWS |
| FE..S.SVTQAGVQW.DLGSLQPPPPGFK.F.CLSL..S..YRR..P.RP...FCIFS....SSCWP..S | |
| Retrocopy | FEMESRSVTQAGVQWHDLGSLQPPPPGFKRFPCLSLLGSCNYRRTKP<RPG*YFCIFSRYGLSSCWPDCS |
| Parental | RSLDLRISGFLSLPKCWDYRREPPRP |
| ...DLR....L.LPKCW.Y.RE.P.P | |
| Retrocopy | *TPDLR*PTLLGLPKCWNYKRESPCP |
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 .12 RPM | 0 .58 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .09 RPM |
| SRP051959_liver | 0 .02 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .02 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_3399 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3399 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3399 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,
|