RetrogeneDB ID: | retro_cjac_3718 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01196893.1:11..301(-) | ||
| 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_3718
TTTTTCAAACGGAGTTTTGCTTTTGTTACCCAGGCTACACTGCAATGGTGCGATCTCAGCTCACGGCAACCTCTGCCTCC
CCAGGTTCAAGGGATTCTCCTGCCCCAGCCTCCCAGGTAGCTGGGATCACAGGCATGCACCACCATGCCCGGCTAATTTT
GTATTTTAGTAGAGACAGGGTTTATTCATATTGGTCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCTGCCTGCCTTG
GCCTCCCAAAGTGCTGGGATTACAGGTATGAGCCACCGCGCCTGGCCTTG
ORF - retro_cjac_3718 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.0 % |
| Parental protein coverage: | 97.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | FFETGSHSVTQAGVQWRDLGSLQPPPPG-FKQFCCLSLPSSWDYRRAPPRPANF-CI-FSKDRVSSCWPG |
| FF......VTQA..QW.DL.S.QP.PP..FK.F.C.SLP.SWD.R.APP.PANF.CI.FS.DRV.S.W.G | |
| Retrocopy | FFKRSFAFVTQATLQWCDLSSRQPLPPQ>FKGFSCPSLPGSWDHRHAPPCPANF<CI<FSRDRVYSYWSG |
| Parental | WSRSLDLRISGFLSLPKCWDYRREPPRPAI |
| WS...DLR.S..L.LPKCWDYR.EPPR.A. | |
| Retrocopy | WS*TPDLR*SACLGLPKCWDYRYEPPRLAL |
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 .24 RPM | 0 .09 RPM |
| SRP051959_heart | 0 .16 RPM | 0 .58 RPM |
| SRP051959_kidney | 0 .20 RPM | 0 .09 RPM |
| SRP051959_liver | 0 .13 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .31 RPM | 0 .21 RPM |
| SRP051959_lymph_node | 0 .37 RPM | 0 .11 RPM |
| SRP051959_skeletal_muscle | 0 .04 RPM | 0 .11 RPM |
| SRP051959_spleen | 0 .46 RPM | 0 .11 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3718 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3718 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3718 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,
|