RetrogeneDB ID: | retro_cjac_3798 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01201910.1:281..579(+) | ||
| 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_3798
TTTTTTGAGTTGGAGTCCCACTCTGTTGCTTAGGCTGGAGTGCAGTGGCACTATCTTGGCTCACTGCAATCTCCACCTCC
TGGGTTGAAGCGATTCTCCTGTCTCAGCCTCCCAAGTAGCTGGCATTACAGGAAGCTGCCACCATGCCCAGCTAATTTTT
TGTACTTTTAGCAGAGATGGGGTTTCACCATGTGGACAAGGCTGGTCTTGAACTCCTGCCCTCAGGTGATCCACCTTCTT
TGGCCTCCCAAAGTGATGGGATTACAGGCATGAGCCACTACAGCCAGAACTCAGTTTC
ORF - retro_cjac_3798 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.0 % |
| Parental protein coverage: | 99.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | FFETGSHSVTQAGVQWRDLGSLQPPPPGFKQFCCLSLPSSWDYRRAPPRPAN-FCIFSKDRVSSCWPGWS |
| FFE..SHSV..AGVQW..LGSLQ.PPPG.K.F.CLSLPSSW.YR..PP.PAN.FC.FS.D.VS.C..GWS | |
| Retrocopy | FFELESHSVA*AGVQWHYLGSLQSPPPGLKRFSCLSLPSSWHYRKLPPCPAN>FCTFSRDGVSPCGQGWS |
| Parental | RSLDLRISGFLSLPKCWDYRREPPRPAIIF |
| ....LR.S.F..LPK.WDYR.EP..P...F | |
| Retrocopy | *TPALR*STFFGLPK*WDYRHEPLQPELSF |
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_3798 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3798 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3798 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 ,
|