RetrogeneDB ID: | retro_cjac_3106 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 8:1648077..1648664(-) | ||
| Located in intron of: | ENSCJAG00000009008 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000034550 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3106
TGTGTGCACGTGCATGTGTGCATGTGTGCCTGCGTGTGTGTGTGTGCGTGCGTGTGTGCACGTGTTGTGTGCGTGTGTGC
GTGCATGTGTGCATGTGTGCGTGCGTGTCTGTGTGCGTGTGTGCGTGCGTGTGTTCACGTGTTGTGTGCTTGTGCGTGCG
TGTGTGCATGTGTGTGTGCGCGTGCGTGTGTGTCTGTGTTGTGCGTGTGCATGTGCACGTGCGTGTGTGCATGTGTGCGT
GCGTGTGTGTCTGTGTGTGTGTGTGCGTGCGTGCACGTGTTGTGTGCGTGTGCGTGCGTGTGCATGTGTGCGTCTGTGTG
TGTGCATGTGTGCACGTGCGTGTGTGCATGTGTGCATGCATGTCTGTGTGTGTGTGTGTGCGTGCGTGTGTGCACGTGTT
GTGTGCGTGTGTGCACGTGTTGTGTGCGTGTGTCTGTGTGTGCGTGCGTGTGCGTGTGTGCATGTGTGCACGTGCGTGTG
CATGTGTGCGTGCATGTGTGTGCGTGTGCGCATGTGTGCGTGCGTGTCTGTGTGTGTGCATGTGTGCGTGCGTGTGTCTG
TGTGCGTGTGTGCACGTGTGTGTGTGC
ORF - retro_cjac_3106 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.63 % |
| Parental protein coverage: | 99.49 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | CVCVCVCVCVCVCLCVCVCVSVSVCVCVCVCVCVSVCVCVCVCVCVSVC-VSVCVSVCVCLCECVCLCV- |
| CV.V.VC.C.CVC.C.CVC..V.VCVC.C.C.CV..C.C.CV..CV.V..V..CV.VC.C.C.CVC.CV. | |
| Retrocopy | CVHVHVCMCACVCVCACVCARV-VCVCACMCACVRACLCACVRACVHVL<VCLCVRVCMCVCACVCVCV> |
| Parental | CVCVCVCVCVCVLCVCVLNVCACMCVSVIGVSVCECECMCFCM-MCEHVCVCICVCAYVCICVNVCL--L |
| CVC.C.CVC.CV...CV..VC.C.CV.V.....C.C.C...C...C.HV.VC.C.C..VC.CV..C...L | |
| Retrocopy | CVCMCTCVCACVRA-CV-SVCVCACVHVLCACACVCMCASVCV<ACVHVRVCMCACMSVCVCVRACVHVL |
| Parental | CACV---CVCVCVCDRVCVCTCMSVCICAACVRVCVCKCVCVYLYMCVCICTCVCACVYMHVYVC |
| CACV...C.CVCVC.RV.VC.C...C.C...VR.CVC.C.CV....CVC.C.CVC.C...HV.VC | |
| Retrocopy | CACVHVLCACVCVCVRVRVCMCARACAC---VRACVCVCACVRACLCVCMCACVCLCACVHVCVC |
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 .02 RPM | 0 .00 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .00 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .02 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .02 RPM |
| SRP051959_lung | 0 .05 RPM | 0 .00 RPM |
| SRP051959_lymph_node | 0 .05 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3106 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3106 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3106 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000034550 | 1 retrocopy |
retro_cjac_3106 ,
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