RetrogeneDB ID: | retro_cjac_2382 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:140289971..140290331(+) | ||
| 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: | ENSCJAG00000032766 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2382
CATCTTCCACAAAGGACAACTTTGGAGAGCAGTCGTAGCCAAAACCTCCCTCTGCCTTTAAGAAGTCTCAGAACTCCAGG
CTACATATCATCTTCTTCATGGGAAAGATGTGGAATTTCCCAGGAACTATCCATCAGGTTGTCTTCTGGGCTGTCTGGAC
CTAACTGGTTGTTTCAGAAGCAATTTAAGGAGCAGTTTCCAGACGTCAGTCAAGAATCACGTTCTCCACTTGTTTTCATC
TCCAAAAATCCTCAGGAAATGGTTGTGGAGTTTCCTATTAAAGAAAATAAAAAAATCTGGAAACTGGATTCCAAGATCCA
CCAAGGAGCAAAGAAGGGGTAAATGAAGCAGAATACAGCT
ORF - retro_cjac_2382 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.85 % |
| Parental protein coverage: | 93.8 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | YTPHRGRLWIAATAKKPSPQ-EVSELQATYRLLRGKDVEFPNDYPSGCLLGCVDLIDCLSQKQFKEQF-P |
| ..P.R..L........P.P..EVSELQATY.LL.GKDVEFP..YPSGCLLGC.DL..C.........F.P | |
| Retrocopy | HLPQRTTLESSRSQNLPLPL>EVSELQATYHLLHGKDVEFPRNYPSGCLLGCLDLTGCF-RSNLRSSF<P |
| Parental | DVSQESDSPFVFICKNPQEMVVKFPVKGNPKIWKLDSKIHQGAKKGLMKQNKA |
| DVSQES.SP.VFI.KNPQEMVV.FP.K.N.KIWKLDSKIHQGAKKG.MKQN.A | |
| Retrocopy | DVSQESRSPLVFISKNPQEMVVEFPIKENKKIWKLDSKIHQGAKKG*MKQNTA |
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 | 3 .57 RPM |
| SRP051959_heart | 0 .02 RPM | 3 .21 RPM |
| SRP051959_kidney | 1 .69 RPM | 2 .57 RPM |
| SRP051959_liver | 0 .06 RPM | 1 .84 RPM |
| SRP051959_lung | 0 .00 RPM | 3 .66 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .11 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .95 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .34 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2382 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2382 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2382 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000032766 | 1 retrocopy |
retro_cjac_2382 ,
|
| Macaca mulatta | ENSMMUG00000009882 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000002322 | 1 retrocopy |