RetrogeneDB ID: | retro_cjac_3801 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01202197.1:2..271(-) | ||
| 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: | ENSCJAG00000019733 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3801
GGGGGCAACCTTGGGGAGAAACAAAATGTTCTCCTCTCCAGAAAAGGGGCGAGAGACACAGACCCAACCCCAACGGCTCT
CGGCCCAGGGGACTAAACTAGGTCAGTCGTCCCTGTTCAACGAGTCGGAAACCAGAGCAGCAGCTCGGACTCGGAGGTGG
AGAGGCGCCGCAGCCCGCTCGGGACACTTTCCAGAAGCCGTGGGACTATTTCGCTCAAGTGAGAGCCCCAGGACGGCGCG
TTCTTAAAGGACTCTCCTACCCTGGGTAC
ORF - retro_cjac_3801 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.1 % |
| Parental protein coverage: | 61.04 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | GDDLGANDELI-PFQDEGGEEQEPSSDSASAQRDLDEV-KSSLVNESE-NQSSSSDSEAERR-PQPARDT |
| G..LG.......P.Q..G..E........S..R.L..V..SSL.NESE.NQSSSSDSE.ERR.PQPARDT | |
| Retrocopy | GGNLGEKQNVL<PLQKRG--ERHRPNPNGSRPRGLN*V<QSSLFNESE<NQSSSSDSEVERR<PQPARDT |
| Parental | FQKPRDYFAEVRRPQDGAFFKGPPYPGY |
| FQKP.DYFA.VR.P......KG..YPGY | |
| Retrocopy | FQKPWDYFAQVRAP-GRRVLKGLSYPGY |
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 .07 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .56 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .16 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .32 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .28 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .16 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .26 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .40 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3801 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3801 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3801 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000019733 | 2 retrocopies |
retro_cjac_371, retro_cjac_3801 ,
|