RetrogeneDB ID: | retro_cjac_660 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 10:11328608..11329061(+) | ||
| 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: | ENSCJAG00000036835 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_660
CAAGAACTACTTGTTGAGGAGCATGGGGAGAAGAAGTCCCAGGTGGCACAGCTCCTAGGGAATGTTCACGCTGCCCTGAA
GCCGTTTTCAGTAAAATTCAATGAGATCACAGATCCCGATAAAAAGCAGATGCTCTAACAGATTCAGCACACAGCGAAGC
TTGCCACGGAGCTGCTTGAGAAAGCTGTGTAGTACAGACTTGGAAAGAAAGCCAACAGCTGTGTGCAAGGATTGTTGGAG
GAGGCCAAGGATTTGCTTTCTGAGTTGCTGGATTCTGCATTCTGGAGTCAGGTGACTGGCAATTTCATTTTCTCCAAACT
GCCCAAGTTCTGGGATGGGGAGTTCCACAAATACATGGAAGCTCTGAATCTCCTCTCTCTGGATGTTTTAACCAGAGTTA
GTGTGTATATGCCAGAAACTGTGAATTTTGACCAAAAGATTGTGGACAATGGT
ORF - retro_cjac_660 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.82 % |
| Parental protein coverage: | 54.87 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | QNHLFRQYREKRPEAAQLLEDVQAALMPFLVKLNETTDADKKQMLERIRHAVQLATEPLEKAVQSRLTGE |
| Q..L.....EK....AQLL..V.AAL.PF.VK.NE.TD.DKKQML..I.H...LATE.LEKAV..RL.G. | |
| Retrocopy | QELLVEEHGEKKSQVAQLLGNVHAALKPFSVKFNEITDPDKKQML*QIQHTAKLATELLEKAV*YRL-GK |
| Parental | EVTSRVEVLLEEAKDLLSDWLDSTLGSDVTDNSIFSELPKFWEGEFHRDMEALNVLPPDVLTRVSEYVPE |
| ...S.V..LLEEAKDLLS..LDS...S.VT.N.IFS.LPKFW.GEFH..MEALN.L..DVLTRVS.Y.PE | |
| Retrocopy | KANSCVQGLLEEAKDLLSELLDSAFWSQVTGNFIFSKLPKFWDGEFHKYMEALNLLSLDVLTRVSVYMPE |
| Parental | IVNFVQKIVDNG |
| .VNF.QKIVDNG | |
| Retrocopy | TVNFDQKIVDNG |
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 .29 RPM |
| SRP051959_heart | 0 .02 RPM | 0 .18 RPM |
| SRP051959_kidney | 0 .02 RPM | 0 .04 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .26 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .16 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .14 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .09 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .19 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_660 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_660 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_660 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 | ENSCJAG00000036835 | 1 retrocopy |
retro_cjac_660 ,
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