RetrogeneDB ID: | retro_cjac_3742 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01198082.1:2459..3203(-) | ||
| 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: | ENSCJAG00000016605 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3742
CTGCTCCCGGGTCTAGTACAGCGCTGGCGCTATGGCAAGGTCTGCCTGGGCTCCTGCTCCACCTTCTCTTTTGGGGGCAG
TGACACACTGTCCGATGCTGCCTTTGAGCCTGTCTACTTGCTGGTAGACAAGGTGATCCGCTGGTTCAGAGTGGTGTTTG
TTGTGCTGGTGATTTTGCTGACAGGCTCCTTTGTGGCTGTCGCCTACCTGTGTGTCCTGCCTCTCATCCTCCGAACCTAT
TCAGTGCCACGACTCTGCTGGCATTTCTTCTCTGCCACCGGAATCTGATCCTCATTGTCTTCCGCTACTACCAGGCCATC
ACCGCTCCGCCTGGATACCCACCCCAGGGCAGGAATGATATTGCCATGGTCTCCATCTGTAAGAAATGCATTTACCCCAA
GCCAGCCAGAACGCACCACTGCAGCATCTGCAACAGGTGTGTGCTGAAGATGGATCATCACTGCCCCCGGCTAAAGAATT
GTGTGGGCCCCTATAACCATCGGTACTTCTTCTCTTTCTGCTTCTTCACGACTCTGGGCTGTGTCTACTGCAGCTATGGA
AGCTGGGACCTTTTCCGGGAGGCTTATGCTGCCATCGAGAAAATGAAGCAGCTTGACAAGAACAAACTACAGGCGGTTGC
CAACCAGACTTCCCACCAGGCCCCACCGCGCACCTTCTCCTTTCAAGAAAGGATGACTCATAGTAGTCATGGTGCTGCTG
ACATGGATGGAGTGCTCGGTGGTA
ORF - retro_cjac_3742 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.6 % |
| Parental protein coverage: | 65.52 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LLRGLVQRWRYGKVCLRSLLYNSFGGSDTAVDAAFEPVYWLVDNVIRWFGVVFVVLVIVLTGSIVAIAYL |
| LL.GLVQRWRYGKVCL.S....SFGGSDT..DAAFEPVY.LVD.VIRWF.VVFVVLVI.LTGS.VA.AYL | |
| Retrocopy | LLPGLVQRWRYGKVCLGSCSTFSFGGSDTLSDAAFEPVYLLVDKVIRWFRVVFVVLVILLTGSFVAVAYL |
| Parental | CVLPLILRTYSVPRLCWHFFYS-HWNLILIVFHYYQAITTPPGYPPQGRNDIAMVSICKKCIYPKPARTH |
| CVLPLILRTYSVPRLCWHFF...H.NLILIVF.YYQAIT.PPGYPPQGRNDIAMVSICKKCIYPKPARTH | |
| Retrocopy | CVLPLILRTYSVPRLCWHFFSA<HRNLILIVFRYYQAITAPPGYPPQGRNDIAMVSICKKCIYPKPARTH |
| Parental | HCSICNRCVLKMDHHCPWLNNCVGHYNHRYFFSFCFFMTLGCVYCSYGSWDLFREAYAAIEKMKQLDKNK |
| HCSICNRCVLKMDHHCP.L.NCVG.YNHRYFFSFCFF.TLGCVYCSYGSWDLFREAYAAIEKMKQLDKNK | |
| Retrocopy | HCSICNRCVLKMDHHCPRLKNCVGPYNHRYFFSFCFFTTLGCVYCSYGSWDLFREAYAAIEKMKQLDKNK |
| Parental | LQAVANQTYHQTPPPTFSFRERMTHKS-LVYL-WFLCSSV |
| LQAVANQT.HQ.PP.TFSF.ERMTH.S..V.L.W..CS.V | |
| Retrocopy | LQAVANQTSHQAPPRTFSFQERMTHSS>MVLLTWMECSVV |
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 | 6 .10 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .86 RPM |
| SRP051959_kidney | 0 .00 RPM | 8 .65 RPM |
| SRP051959_liver | 0 .02 RPM | 6 .93 RPM |
| SRP051959_lung | 0 .00 RPM | 7 .47 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 8 .06 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 6 .97 RPM |
| SRP051959_spleen | 0 .04 RPM | 7 .61 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3742 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3742 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3742 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016605 | 2 retrocopies |
retro_cjac_3503, retro_cjac_3742 ,
|
| Rattus norvegicus | ENSRNOG00000046530 | 1 retrocopy |