RetrogeneDB ID: | retro_cjac_1302 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 14:82346944..82347325(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | PPIL1 | ||
| Ensembl ID: | ENSCJAG00000016094 | ||
| Aliases: | None | ||
| Description: | peptidylprolyl isomerase (cyclophilin)-like 1 [Source:HGNC Symbol;Acc:9260] |
Retrocopy-Parental alignment summary:
>retro_cjac_1302
GCTGAGACGGCTCGTCGAGGTGACTACAGTGGCACAAAATTCCACAGAATCATCAAAGATTTCGTGATCCAAAAAGGAGA
CCCAACGGGGGCAGGTTGAGGCGGTGCATTTATCTATGGCACACAGTTTGAAGATGAACTTCATCCAGACCTGAAATTCA
CGGTCGCTGGAATTCTCACAATGACCAATGCAGGGCCAGACACCAATGGCAGCCAGTTCTTTGTGACCCTTGCCCCCACC
CAGTGGCTCAATAGCAAACACACCATTCTTGGCCGAGTGTGCCAGGGGATAGGAAGGGTGAACTGAGTAGGAATGGTATC
AACAGAGCCCCAGGACTGCCCTGTGAACAATGTGAAGATTATTAAGGCATACCCTTCTGGG
GCTGAGACGGCTCGTCGAGGTGACTACAGTGGCACAAAATTCCACAGAATCATCAAAGATTTCGTGATCCAAAAAGGAGA
CCCAACGGGGGCAGGTTGAGGCGGTGCATTTATCTATGGCACACAGTTTGAAGATGAACTTCATCCAGACCTGAAATTCA
CGGTCGCTGGAATTCTCACAATGACCAATGCAGGGCCAGACACCAATGGCAGCCAGTTCTTTGTGACCCTTGCCCCCACC
CAGTGGCTCAATAGCAAACACACCATTCTTGGCCGAGTGTGCCAGGGGATAGGAAGGGTGAACTGAGTAGGAATGGTATC
AACAGAGCCCCAGGACTGCCCTGTGAACAATGTGAAGATTATTAAGGCATACCCTTCTGGG
ORF - retro_cjac_1302 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.89 % |
| Parental protein coverage: | 76.51 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | AELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYGKQFEDELHPDLKFTGAGILAMANAGPDTNG |
| AE.ARRG.Y.GTKFHRIIKDF.IQ.GDPTG.G.GGA.IYG.QFEDELHPDLKFT.AGIL.M.NAGPDTNG | |
| Retrocopy | AETARRGDYSGTKFHRIIKDFVIQKGDPTGAG*GGAFIYGTQFEDELHPDLKFTVAGILTMTNAGPDTNG |
| Parental | SQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPSG |
| SQFFVTLAPTQWL..KHTI.GRVCQGIG.VN.VGMV.T..QD.PV..VKIIKAYPSG | |
| Retrocopy | SQFFVTLAPTQWLNSKHTILGRVCQGIGRVN*VGMVSTEPQDCPVNNVKIIKAYPSG |
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 | 6 .88 RPM |
| SRP051959_heart | 0 .02 RPM | 5 .60 RPM |
| SRP051959_kidney | 0 .00 RPM | 6 .10 RPM |
| SRP051959_liver | 0 .00 RPM | 4 .07 RPM |
| SRP051959_lung | 0 .00 RPM | 5 .63 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 8 .58 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .88 RPM |
| SRP051959_spleen | 0 .00 RPM | 7 .42 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1302 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1302 was not experimentally validated.