RetrogeneDB ID: | retro_cjac_1458 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 16:27515257..27516048(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ISP | ||
| Ensembl ID: | ENSCJAG00000001887 | ||
| Aliases: | None | ||
| Description: | Ubiquinol-cytochrome c reductase iron-sulfur subunit [Source:UniProtKB/TrEMBL;Acc:F7ABQ4] |
Retrocopy-Parental alignment summary:
>retro_cjac_1458
TTTGCGCCCGTCCTGTCGGCCATGTCCCGCGGGGTGGCGGGTGCACTGAGGCCCCTGGTGCAGGCCGAGGTGCCCGCCAC
CCCGGCGCCACCTGTGCTGGACCCAAAGTGGCCCATCTTGAACCAGGAGTGGCTGAGCGGCCAGACCGCGCGCCAGCCTT
TGGTCGTCTCCGTGAGCCTCAATGTCCCTGCTTCTGTTCATTATTCCCATACAGACATCAAGGTGCCTGACTTCTCTGAC
TACCGCCACTCTGAAGTTTTAGATAAAATAAAGTCTTCAAGAGAAAGCAGCGATGCTAGAAAGGTTTCTCCTATTTGGTA
ATGGCAGCAACTGCTGTGGGTGTCACGTATGCTGCCAAGAGTATCGTCACCTAGTTCGTTTCCTCCATGAGTGCTTCTGC
TGATGTGTTGGCCATGTCAAAAATCAAAATCAAGTTGTCTGATATTCAAGAAGGCAAGAACATGGCTTTCAAATGGAGGG
GGAAACCCCTGTTTGTGTGTCATAGAACCCAGAAGGAAACTGAGCAGGAAGCTGCATTAGAATTGTCCCAGTTGGGGGAC
CCACAGCATGTTCTAGATCGAGTAAAGAAACCCGAATGGATGATCCTCATTGGTGTTTGCATGCATCTTGGTTGTGTACC
CATTGCAAATTCAGGAGATTTTGGTGGTTATTACTGCCCTTGCCATGGGTCACACTATGATGCGTCTGGCAGGATCAGGA
AGGGGCCTGCACCTCTCAACCTAGAAGTCCCTACCTATGAGTTCACCAGTGACGATATGGTCATTGTTGGC
ORF - retro_cjac_1458 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.77 % |
| Parental protein coverage: | 96.35 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | FAPVLSATSRGVVHFTSSQHQSGRCIRTAPPVLDPKRPILSRESLSGQAARRPLVASVGLNVPASVRYSH |
| FAPVLSA.SRGV........Q.......APPVLDPK.PIL..E.LSGQ.AR.PLV.SV.LNVPASV.YSH | |
| Retrocopy | FAPVLSAMSRGVAGALRPLVQAEVPATPAPPVLDPKWPILNQEWLSGQTARQPLVVSVSLNVPASVHYSH |
| Parental | TDIKVPDFADYRRSEVLDKAKSSRESSDARK-GFSYLVTAATAVGVTYAAKGIVTQFVSSMSASADVLAM |
| TDIKVPDF.DYR.SEVLDK.KSSRESSDARK.GFSYLV.AATAVGVTYAAK.IVT.FVSSMSASADVLAM | |
| Retrocopy | TDIKVPDFSDYRHSEVLDKIKSSRESSDARK<GFSYLVMAATAVGVTYAAKSIVT*FVSSMSASADVLAM |
| Parental | SKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDPQHDLDRVKKPEWMILIGVCTH |
| SKI.IKLSDI.EGKNMAFKWRGKPLFV.HRTQKE.EQEAA.ELSQL.DPQH.LDRVKKPEWMILIGVC.H | |
| Retrocopy | SKIKIKLSDIQEGKNMAFKWRGKPLFVCHRTQKETEQEAALELSQLGDPQHVLDRVKKPEWMILIGVCMH |
| Parental | LGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPTYEFTGDDMVVVG |
| LGCVPIAN.GDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPTYEFT.DDMV.VG | |
| Retrocopy | LGCVPIANSGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPTYEFTSDDMVIVG |
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 | 23 .81 RPM |
| SRP051959_heart | 0 .16 RPM | 57 .50 RPM |
| SRP051959_kidney | 0 .09 RPM | 35 .70 RPM |
| SRP051959_liver | 0 .02 RPM | 29 .68 RPM |
| SRP051959_lung | 0 .00 RPM | 7 .84 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 8 .33 RPM |
| SRP051959_skeletal_muscle | 0 .04 RPM | 44 .86 RPM |
| SRP051959_spleen | 0 .00 RPM | 9 .45 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1458 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1458 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1458 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 | ENSCJAG00000001887 | 1 retrocopy |
retro_cjac_1458 ,
|
| Gorilla gorilla | ENSGGOG00000012978 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000010777 | 1 retrocopy |