RetrogeneDB ID: | retro_cjac_4028 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL289951.1:215747..216291(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000032770 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000016528 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_4028
CCGCACGTCGTTCCCGACCAGAGAAGCAAGTTGGAGAACTAGGAGTTCTTCAAGAAGCTGAGCCGCGAGTGTTAGATTAA
GTACACGGGATTCAGGGACCGGCCCCATGAGGAGCGCCAGGCGTACTTCCAGAACGCCTGCCGCGACGGCCGCTCGGAAA
TCGCTTTTGTGGCCACAGGAACCAACCTCTCTCTGCAGTTTTTTCCGGCCGGCTGCCAGGGGAGAACAGCGACAAACACC
TAGCCGAGAGTATGTCGACCTAGAAAGAGAAGCAGGCAAGGTATATTTGAAGGCTCCCATGATTCTGAATGGAGTCTGTG
TTACCAGCAAAGGCTGGATTGATCTCCAGAGACGGGATGGGATGGGCTGTCTGGAGTTTGATGAGGAGCGAGCCCTGCAG
GAGGACGCATTAGCCCAACAGGCCTTTGAAGAGACTCAGAGAAGGACACGAGAATTTGAAGAGAGAGACACGTCTCATCG
GGAGGAAATGGAGGTGAGAGTTTCACAGCTGCTGGCAGTAACTGACAAGAAGACAACAAGACCC
ORF - retro_cjac_4028 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.66 % |
| Parental protein coverage: | 99.45 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPA |
| P.VVPDQRSK.EN.EFF.KLSREC.IKYTGFRDRPHEERQA.FQNACRDGRSEIAFVATGTNLSLQFFPA | |
| Retrocopy | PHVVPDQRSKLEN*EFFKKLSREC*IKYTGFRDRPHEERQAYFQNACRDGRSEIAFVATGTNLSLQFFPA |
| Parental | SWQ-GEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQ |
| ..Q.GEQRQTPSREYVDLEREAGKVYLKAPMILNGVCV..KGWIDLQR.DGMGCLEFDEERA.QEDALAQ | |
| Retrocopy | GCQ>GEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVTSKGWIDLQRRDGMGCLEFDEERALQEDALAQ |
| Parental | QAFEETRRRTREFEDRDRSHREEMEVRVSQLLAVTGKKTTRP |
| QAFEET.RRTREFE.RD.SHREEMEVRVSQLLAVT.KKTTRP | |
| Retrocopy | QAFEETQRRTREFEERDTSHREEMEVRVSQLLAVTDKKTTRP |
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 | 29 .18 RPM |
| SRP051959_heart | 0 .02 RPM | 20 .68 RPM |
| SRP051959_kidney | 0 .00 RPM | 19 .50 RPM |
| SRP051959_liver | 0 .00 RPM | 14 .62 RPM |
| SRP051959_lung | 0 .00 RPM | 41 .94 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 73 .51 RPM |
| SRP051959_skeletal_muscle | 0 .04 RPM | 13 .93 RPM |
| SRP051959_spleen | 0 .02 RPM | 48 .21 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4028 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4028 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4028 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 | ENSCJAG00000016528 | 2 retrocopies |
retro_cjac_1228, retro_cjac_4028 ,
|