RetrogeneDB ID: | retro_cjac_433 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:81750641..81751275(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RTDR1 | ||
| Ensembl ID: | ENSCJAG00000009770 | ||
| Aliases: | None | ||
| Description: | rhabdoid tumor deletion region gene 1 [Source:HGNC Symbol;Acc:13437] |
Retrocopy-Parental alignment summary:
>retro_cjac_433
CAAACCCTGAAGATTTACACTGGGGCTGAAGAAACCATCAGCAAAGGCTGATCTCCCCGCTGGTATGAAGCTGCAGGGCA
AGTGGAGGAGGAGTTCCAGGAGCTCATCCTAGACACTCTGGTGCTCTGCCTGTGGGAAGATGCCACCAAGGCCCTGAATA
GCAACGTGGTGCCCATCCTGAAGCAGAAGCTCATCAGCACCAACGAGAACATCCGAAGCAAGGCTGCTGGTGCGCTCCTT
AATGTCAGCATATCTCGTGTGGGCAAGAAACAGGTGTGTCAGTTTGACGTCATCCCCATCTGGTGCATCTACCGAAAGAC
CCAGTGGACCATGTGAGGTCTAACGCTGCTGGGGCCTTGATGTTCGCCACGGTGATCACCGAAGGGAATATGCGGCCCTG
GAGGCAGAAGCCATCAGCCCGCTTCTGGAGCTGCTGCATTCCCCCATGACTGTAGTGCACCTGAACGCCACCAAGGCCCT
CACCATGCTGGTGGAGGCTCCTGAGGACCGCAAGGTCCTACAGGCACATGTGCCCACCTTCCGTGCCATGGAAGTGGAGC
CTCACAAAAAGCTTCACATGGCCGAAGCCTTACAGCGGGCGGCCCGGATTGCTGTCAGTGTCATCAAGTTCAAA
ORF - retro_cjac_433 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.7 % |
| Parental protein coverage: | 61.38 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | QLVQVPRGAEEIISKG-LISPLV-WKLQG-EVEEEFQELILDTLVLCLWEDATEALNSNVVPILKQKLIS |
| Q......GAEE.ISKG.LISPLV..KLQG..VEEEFQELILDTLVLCLWEDAT.ALNSNVVPILKQKLIS | |
| Retrocopy | QTLKIYTGAEETISKG<LISPLV<MKLQG<QVEEEFQELILDTLVLCLWEDATKALNSNVVPILKQKLIS |
| Parental | TNENIRSKAARALLNVSISRVGKKQVCQFDVIPI-LVHLLKDPVEHVRSNAAGALMFALVITEG-KYAAL |
| TNENIRSKAA.ALLNVSISRVGKKQVCQFDVIPI.LVHL.KDPV.HVRSNAAGALMFA.VITEG..YAAL | |
| Retrocopy | TNENIRSKAAGALLNVSISRVGKKQVCQFDVIPI<LVHLPKDPVDHVRSNAAGALMFATVITEG<EYAAL |
| Parental | EAEAIGPLLELLHSPMTVARLNATKALTMLAEAPEGRKVLQAHVPTFRAMEVEPHEKPHIAEALQRAARI |
| EAEAI.PLLELLHSPMTV..LNATKALTML.EAPE.RKVLQAHVPTFRAMEVEPH.K.H.AEALQRAARI | |
| Retrocopy | EAEAISPLLELLHSPMTVVHLNATKALTMLVEAPEDRKVLQAHVPTFRAMEVEPHKKLHMAEALQRAARI |
| Parental | AVSVIEFK |
| AVSVI.FK | |
| Retrocopy | AVSVIKFK |
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 .04 RPM | 0 .16 RPM |
| SRP051959_heart | 0 .02 RPM | 0 .14 RPM |
| SRP051959_kidney | 0 .02 RPM | 0 .64 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .16 RPM | 0 .73 RPM |
| SRP051959_lymph_node | 0 .18 RPM | 0 .34 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 0 .04 RPM |
| SRP051959_spleen | 0 .02 RPM | 0 .08 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_433 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_433 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_433 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 | ENSCJAG00000009770 | 2 retrocopies |
retro_cjac_3818, retro_cjac_433 ,
|