RetrogeneDB ID: | retro_cjac_1135 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 13:38423086..38424155(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000006505 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CYP3A21 | ||
| Ensembl ID: | ENSCJAG00000035708 | ||
| Aliases: | CYP3A4, CYP3A21, CYPIIIA21 | ||
| Description: | Cytochrome P450 3A21 [Source:UniProtKB/Swiss-Prot;Acc:O18993] |
Retrocopy-Parental alignment summary:
>retro_cjac_1135
GTCCCTATCTTTGCCCAGTATGGAGAGGTGTTGGTGAAAAACCTGAGGCGGGAAGCAGAGAAAGGCAAGGAATCAACATG
AAAGACATCTTTGGGGCCTACAGCATGGATGTGATCACTGACACGTCATTTGGAGTGAACAACAACTCTCTCAACAATCC
ACAAGACCCCTTTGTGGAAAGCACCAAGAAGCTTTTAAGATTTGATGTTTCAGATCCATTCTTTCTCTCAATAACAATCT
TTCCATTCCTTACCCCAATTCTTGAAGCATTAAATATTTCTGTGTTTCCAAGAGATTCTACAAGTTTTTTAAGAAAATCT
ATAAAAAGGATAAAAGAAAGTCGTCTCAAAGATACACATAAGCACCGAGTGGATTTCCTTCAGCTGATGATTGACTCCCA
GAATTCGAAAGAAACTGAGTCCCACAAAGCTCTGTCTGATCTGGAGCTCATGGCCCAATCAATTATCTTCATTTTTACTG
GCTATGAAACCACCAGCAGTAGTCTTTTCTTCGTTATGTATGAACTGGCCACTCACCCTGATGTCCAGCAGAAACCGCAG
GAGGAAATTGATGCAGTTTTACCCAACAAGGCACCAGCCACCTATGATACTGTGCTACAGATGGAGTATCTTGACATGGT
GGTGAATGAAACACTCAGATTATTCCCACTTGCTATGAGACTTGAGAGGATCTGCAAAAAAGATGTTGAAATCAATGGGA
TGTTGATTCCCAAAGGGGTAGTGGTGATGAATCCAAGCTATGCTCTTCACTATGACCCAAAGTACTGGACAGAGACTGAG
AAGTTCCTCCCTGAAAGGTTCAGTAAGAATAACAAGGACAACACAGATAGCACATATACACATCCTTTAGAACTGGACCC
AGAAACTGCATTGGCATGAGGTTTGCTCTCATGAACATGGTACTTGCTCTAATCAGAGTCCTTCAGAACTTGTCCTTCAA
ACCTTGTAAAGAAATACAGATCCCCCTGAAATTATGCTTAGGAGGACTTCTTCAAACAGAAAAACCTATTGTTCTAAAGG
TTGAGTCAAGGGATGGGACTGTAAGTGGA
ORF - retro_cjac_1135 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.81 % |
| Parental protein coverage: | 70.97 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VPIIAQYGEVLVRNLRREAEKGKP-INMKDIFGAYSMDVITGTSFGVNIDSLNNPQDPFVESTKKLLRFD |
| VPI.AQYGEVLV.NLRREAEKGK..INMKDIFGAYSMDVIT.TSFGVN..SLNNPQDPFVESTKKLLRFD | |
| Retrocopy | VPIFAQYGEVLVKNLRREAEKGKE<INMKDIFGAYSMDVITDTSFGVNNNSLNNPQDPFVESTKKLLRFD |
| Parental | FLDPFFLSITIFPFLTPILEALNISMFPRDSTSFLRKSIKRIKESRLKDTHKHRVDFLQLMIDSQNSKET |
| ..DPFFLSITIFPFLTPILEALNIS.FPRDSTSFLRKSIKRIKESRLKDTHKHRVDFLQLMIDSQNSKET | |
| Retrocopy | VSDPFFLSITIFPFLTPILEALNISVFPRDSTSFLRKSIKRIKESRLKDTHKHRVDFLQLMIDSQNSKET |
| Parental | ESDKALSDLELVAQSIIFIFAGYETTSSTLSFIMYELATHPDVQQKLQEEIDAVLPNKAPATYDTVLQME |
| ES.KALSDLEL.AQSIIFIF.GYETTSS.L.F.MYELATHPDVQQK.QEEIDAVLPNKAPATYDTVLQME | |
| Retrocopy | ESHKALSDLELMAQSIIFIFTGYETTSSSLFFVMYELATHPDVQQKPQEEIDAVLPNKAPATYDTVLQME |
| Parental | YLDMVVNETLRLFPLAMRLERVCKKDVEINGVFIPKGVVVMIPSYALHYDPKYWTEPEKFLPERFSKNNK |
| YLDMVVNETLRLFPLAMRLER.CKKDVEING..IPKGVVVM.PSYALHYDPKYWTE.EKFLPERFSKNNK | |
| Retrocopy | YLDMVVNETLRLFPLAMRLERICKKDVEINGMLIPKGVVVMNPSYALHYDPKYWTETEKFLPERFSKNNK |
| Parental | DNIDP-YIYTPFGTGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLRLGGLLQTEKPIVLKV |
| DN.D...IYT.F.TGPRNCIGMRFALMNM.LALIRVLQN.SFKPCKE.QIPLKL.LGGLLQTEKPIVLKV | |
| Retrocopy | DNTDS<HIYTSFRTGPRNCIGMRFALMNMVLALIRVLQNLSFKPCKEIQIPLKLCLGGLLQTEKPIVLKV |
| Parental | EPRDGTVSG |
| E.RDGTVSG | |
| Retrocopy | ESRDGTVSG |
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 | 11 .45 RPM |
| SRP051959_heart | 0 .00 RPM | 6 .12 RPM |
| SRP051959_kidney | 0 .07 RPM | 7 .12 RPM |
| SRP051959_liver | 0 .65 RPM | 738 .28 RPM |
| SRP051959_lung | 0 .02 RPM | 9 .27 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 17 .08 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 7 .12 RPM |
| SRP051959_spleen | 0 .04 RPM | 8 .38 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1135 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1135 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1135 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 | ENSCJAG00000035708 | 1 retrocopy |
retro_cjac_1135 ,
|
| Procavia capensis | ENSPCAG00000001718 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000028864 | 1 retrocopy |