RetrogeneDB ID: | retro_cjac_1619 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 18:686527..687032(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSCJAG00000019989 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | ALKBH4 | ||
| Ensembl ID: | ENSCJAG00000016185 | ||
| Aliases: | None | ||
| Description: | alkB, alkylation repair homolog 4 (E. coli) [Source:HGNC Symbol;Acc:21900] |
Retrocopy-Parental alignment summary:
>retro_cjac_1619
GCGGCGGCGGCTGCAGCCGAGGTCCCTGAGGTCCGGGAATGCGGTTGCAAGGGCATCCGGACCTGTCTTATCTGCGAGCG
GCGGAGACCCGCCCGGCACCTGCCCGCAGCGAAAACGCACCGTTTCAGGTCCTGCTCTGACACCGGCTGGCCGCGGGCTC
AGAGGAGTCTGACTTTGAGGGCTGGGCCTTCCCCTTCCCAGGAGTGATGCTGATGACTCGGGAGGAAGAAGCCCAGTTGG
TGAGGCCCATGGACTGTGACCCCTGGAAGCTCTCCCGGTCTGCACGGAGGAAGCAGGACTATGGCCCCAAAGTCAACTTT
CGGAAACAGACGCTAAAGACCGAGGGCTTCTGCGGCCTCCCCAGCTTCAGCCGGGAGGTGGTGCGGAGGGTGGGCCTCTA
CCCCGGGGCTGGGGGCTTCTGGCCCGGCGAGCAGTGCAACCTGCACTACGCCCCGAGCTCGGCCCGGCCATCGACCCGCA
CCTGGACGACGCGTGGCTGTGGGGG
GCGGCGGCGGCTGCAGCCGAGGTCCCTGAGGTCCGGGAATGCGGTTGCAAGGGCATCCGGACCTGTCTTATCTGCGAGCG
GCGGAGACCCGCCCGGCACCTGCCCGCAGCGAAAACGCACCGTTTCAGGTCCTGCTCTGACACCGGCTGGCCGCGGGCTC
AGAGGAGTCTGACTTTGAGGGCTGGGCCTTCCCCTTCCCAGGAGTGATGCTGATGACTCGGGAGGAAGAAGCCCAGTTGG
TGAGGCCCATGGACTGTGACCCCTGGAAGCTCTCCCGGTCTGCACGGAGGAAGCAGGACTATGGCCCCAAAGTCAACTTT
CGGAAACAGACGCTAAAGACCGAGGGCTTCTGCGGCCTCCCCAGCTTCAGCCGGGAGGTGGTGCGGAGGGTGGGCCTCTA
CCCCGGGGCTGGGGGCTTCTGGCCCGGCGAGCAGTGCAACCTGCACTACGCCCCGAGCTCGGCCCGGCCATCGACCCGCA
CCTGGACGACGCGTGGCTGTGGGGG
ORF - retro_cjac_1619 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.89 % |
| Parental protein coverage: | 58.61 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | AAAAASEVPEVLRECGCKGIRTCLICERQRGGDPPWKLPPAKTHRFIYSSDTGW-AVGSEESDFEGWAFP |
| AAAAA.EVPEV.RECGCKGIRTCLICER.R...P...LP.AKTHRF...SDTGW.A.GSEESDFEGWAFP | |
| Retrocopy | AAAAAAEVPEV-RECGCKGIRTCLICERRR---PARHLPAAKTHRFRSCSDTGW<AAGSEESDFEGWAFP |
| Parental | FPGVMLIEDFVTREEEAELVRLMDCDPWKLSQSGRRKQDYGPKVNFRKQKLKTEGFCGLPSFSREVVRRM |
| FPGVML.....TREEEA.LVR.MDCDPWKLS.S.RRKQDYGPKVNFRKQ.LKTEGFCGLPSFSREVVRR. | |
| Retrocopy | FPGVML----MTREEEAQLVRPMDCDPWKLSRSARRKQDYGPKVNFRKQTLKTEGFCGLPSFSREVVRRV |
| Parental | GLYPGLEGFRPVEQCNLDYC-PERGSSIDPHLDDAWLWG |
| GLYPG..GF.P.EQCNL.Y..PE.G..IDPHLDDAWLWG | |
| Retrocopy | GLYPGAGGFWPGEQCNLHYA<PELGPAIDPHLDDAWLWG |
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 | 2 .48 RPM |
| SRP051959_heart | 0 .00 RPM | 2 .75 RPM |
| SRP051959_kidney | 0 .00 RPM | 3 .59 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .51 RPM |
| SRP051959_lung | 0 .00 RPM | 3 .35 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .79 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .49 RPM |
| SRP051959_spleen | 0 .00 RPM | 2 .29 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1619 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1619 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1619 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016185 | 1 retrocopy |
retro_cjac_1619 ,
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