RetrogeneDB ID: | retro_pcap_406 | ||
Retrocopy location | Organism: | Hyrax (Procavia capensis) | |
| Coordinates: | scaffold_70511:233..901(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AS3MT | ||
| Ensembl ID: | ENSPCAG00000000867 | ||
| Aliases: | None | ||
| Description: | arsenic (+3 oxidation state) methyltransferase [Source:HGNC Symbol;Acc:17452] |
Retrocopy-Parental alignment summary:
>retro_pcap_406
TCAAATTGTGTCTTTAACCTTATGCCTAATAAACAACAAGTGCTGCAAGAGTATATCAAGTATTGAAGCATGGTGGGAGC
TGTATTTCAGTCACATCTGTACTATCCTTGAAATGTCAGAAGAAATCATGAAACACAAAGTTTTATGGGGTGAGTGCCTC
AGTGGTGCTTTGTACTGGAAAGACCTTGCCATCCTTGCCCAGAAAAGTGGATTCTGCCACTTCCACACTTGGTCCCTGCC
AACCTGATTATGATACAGAACAAGGAAATAGAAAGAGTTGTTGGTGACAGTAGTTTTGTTTCTGCAACATTTCACCTTTT
CAAAGTCCCTAAGACAGGAACTGTCCCCAAGAAGTCAGGCTGTTCACAACGGAGGAATCACAGAACATGAAAAGGAACTA
ATATTTGATGCAAATTTCACATTTAAGGAAGGTGACCTCGTTGAAGTACATGATGAAACTGCAGCTATCTTGAAGAATTC
ACGATTTGCCCAAGATTTTCTTGATTACACGAATTAGAGAGAGGTGGCCATAATCTGGAAGTTATTCTGCTTTAGCATCA
AAGGATATCATCACAGATCCATTCAAACTTGCAGAAGACTCTCACAGCACCGAGTCCAGATGTCTCCCTGATGCTGCCGG
AGACTGCTGTTCTCCAAGGGAAAGGTGC
ORF - retro_pcap_406 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.91 % |
| Parental protein coverage: | 57.6 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | SNCVINLVPDKQQVLQE-AYRVLKHGG-ELYFSDVYGSLEMPEEIREQKALWGE-LGGALYW-KGLGILA |
| SNCV.NL.P.KQQVLQE..Y.VLKHGG.ELYFS.....LEM.EEI...K.LWGE.L.GALYW.K.L..L. | |
| Retrocopy | SNCVFNLMPNKQQVLQE<VYQVLKHGG<ELYFSHICTILEMSEEIMKHKVLWGECLSGALYW>KTLPSLP |
| Parental | QKIGFCR-PRLVTANVITIQNKEI--LVGDCRFVSATFRLFKLPKTGP-ATRSQVVYDGGIMGHEKELIF |
| .K......P.LV.AN.I.IQNKEI...VGD..FVSATF.LFK.PKTG....RSQ.V..GGI..HEKELIF | |
| Retrocopy | RKVDSAT>PHLVPANLIMIQNKEIERVVGDSSFVSATFHLFKVPKTGT>SPRSQAVHNGGITEHEKELIF |
| Parental | DANFTFTE---VEVDEETAAILKNSRFAQDFL-IKPVRERLPLSGSCSALESKDFISDPFKLAEDSHNTK |
| DANFTF.E...VEV..ETAAILKNSRFAQDFL.I...RER.P.SGS.SAL.SKD.I.DPFKLAEDSH.T. | |
| Retrocopy | DANFTFKEGDLVEVHDETAAILKNSRFAQDFL>ITRIRERWP*SGSYSALASKDIITDPFKLAEDSHSTE |
| Parental | SRCSLGVAGGCWGTKKSC |
| SRC....AG.C......C | |
| Retrocopy | SRCLPDAAGDCCSPRERC |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Procavia capensis was not studied using RNA-Seq expression data.
Procavia capensis was not studied using ChIP-Seq data.
Procavia capensis was not studied using EST data.
Procavia capensis was not studied using FANTOM5 data.
retro_pcap_406 was not experimentally validated.
Retrocopy orthology:
Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000000626 | 1 retrocopy | |
| Procavia capensis | ENSPCAG00000000867 | 1 retrocopy |
retro_pcap_406 ,
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