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 symbol: AS3MT
• Ensembl ID: ENSPCAG00000000867
• Aliases: None
• Description: arsenic (+3 oxidation state) methyltransferase [Source:HGNC Symbol;Acc:17452]

Sequence

>retro_pcap_406
TCAAATTGTGTCTTTAACCTTATGCCTAATAAACAACAAGTGCTGCAAGAGTATATCAAGTATTGAAGCATGGTGGGAGC
TGTATTTCAGTCACATCTGTACTATCCTTGAAATGTCAGAAGAAATCATGAAACACAAAGTTTTATGGGGTGAGTGCCTC
AGTGGTGCTTTGTACTGGAAAGACCTTGCCATCCTTGCCCAGAAAAGTGGATTCTGCCACTTCCACACTTGGTCCCTGCC
AACCTGATTATGATACAGAACAAGGAAATAGAAAGAGTTGTTGGTGACAGTAGTTTTGTTTCTGCAACATTTCACCTTTT
CAAAGTCCCTAAGACAGGAACTGTCCCCAAGAAGTCAGGCTGTTCACAACGGAGGAATCACAGAACATGAAAAGGAACTA
ATATTTGATGCAAATTTCACATTTAAGGAAGGTGACCTCGTTGAAGTACATGATGAAACTGCAGCTATCTTGAAGAATTC
ACGATTTGCCCAAGATTTTCTTGATTACACGAATTAGAGAGAGGTGGCCATAATCTGGAAGTTATTCTGCTTTAGCATCA
AAGGATATCATCACAGATCCATTCAAACTTGCAGAAGACTCTCACAGCACCGAGTCCAGATGTCTCCCTGATGCTGCCGG
AGACTGCTGTTCTCCAAGGGAAAGGTGC

Alignment

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

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_406 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000000626	1 retrocopy	retro_ocun_1111,
Procavia capensis	ENSPCAG00000000867	1 retrocopy	retro_pcap_406 ,