RetrogeneDB ID: retro_pcap_380

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_59492:309..639(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000010486
• Aliases: None
• Description: None

Sequence

>retro_pcap_380
AAAAACTTTGCCCTAGCCAAGACATGGATGTAGGAACTACACTGACAGACCAGTTACAGTGCTGTTATTGCCCTGCTGGA
AAACAAGGCTGACCTGGTCAGCAAATGCGTGGTGGAGTGTGAAGAGGACAAGGCATATGCAGATAACAGCAGCTTCTTTT
TTATGGGAACTTCAGCCAAGACAGCTATGAACATGAATGATCCCTTCCTGGTAATTGCTAAGAAGTTGCCAAAGAGTGAA
CCTCAGAATCTGGGGGGTACAGCAGGCCAAAGTCGGGGTGTGGATCTCCATGAGCAGTCTGAGCACAACAAGAGCCAGTG
TTGTAGCAAC

Alignment

ORF - retro_pcap_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.82 %
• Parental protein coverage: 51.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETFARAKTWVKELQRQASPSIVIALAGNKADLANKRMVEYEEAQAYADDNSLLFMETSAKTAMNVNDLFL
          ..FA.AKTW..EL..Q.S.S.VIAL..NKADL..K..VE.EE..AYAD..S..FM.TSAKTAMN.ND.FL
Retrocopy KNFALAKTWM*ELH*QTSYSAVIALLENKADLVSKCVVECEEDKAYADNSSFFFMGTSAKTAMNMNDPFL

Parental  AIAKKLPKSEPQNLGGTACRSRGVDLHEQSQQNKSQCCSN
          .IAKKLPKSEPQNLGGTA..SRGVDLHEQS..NKSQCCSN
Retrocopy VIAKKLPKSEPQNLGGTAGQSRGVDLHEQSEHNKSQCCSN

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_380 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879,
Dasypus novemcinctus	ENSDNOG00000016952	1 retrocopy	retro_dnov_350,
Equus caballus	ENSECAG00000023306	1 retrocopy	retro_ecab_280,
Echinops telfairi	ENSETEG00000009603	2 retrocopies	retro_etel_617, retro_etel_698,
Mus musculus	ENSMUSG00000000711	1 retrocopy	retro_mmus_2081,
Nomascus leucogenys	ENSNLEG00000017570	1 retrocopy	retro_nleu_2531,
Oryctolagus cuniculus	ENSOCUG00000013895	1 retrocopy	retro_ocun_1193,
Ochotona princeps	ENSOPRG00000007883	3 retrocopies	retro_opri_1061, retro_opri_1116, retro_opri_299,
Procavia capensis	ENSPCAG00000010486	1 retrocopy	retro_pcap_380 ,