RetrogeneDB ID: retro_pcap_144

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_110432:929..1261(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX5
• Ensembl ID: ENSPCAG00000010811
• Aliases: None
• Description: peroxiredoxin 5 [Source:HGNC Symbol;Acc:9355]

Sequence

>retro_pcap_144
TTTATGCTAGGTTGTTCTGAGACCCACATACCAAAGTTTGTGGAACAGCCTGGAGCTCTGCAGGCCCACGGGTCCAGGTG
GTCTGAGCAGCAGTGAGTGACTTCTCTGTGACTGCTGAGTGGGGGCAAGCTCACAACGCAGAAAGCAAGGATCTGCTCCT
GGCTATATACACTCAGGCCTTTGGGAAAGAGACAGATTTGTTGCTAGGTGATTTGTTGGTATTACTGCTAGGGAACTGAT
AGCTCCACAGTTTTTCCATGATGATAGAAAGCATGGTAAAGACTTTCAACATGGAGCCAGAGGTTAAAGGCATCACCTGC
AGCCTGGTCCCC

Alignment

ORF - retro_pcap_144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.89 %
• Parental protein coverage: 51.83 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FTPGCSKTHLPGYVEQAGDLKAKGA-QVVACLTVNDVFVTDEWGKAHHAEGKVRLLADPTGAFGKETDLL
          F..GCS.TH.P..VEQ.G.L.A.G..QVV....V.D..VT.EWG.AH.AE.K..LLA..T.AFGKETDLL
Retrocopy FMLGCSETHIPKFVEQPGALQAHGS<QVV*A-AVSDFSVTAEWGQAHNAESKDLLLAIYTQAFGKETDLL

Parental  LDDSLVPLFGNQRLKRFSMVIEDGVVKALNVEPDGTGLTCSLAP
          L.D.LV.L.GN..L..FSM.IE...VK..N.EP...G.TCSL.P
Retrocopy LGDLLVLLLGN**LHSFSMMIE-SMVKTFNMEPEVKGITCSLVP

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_144 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 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017959	1 retrocopy	retro_amel_753,
Bos taurus	ENSBTAG00000008648	1 retrocopy	retro_btau_1364,
Callithrix jacchus	ENSCJAG00000018014	1 retrocopy	retro_cjac_3013,
Dasypus novemcinctus	ENSDNOG00000004647	1 retrocopy	retro_dnov_2664,
Equus caballus	ENSECAG00000017747	2 retrocopies	retro_ecab_823, retro_ecab_844,
Echinops telfairi	ENSETEG00000000264	3 retrocopies	retro_etel_1821, retro_etel_662, retro_etel_740,
Felis catus	ENSFCAG00000028856	3 retrocopies	retro_fcat_1189, retro_fcat_410, retro_fcat_727,
Homo sapiens	ENSG00000126432	1 retrocopy	retro_hsap_408,
Gorilla gorilla	ENSGGOG00000001337	1 retrocopy	retro_ggor_404,
Loxodonta africana	ENSLAFG00000025661	2 retrocopies	retro_lafr_132, retro_lafr_250,
Macaca mulatta	ENSMMUG00000013397	1 retrocopy	retro_mmul_504,
Mustela putorius furo	ENSMPUG00000012907	1 retrocopy	retro_mputfur_1360,
Nomascus leucogenys	ENSNLEG00000005003	2 retrocopies	retro_nleu_1007, retro_nleu_2228,
Procavia capensis	ENSPCAG00000010811	1 retrocopy	retro_pcap_144 ,
Pongo abelii	ENSPPYG00000003106	1 retrocopy	retro_pabe_310,
Pan troglodytes	ENSPTRG00000003835	1 retrocopy	retro_ptro_313,
Sus scrofa	ENSSSCG00000013030	2 retrocopies	retro_sscr_1041, retro_sscr_888,