RetrogeneDB ID: retro_pcap_181

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_13918:30770..31256(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000015914
• Aliases: None
• Description: None

Sequence

>retro_pcap_181
GTAAAGAGTCAATATCCTGTGCAGGATACAGATGAATTTATTTTGCCAACTGGAGTTGATAAAACTTGGGGCAGATTTGA
ACTGATCTTCTTTACCACAGGAAGATGCTGTGTGACAAGAGCTACATTTGAGCCAATGGATGGTCTACAGTGAGGATTGA
AGGGAACCCAAAATACAGCTTGGTCTAAACCAAGAAAAGTACAGATTTTGAATATGGTGACCAGGTGAGGGGCACTTTGA
GCTAATACTCTAAGGTCTCTGCTTTGCTCTGTAGTGCATTTGGTGTCATCACTGAGGAAATCTGAGGTGCAGGGGATAGC
TTCAATATGATATCAGCTAGAATAAAGACAGATGTGTTGTCTAAATGCACAGACGGTCTTCAGAAGGACAGCACAAGGTG
GCGTAGCAGGACTGACACTTACCAGCCTCTATGCACTATATAGAAACTGGAAGCGCATGAAAGCATCCTTGACCCAACAG
TCACTC

Alignment

ORF - retro_pcap_181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.46 %
• Parental protein coverage: 77.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VDPRYLVQDTDEFILPTGANKTRGRFELAFFTIGGCCMTGAAFGALNGLRLGLKETQNMAWSKPRNVQIL
          V...Y.VQDTDEFILPTG..KT.GRFEL.FFT.G.CC.T.A.F....GL..GLK.TQN.AWSKPR.VQIL
Retrocopy VKSQYPVQDTDEFILPTGVDKTWGRFELIFFTTGRCCVTRATFEPMDGLQ*GLKGTQNTAWSKPRKVQIL

Parental  NMVTRQGALWANTLGSL-ALLYSAFGVIIEKTRGAEDDLNTVAAGTMTGMLYKCPGGL-RGIARGGIAGL
          NMVTR.GAL.ANTL.SL.ALL.SAFGVI.E...GA.D..N...A...T..L.KC..GL.R..A.GG.AGL
Retrocopy NMVTR*GAL*ANTLRSL<ALLCSAFGVITEEI*GAGDSFNMISARIKTDVLSKCTDGL>RRTAQGGVAGL

Parental  TLTSLYALYNNWEHMKGSLIQQSL
          TLTSLYALY.NW..MK.SL.QQSL
Retrocopy TLTSLYALYRNWKRMKASLTQQSL

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_181 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 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007501	1 retrocopy	retro_amel_1488,
Canis familiaris	ENSCAFG00000029477	1 retrocopy	retro_cfam_329,
Choloepus hoffmanni	ENSCHOG00000007073	1 retrocopy	retro_chof_797,
Callithrix jacchus	ENSCJAG00000013336	1 retrocopy	retro_cjac_2965,
Cavia porcellus	ENSCPOG00000019917	2 retrocopies	retro_cpor_1013, retro_cpor_321,
Monodelphis domestica	ENSMODG00000002661	2 retrocopies	retro_mdom_1202, retro_mdom_860,
Mus musculus	ENSMUSG00000013701	1 retrocopy	retro_mmus_2,
Oryctolagus cuniculus	ENSOCUG00000000525	1 retrocopy	retro_ocun_73,
Otolemur garnettii	ENSOGAG00000015393	1 retrocopy	retro_ogar_2627,
Ochotona princeps	ENSOPRG00000005255	2 retrocopies	retro_opri_520, retro_opri_920,
Procavia capensis	ENSPCAG00000015914	1 retrocopy	retro_pcap_181 ,
Rattus norvegicus	ENSRNOG00000019811	3 retrocopies	retro_rnor_1804, retro_rnor_225, retro_rnor_661,
Sorex araneus	ENSSARG00000010335	1 retrocopy	retro_sara_86,
Sus scrofa	ENSSSCG00000025276	1 retrocopy	retro_sscr_404,
Ictidomys tridecemlineatus	ENSSTOG00000007041	1 retrocopy	retro_itri_1043,