RetrogeneDB ID: retro_pcap_43

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_2094:60341..60835(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000009309
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WDR5
• Ensembl ID: ENSPCAG00000013476
• Aliases: None
• Description: WD repeat domain 5 [Source:HGNC Symbol;Acc:12757]

Sequence

>retro_pcap_43
CCTGAAAGCCCAAACTATGCCCTCCAGTTTACTCTCGTGGGACACACGGAAGCAGTATCATCGGTTAAGTTTAGTCCTAA
TGGAGACTGGCTAGCAAGTTCTTCTGCTGATAAACTAATTAAAATCTGGAGTGTCTATGACGGGAAACATGAGAAAACGC
TGTGTGGTCACAGTCTGGAAATATCAGATGTCTCCTGGTCATCAGATTCCAGTCGTCTTGTTTCAGCCTCAGATGATAAA
ACTCTAACGATATGGGATGTGAGATCTGGAAAATGTTTGAAAACACTAAAAGGACACAGTAATTATGTCTTTTGCTGTAA
TTTCAACCCGGCATCCAACTTGTCATTTCAGATCTTTCGATGAGAGTTGTGAAAATATGGGAGGTGAAAACAGGAAAGTG
TCTGAAGACTTTGTCTGCTCATTCTGACCCCGTCTCTGCTGTTCATTTTAATTGCAGTGGGTCCTTGATAGTATCGGGTA
GCTATGACGGTCTC

Alignment

ORF - retro_pcap_43 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.52 %
• Parental protein coverage: 54.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDS
          P..PNYAL.FTL.GHT.AVSSVKFSPNG.WLASSSADKLIKIW..YDGK.EKT..GH.L.ISDV.WSSDS
Retrocopy PESPNYALQFTLVGHTEAVSSVKFSPNGDWLASSSADKLIKIWSVYDGKHEKTLCGHSLEISDVSWSSDS

Parental  NLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSN-LIVSGSFDESVRIWDVKTGKCLKTLP
          ..LVSASDDKTL.IWDV.SGKCLKTLKGHSNYVFCCNFNP.SN.L..S......V.IW.VKTGKCLKTL.
Retrocopy SRLVSASDDKTLTIWDVRSGKCLKTLKGHSNYVFCCNFNPASN<LVISDLSMRVVKIWEVKTGKCLKTLS

Parental  AHSDPVSAVHFNRDGSLIVSSSYDGL
          AHSDPVSAVHFN..GSLIVS.SYDGL
Retrocopy AHSDPVSAVHFNCSGSLIVSGSYDGL

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_43 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 26 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011179	1 retrocopy	retro_amel_29,
Bos taurus	ENSBTAG00000047031	1 retrocopy	retro_btau_299,
Canis familiaris	ENSCAFG00000019830	1 retrocopy	retro_cfam_128,
Callithrix jacchus	ENSCJAG00000010123	1 retrocopy	retro_cjac_1,
Cavia porcellus	ENSCPOG00000014790	1 retrocopy	retro_cpor_12,
Dipodomys ordii	ENSDORG00000015010	1 retrocopy	retro_dord_7,
Equus caballus	ENSECAG00000017389	1 retrocopy	retro_ecab_82,
Echinops telfairi	ENSETEG00000015731	1 retrocopy	retro_etel_15,
Felis catus	ENSFCAG00000005712	1 retrocopy	retro_fcat_119,
Homo sapiens	ENSG00000196363	1 retrocopy	retro_hsap_11,
Gorilla gorilla	ENSGGOG00000004997	2 retrocopies	retro_ggor_171, retro_ggor_2023,
Loxodonta africana	ENSLAFG00000011192	1 retrocopy	retro_lafr_55,
Microcebus murinus	ENSMICG00000008085	1 retrocopy	retro_mmur_34,
Myotis lucifugus	ENSMLUG00000002236	1 retrocopy	retro_mluc_11,
Macaca mulatta	ENSMMUG00000014159	1 retrocopy	retro_mmul_190,
Mustela putorius furo	ENSMPUG00000012184	1 retrocopy	retro_mputfur_2,
Mus musculus	ENSMUSG00000026917	1 retrocopy	retro_mmus_132,
Nomascus leucogenys	ENSNLEG00000013472	1 retrocopy	retro_nleu_63,
Otolemur garnettii	ENSOGAG00000008960	1 retrocopy	retro_ogar_86,
Procavia capensis	ENSPCAG00000013476	1 retrocopy	retro_pcap_43 ,
Pan troglodytes	ENSPTRG00000023653	2 retrocopies	retro_ptro_18, retro_ptro_1975,
Pteropus vampyrus	ENSPVAG00000001666	1 retrocopy	retro_pvam_112,
Rattus norvegicus	ENSRNOG00000008212	1 retrocopy	retro_rnor_258,
Sus scrofa	ENSSSCG00000024912	1 retrocopy	retro_sscr_1,
Ictidomys tridecemlineatus	ENSSTOG00000015899	1 retrocopy	retro_itri_117,
Drosophila melanogaster	FBgn0040066	1 retrocopy	retro_dmel_69,