RetrogeneDB ID: retro_pcap_88

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_5206:65408..66278(-)
• Located in intron of: ENSPCAG00000005295

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPR
• Ensembl ID: ENSPCAG00000010462
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein R [Source:HGNC Symbol;Acc:5047]

Sequence

>retro_pcap_88
GTAACAGACGGCCTGACAGATGTCATTTTATACCACCAATCAGATAGCAATGAAAAAACATACTTTTGCTCCCCTAAATA
TGAAAGGTCACAAAACAGCTGTGCAGGCAAGACGTAGGTTGGTAAAGTCAGAGTCTGGGGAAGTGTTGGACTGTTGAATG
GGCTGATCCTATTGAAGATCCTGATCGTGAGATTGTAGCAATGGGAAAATGCTGTTTGTCTGCAACCTTGTCAGTACTGT
AACAGAAGGGATTTTAGAAAAAGCATTCAGTCAATTTGGGAAACTGGAATGAGTGAACAAACTAAAAGATTATGCTTTCA
TTCATTTTGATGAGCAAGATAATGCTATCAAGGCTATGGAAGAAATGAATGGCAAAAACTTAGAAGGAGAATGTATTGAG
ATTGTGTTTGCTAAGCCAACTGATCAGAAAAGAAAAAAGAAAAGCTCAGAGGTAAGCAGCAAAAGAGTCAAGTGTATGCT
GATTACCACTCTTATGGTCCACCTTGTCTACTCCCTTCAACAAGTGGTCAAGGGTGTGGAGGTAGATGTGGTTATGGGTA
TACTCCAGATTATTAGGGATGTGAAGATCATTATAATTATTACGGCTATGATTACCATAACTATTGTGAATGTGAAGATC
CACATTATGGTTATAAAGATTTTCAAGTTATAGGTAGAGGAAGGAGTAGTAAAGGAGCAAGGGGTGCTGCTCCATTTAGA
GATTGCAGGGCTGTTCCTCCTTTTGATAGAGCTGATTATTCACAGACAGGAGGTCCTGGATCAGCAAGAGGCATTCCATG
TGTGAGAGGAGAGAAGGTGCTTAAGAACAGAGAGTTGTGGTCAGGGAAGACAGGCCAAGGCAGAGGTGGA

Alignment

ORF - retro_pcap_88 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.32 %
• Parental protein coverage: 51.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQARRRLMSGKVKVWGNVV-TVEWADPVEEPDPEVM
          .T.GL.DVILYHQ.D...K...FC...YE..............GKV.VWG.V..TVEWADP.E.PD.E..
Retrocopy VTDGLTDVILYHQSDSNEKTY-FCSPKYERSQNSCAGKT*V--GKVRVWGSVG<TVEWADPIEDPDREIV

Parental  A-KVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMNGKKIEGEEIEI
          A...K.LFV.NL..TVTE.ILEK.FS.FGKLE.V.KLKDYAF.HF.....A.KAM.EMNGK..EGE.IEI
Retrocopy A<NGKMLFVCNLVSTVTEGILEKAFSQFGKLE*VNKLKDYAFIHFDEQDNAIKAMEEMNGKNLEGECIEI

Parental  VLAKPPDKKRKERQAARQASR-STAYEDYYYHPPPRMPPPIRGRGRGGGRGGYGYPPDYYGYEDYYDDYY
          V.AKP.D.KRK.........R.S..Y.DY....PP...P...G.G..GGR.GYGY.PDY.G.ED.Y..YY
Retrocopy VFAKPTDQKRKKKSSEVSSKR<SQVYADYHSYGPPCLLPSTSGQG-CGGRCGYGYTPDY*GCEDHY-NYY

Parental  GYDYHDYRGGYEDPYYGYDDGYAVRGRGGGRGGRGAPPPPRGRGAPPPRGRAGYSQRGAPLGPPRGSRGG
          GYDYH.Y....EDP.YGY.D...V.GRG....G.....P.R...A.PP..RA.YSQ.G.P.G..RG....
Retrocopy GYDYHNY-CECEDPHYGYKD-FQVIGRGRSSKGARGAAPFRDCRAVPPFDRADYSQTGGP-GSARGIPCV

Parental  RGGPAQQQRGRGSRGARGNRGG
          RG......R...S......RGG
Retrocopy RGEKVLKNRELWSGKTGQGRGG

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_88 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000125944	1 retrocopy	retro_hsap_651,
Gorilla gorilla	ENSGGOG00000013250	1 retrocopy	retro_ggor_568,
Macaca mulatta	ENSMMUG00000010970	1 retrocopy	retro_mmul_2433,
Monodelphis domestica	ENSMODG00000016144	1 retrocopy	retro_mdom_240,
Mus musculus	ENSMUSG00000066037	1 retrocopy	retro_mmus_458,
Otolemur garnettii	ENSOGAG00000009179	1 retrocopy	retro_ogar_3144,
Procavia capensis	ENSPCAG00000010462	1 retrocopy	retro_pcap_88 ,
Pan troglodytes	ENSPTRG00000000324	1 retrocopy	retro_ptro_474,
Tupaia belangeri	ENSTBEG00000002251	1 retrocopy	retro_tbel_4256,