RetrogeneDB ID: retro_pcap_45

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_2394:52269..52739(+)
• Located in intron of: ENSPCAG00000013745

Retrocopy information

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

Parental gene information

• Parental gene symbol: SARNP
• Ensembl ID: ENSPCAG00000009477
• Aliases: None
• Description: SAP domain containing ribonucleoprotein [Source:HGNC Symbol;Acc:24432]

Sequence

>retro_pcap_45
GAAGAAAATGCTGACGAAAACTCACTGGGAGATGAAATACAGGAAAAACCAAAGCCCATAGAACTACCCATCAAAGAGGA
AGATCTCTGTGAGAAAACTGTCAATCTGGCAGCAGAGAAGGAAGTGGTAAAAATTAAATCTGAAATACCAAAGACTAAAA
GAATGCAGAAGAGGGCTGAACAATCCAACATACCTGTGAGTTTGGAGGGTAAGGAAGCTTCCCAGGCAGCTAGGTTTGGC
ATTTCTTCACTTCCAACAACTGAAGACACCAGGCCTATGGTCAACCTGGATAAGCGTGAGAAAAGAGTTCAAAGATTTAG
TTTGAATGCATCTTCAATCTCCGAGAAGTCTGAAGTGAAAAGAAACTGAAAAATAGGAAGGAGCAATTTGGGGTTGTCGC
TAATTCAGCTGGAACTAGAACCACAAAGGGTACAGATGCAAAAAAGAGGAAGAGAACAGAGCACTTTGGG

Alignment

ORF - retro_pcap_45 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.26 %
• Parental protein coverage: 76.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEANEEDVLGDETEEEEAKPIELPVKEEEPPEKTVDMAAEKKVVKITSEISQTERMQKRAERFNVPVSLE
          EE...E..LGDE..E...KPIELP.KEE...EKTV..AAEK.VVKI.SEI..T.RMQKRAE..N.PVSLE
Retrocopy EENADENSLGDEIQEKP-KPIELPIKEEDLCEKTVNLAAEKEVVKIKSEIPKTKRMQKRAEQSNIPVSLE

Parental  SKKAARAARSMFSSVPTKGLSSDTKPMINLDKLKERAQRFGLNVSSISRKSE-DDEKLKKRKERFGIVTS
          .K.A..AAR...SS.PT.....DT.PM.NLDK...R.QRF.LN.SSIS.KSE....KLK.RKE.FG.V..
Retrocopy GKEASQAARFGISSLPT---TEDTRPMVNLDKREKRVQRFSLNASSISEKSE<SEKKLKNRKEQFGVVAN

Parental  SVGTGTTEDTEXXXXKRAERFG
          S.GT.TT..T.....KR.E.FG
Retrocopy SAGTRTTKGTDAKKRKRTEHFG

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_45 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 21 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011769	2 retrocopies	retro_amel_1602, retro_amel_347,
Bos taurus	ENSBTAG00000020662	1 retrocopy	retro_btau_202,
Choloepus hoffmanni	ENSCHOG00000005081	5 retrocopies	retro_chof_1001, retro_chof_1749, retro_chof_410, retro_chof_705, retro_chof_93,
Callithrix jacchus	ENSCJAG00000007853	8 retrocopies	retro_cjac_1070, retro_cjac_1487, retro_cjac_1801, retro_cjac_2439, retro_cjac_2560, retro_cjac_389, retro_cjac_4139, retro_cjac_731,
Cavia porcellus	ENSCPOG00000011755	1 retrocopy	retro_cpor_1313,
Dipodomys ordii	ENSDORG00000001065	1 retrocopy	retro_dord_80,
Erinaceus europaeus	ENSEEUG00000015176	1 retrocopy	retro_eeur_549,
Homo sapiens	ENSG00000205323	1 retrocopy	retro_hsap_3882,
Gorilla gorilla	ENSGGOG00000013217	2 retrocopies	retro_ggor_2613, retro_ggor_2753,
Loxodonta africana	ENSLAFG00000015053	1 retrocopy	retro_lafr_1024,
Microcebus murinus	ENSMICG00000010902	1 retrocopy	retro_mmur_358,
Myotis lucifugus	ENSMLUG00000003565	2 retrocopies	retro_mluc_1915, retro_mluc_484,
Monodelphis domestica	ENSMODG00000028949	1 retrocopy	retro_mdom_1909,
Mustela putorius furo	ENSMPUG00000000885	1 retrocopy	retro_mputfur_617,
Mus musculus	ENSMUSG00000078427	1 retrocopy	retro_mmus_54,
Nomascus leucogenys	ENSNLEG00000017599	2 retrocopies	retro_nleu_2779, retro_nleu_569,
Otolemur garnettii	ENSOGAG00000001693	3 retrocopies	retro_ogar_1630, retro_ogar_2272, retro_ogar_2333,
Procavia capensis	ENSPCAG00000009477	2 retrocopies	retro_pcap_262, retro_pcap_45 ,
Pongo abelii	ENSPPYG00000004630	2 retrocopies	retro_pabe_3116, retro_pabe_3358,
Pan troglodytes	ENSPTRG00000029747	2 retrocopies	retro_ptro_2644, retro_ptro_2782,
Rattus norvegicus	ENSRNOG00000030520	2 retrocopies	retro_rnor_1326, retro_rnor_471,