RetrogeneDB ID: retro_pcap_23

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_9076:32284..32812(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000008202
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSPCAG00000014202
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_pcap_23
ATGGGGAAGGTGCTATCTAAAATCTTCGGGAACAAGGAAATGCGGATCCTCATGCTGGGGCTGGACGCGGCTGGCAAGAC
CACAATCCTGTACAAGTTGAAGCTGGGCCAGTCGGTGACCACCATCCCCACCGTGGGTTTCAACGTGGAGACGGTGACTT
ACAAAAACGTCAAGTTCAACGTGTGGGATGTGGGCGGCCAGGACAAGATCCGGCCGCTCTGGCGGCATTATTACACCGGG
ACCCAAGGTCTGATCTTCGTAGTGGACTGTGCCGACCGCGACCGCATCGATGAGGCCCGCCAGGAGCTGCACCGCATTAT
CAATGACCGGGAGATGAGGGACGCCATAATCCTCATCTTCGCCAACAAGCAGGACCTGCCTGATGCCATGAAACCCCACG
AGATCCAGGAGAAACTGGGCCTGACCCGGATTCGGGACAGGAACTGGTATGTGCAGCCCTCCTGTGCCACCTCAGGGGAT
GGACTCTATGAGGGGCTCACATGGTTAACCTCTAACTACAAATCCTAA

Alignment

ORF - retro_pcap_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 92.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHY
          .FG.KEMRILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIRPLWRHY
Retrocopy IFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHY

Parental  FQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHR
          ...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.FANKQDLP.AM...EI..KLGL...R.R
Retrocopy YTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDR

Parental  NWYIQATCATSGDGLYEGLDWLSNQLRN
          NWY.Q..CATSGDGLYEGL.WL......
Retrocopy NWYVQPSCATSGDGLYEGLTWLTSNYKS

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_23 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 27 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000004509	1 retrocopy	retro_apla_4,
Bos taurus	ENSBTAG00000007725	2 retrocopies	retro_btau_1257, retro_btau_1390,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Dasypus novemcinctus	ENSDNOG00000010454	3 retrocopies	retro_dnov_2375, retro_dnov_2459, retro_dnov_26,
Dipodomys ordii	ENSDORG00000007603	4 retrocopies	retro_dord_31, retro_dord_351, retro_dord_409, retro_dord_573,
Erinaceus europaeus	ENSEEUG00000004638	4 retrocopies	retro_eeur_328, retro_eeur_660, retro_eeur_684, retro_eeur_76,
Ficedula albicollis	ENSFALG00000001088	1 retrocopy	retro_falb_2,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Nomascus leucogenys	ENSNLEG00000014137	3 retrocopies	retro_nleu_210, retro_nleu_227, retro_nleu_2929,
Otolemur garnettii	ENSOGAG00000010974	4 retrocopies	retro_ogar_2431, retro_ogar_295, retro_ogar_3353, retro_ogar_974,
Ochotona princeps	ENSOPRG00000015063	2 retrocopies	retro_opri_317, retro_opri_759,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23 ,
Pongo abelii	ENSPPYG00000000148	3 retrocopies	retro_pabe_3159, retro_pabe_849, retro_pabe_965,
Pelodiscus sinensis	ENSPSIG00000009767	1 retrocopy	retro_psin_12,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Pteropus vampyrus	ENSPVAG00000007383	1 retrocopy	retro_pvam_1324,
Rattus norvegicus	ENSRNOG00000030591	3 retrocopies	retro_rnor_1268, retro_rnor_1348, retro_rnor_1950,
Sarcophilus harrisii	ENSSHAG00000014599	3 retrocopies	retro_shar_106, retro_shar_462, retro_shar_725,
Sus scrofa	ENSSSCG00000013992	2 retrocopies	retro_sscr_429, retro_sscr_82,
Ictidomys tridecemlineatus	ENSSTOG00000009288	3 retrocopies	retro_itri_1754, retro_itri_273, retro_itri_363,
Taeniopygia guttata	ENSTGUG00000000233	1 retrocopy	retro_tgut_2,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Vicugna pacos	ENSVPAG00000003224	4 retrocopies	retro_vpac_281, retro_vpac_328, retro_vpac_6, retro_vpac_78,