RetrogeneDB ID: retro_pabe_2711

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:182191802..182192318(+)
• Located in intron of: ENSPPYG00000016120

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX2
• Ensembl ID: ENSPPYG00000009607
• Aliases: None
• Description: Peroxiredoxin-2 [Source:UniProtKB/Swiss-Prot;Acc:Q5RC63]

Sequence

>retro_pabe_2711
CTCGGAAAGCCAGCCCCTGACTTCAAGGCCACTGCCCTGGTGGGTGGCGCCTTCCAGGAGGTGAAGCTGTGGGCTACAAA
GGGAGGTACCTCGTCCTCTTTTTCTACCCTCTGGACTTCACTTTTCTGTGGCCCATGGAGAACATCGCGTTCAGCAACCA
TGCCGAGGATTTCCGCAAGCTGGGCTGCGAAGTGCTGGGTGTCTCGGTGGACTCAGTTCACCCACCTGGCTTGGATCAAC
AACCCCCAGAAGTAGGGAGGCTTGGGCCCCCGAGCATCCCCCACCCGCTGATGTGACGGGAAGCTTGTCTGAGGATTACT
GTGTGCTGAAAACCAATGAGGGCATTGCCTACCCTGCCTCTTTATCGTCGATGGCAAGGGTGACTTTTGCCAGATCACTG
TTAATGATTTGCCTGTGGGGTGCTCCATGGATGAGGCTCTGCAGCTGGTCCAGGCCTTCCAGTACACAGACGAGCACGGG
GAGGTTTGTCCCACTGGCTGGAAGCCTGGTAGCGAC

Alignment

ORF - retro_pabe_2711 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 87.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  IGKPAPDFKATAVVDGAFKEVKL-SDYKGKYVVLFFYPLDFTFVCPTEIIAFSNRAED-FHKLGCEVLG-
          .GKPAPDFKATA.V.GAF.EVKL...YKG.Y.VLFFYPLDFTF..P.E.IAFSN.AED.F...G....G.
Retrocopy LGKPAPDFKATALVGGAFQEVKL<VGYKGRYLVLFFYPLDFTFLWPMENIAFSNHAED<FPQAGLRSAG<

Parental  VSVDSQFTHLAWINTPRKEGGL-GPLNI-PLLADVTRRLSEDYGVLKTDEGIAYRG-LFIIDGKGVLRQI
          VS...QFTHLAWIN.P.K.GGL.GP..I.P..ADVT..LSEDY.VLKT.EGIAY...LFI.DGKG...QI
Retrocopy VSRWTQFTHLAWINNPQK*GGL<GPPSI<PPPADVTGSLSEDYCVLKTNEGIAYPA<LFIVDGKGDFCQI

Parental  TVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPGSD
          TVNDLPVG.S.DEAL.LVQAFQYTDEHGEVCP.GWKPGSD
Retrocopy TVNDLPVGCSMDEALQLVQAFQYTDEHGEVCPTGWKPGSD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	125.73 RPM
SRP007412_cerebellum	0.49 RPM	85.85 RPM
SRP007412_heart	0.06 RPM	96.96 RPM
SRP007412_kidney	0.07 RPM	92.78 RPM
SRP007412_liver	0.12 RPM	47.95 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2711 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2711 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2711 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3278
Pan troglodytes	retro_ptro_2217
Callithrix jacchus	retro_cjac_1795

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012307	3 retrocopies	retro_amel_1188, retro_amel_1710, retro_amel_55,
Canis familiaris	ENSCAFG00000017163	3 retrocopies	retro_cfam_1603, retro_cfam_1624, retro_cfam_1739,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
Callithrix jacchus	ENSCJAG00000004882	4 retrocopies	retro_cjac_1269, retro_cjac_1795, retro_cjac_2356, retro_cjac_2392,
Dipodomys ordii	ENSDORG00000009005	1 retrocopy	retro_dord_176,
Felis catus	ENSFCAG00000000473	1 retrocopy	retro_fcat_1755,
Homo sapiens	ENSG00000167815	3 retrocopies	retro_hsap_1184, retro_hsap_3278, retro_hsap_3500,
Gorilla gorilla	ENSGGOG00000025089	3 retrocopies	retro_ggor_2366, retro_ggor_2833, retro_ggor_923,
Macaca mulatta	ENSMMUG00000005689	2 retrocopies	retro_mmul_1780, retro_mmul_2061,
Monodelphis domestica	ENSMODG00000006978	1 retrocopy	retro_mdom_1770,
Mustela putorius furo	ENSMPUG00000004591	2 retrocopies	retro_mputfur_28, retro_mputfur_660,
Mus musculus	ENSMUSG00000005161	2 retrocopies	retro_mmus_2403, retro_mmus_472,
Nomascus leucogenys	ENSNLEG00000012800	2 retrocopies	retro_nleu_2110, retro_nleu_2883,
Otolemur garnettii	ENSOGAG00000024998	2 retrocopies	retro_ogar_1993, retro_ogar_244,
Pongo abelii	ENSPPYG00000001411	1 retrocopy	retro_pabe_3409,
Pongo abelii	ENSPPYG00000002700	1 retrocopy	retro_pabe_1906,
Pongo abelii	ENSPPYG00000009607	3 retrocopies	retro_pabe_2711 , retro_pabe_2892, retro_pabe_988,
Pan troglodytes	ENSPTRG00000010541	3 retrocopies	retro_ptro_2217, retro_ptro_2372, retro_ptro_812,
Rattus norvegicus	ENSRNOG00000003520	2 retrocopies	retro_rnor_2288, retro_rnor_497,
Sorex araneus	ENSSARG00000000146	1 retrocopy	retro_sara_96,
Sarcophilus harrisii	ENSSHAG00000015596	1 retrocopy	retro_shar_305,
Sus scrofa	ENSSSCG00000013736	2 retrocopies	retro_sscr_155, retro_sscr_962,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842,