RetrogeneDB ID: retro_pabe_310

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:152806497..152807010(+)
• Located in intron of: ENSPPYG00000001227

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX5
• Ensembl ID: ENSPPYG00000003106
• Aliases: None
• Description: peroxiredoxin 5 [Source:HGNC Symbol;Acc:9355]

Sequence

>retro_pabe_310
GGGACCCACGATTTCAGCAGTACCTTTGCAGCCATGGCGCCTGTCATGGTGGGAGATGCTATCCTGGCATTAGTGGTGTT
TGAAAGGGAGCCTGGGAACAAGGTGGACCTGACAGAACTATGCCAGGGAAAGAAGGGTGTGCTGTTCAGAATCCCCGGGG
CTTCCACTCTAACTGTCAAAGACCCACCTGCTTGGGTTTGGGGAGTAGGCTGGGGCTCTGAAGGTCAAGGGGGGCCAGAT
CCATGTCTAAGTGCCTCTGTCTTTGTGTCTTTGTGACTGGTGAGTGGGGACAGGCCACAGGGCAGAAGGCCAAGGCCAGC
TCATGGGTGGCAGCCCTGGGGCCTCTGGGAAGGAGACTGATTTGTTACTAGATGATTTGCTGTTGCCACTCTTTGGGGAT
GAGAGCTTGAGAGGTTCTTCCTGGTGATAGAGGATGGTGTGGTGAAGACCTTGCCTGAGCCTGACCGTACAGGCCTCACC
TGCAGCCTGGTCCCCAGCTCCAACTCACAGGTC

Alignment

ORF - retro_pabe_310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.41 %
• Parental protein coverage: 50.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GVRSFSRAAAAMAPIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGA-FTPGCSK-THLPGFV
          G...FS...AAMAP..VGDAI.A..VFE.EPGNKV.L.EL..GKKGVLF..PGA.F...C...THL.GF.
Retrocopy GTHDFSSTFAAMAPVMVGDAILALVVFEREPGNKVDLTELCQGKKGVLFRIPGA<FHSNCQR<THLLGFG

Parental  EQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETDLLLDDSLVSIFGNR-RL
          E.A.ALK.KG.Q................G..H.AEG...L.....GA.GKETDLLLDD.L...FG....L
Retrocopy E*AGALKVKGGQIHV*VPLSLCLCDW*VGTGHRAEGQGQLMGGSPGASGKETDLLLDDLLLPLFGDE<EL

Parental  KRFSMVVQDGIVKALNVEPDGTGLTCSLAPNIISQL
          .RF..V..DG.VK.L..EPD.TGLTCSL.P...SQ.
Retrocopy ERFFLVIEDGVVKTL-PEPDRTGLTCSLVPSSNSQV

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	112.46 RPM
SRP007412_cerebellum	0.00 RPM	99.10 RPM
SRP007412_heart	0.00 RPM	62.68 RPM
SRP007412_kidney	0.00 RPM	125.69 RPM
SRP007412_liver	0.00 RPM	54.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_310 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_310 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_310 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_408
Pan troglodytes	retro_ptro_313
Gorilla gorilla	retro_ggor_404
Macaca mulatta	retro_mmul_504
Callithrix jacchus	retro_cjac_3013
Sus scrofa	retro_sscr_888
Canis familiaris	retro_cfam_1806
Equus caballus	retro_ecab_844

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017959	1 retrocopy	retro_amel_753,
Bos taurus	ENSBTAG00000008648	1 retrocopy	retro_btau_1364,
Callithrix jacchus	ENSCJAG00000018014	1 retrocopy	retro_cjac_3013,
Dasypus novemcinctus	ENSDNOG00000004647	1 retrocopy	retro_dnov_2664,
Equus caballus	ENSECAG00000017747	2 retrocopies	retro_ecab_823, retro_ecab_844,
Echinops telfairi	ENSETEG00000000264	3 retrocopies	retro_etel_1821, retro_etel_662, retro_etel_740,
Felis catus	ENSFCAG00000028856	3 retrocopies	retro_fcat_1189, retro_fcat_410, retro_fcat_727,
Homo sapiens	ENSG00000126432	1 retrocopy	retro_hsap_408,
Gorilla gorilla	ENSGGOG00000001337	1 retrocopy	retro_ggor_404,
Loxodonta africana	ENSLAFG00000025661	2 retrocopies	retro_lafr_132, retro_lafr_250,
Macaca mulatta	ENSMMUG00000013397	1 retrocopy	retro_mmul_504,
Mustela putorius furo	ENSMPUG00000012907	1 retrocopy	retro_mputfur_1360,
Nomascus leucogenys	ENSNLEG00000005003	2 retrocopies	retro_nleu_1007, retro_nleu_2228,
Procavia capensis	ENSPCAG00000010811	1 retrocopy	retro_pcap_144,
Pongo abelii	ENSPPYG00000003106	1 retrocopy	retro_pabe_310 ,
Pan troglodytes	ENSPTRG00000003835	1 retrocopy	retro_ptro_313,
Sus scrofa	ENSSSCG00000013030	2 retrocopies	retro_sscr_1041, retro_sscr_888,