RetrogeneDB ID: retro_sscr_1041

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:123898586..123898920(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX5
• Ensembl ID: ENSSSCG00000013030
• Aliases: None
• Description: peroxiredoxin 5 [Source:HGNC Symbol;Acc:9355]

Sequence

>retro_sscr_1041
AAGGAAGATGTGCTATTTGAAGTCCTTGGAGACTTTACCATCAGGTGTCCCTAGATTCACCCAGGGTTCGTGGAGGAGGC
TGAGGCTCTGAAGGTGGAGGAGGTAAATGTGGTGGCAGGCTGGGGTGTGAATGATGTCTCCATGACTGGTGGGAAGGGAT
GACCCATTACCAGAAAGGCAAGGGTGAACTCCCGGTTGGCTCTACTGGGGCTTCTGGGAAGGAGACACATTTGTTTCTAG
ATGATTCCTTGTCATTTCTCTTCAGGAACTGATGCCTCAAGAGATTCTGCCTGTGACAGAGAGAGGTGGAGCAAAGTCCA
TGAACAGCAGCCCA

Alignment

ORF - retro_sscr_1041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.17 %
• Parental protein coverage: 69.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKGVLFGVPGAFTPGCSKTHLPGFVEQAEALKAKGIQVVACLSVNDVFVTEMWG-RAHNTEGKVRLLADP
          K..VLF.V.G.FT..C...H.PGFVE.AEALK.....VVA...VNDV..T...G...H...GK..L....
Retrocopy KEDVLFEVLGDFTIRCP*IH-PGFVEEAEALKVEEVNVVAGWGVNDVSMTGGKG<MTHYQKGKGELPVGS

Parental  TGAFGKETDLLLDDSLVSLFGNRRLKRFSM-VIEDGIVKSLNVEP
          TGA.GKET.L.LDDSL..LF.N..LKRF...V.E.G..KS.N..P
Retrocopy TGASGKETHLFLDDSLSFLFRN*CLKRFCL<VTERGGAKSMNSSP

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
SRP014902_placenta	0.00 RPM	12.61 RPM
SRP014902_testis	0.00 RPM	43.71 RPM
SRP018288_heart	0.00 RPM	7.28 RPM
SRP018288_kidney	0.00 RPM	142.83 RPM
SRP018288_liver	0.00 RPM	116.73 RPM
SRP018288_lung	0.00 RPM	115.98 RPM
SRP018856_adipose	0.00 RPM	94.93 RPM
SRP035408_brain	0.00 RPM	108.91 RPM
SRP035408_liver	0.00 RPM	333.63 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1041 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1041 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1041 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1364
Equus caballus	retro_ecab_823

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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,