RetrogeneDB ID: retro_btau_1364

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:109203770..109204167(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX5
• Ensembl ID: ENSBTAG00000008648
• Aliases: PRDX5, Prx V
• Description: Peroxiredoxin-5, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9BGI1]

Sequence

>retro_btau_1364
GGGATCAGTGGTTTCAGAAGCGCCCCCGTATCTGTGGTCCCATCAAGGTGGGAGCGGCCATTCAGCCGTCGGTGGTGGTG
TGTGAAGGTGAGCCTGGAACAAGTTGAACCTGGCAGAGTTCAAGGGCAAGGAGGAGGTGCAGTTTGGAGTCCTCGGGGCC
TTTACTCTCAGCACTACCTAGACCCCACTTTCCAGGGTTTGCAGGGCAGCTTGGAGCTCCAAAGGTTGAGGGGTCCAGAT
ATTGGCAGGTCTGAGGGTGAACGATGTCTTTGTGACTGAAGAGCGGGGATGAGCCCACAATGCAAAAGGCAAGGGTGGGC
TCCCTGCAGACCCCACTGGGGACTTTGGTGTTCCTGTTTGGGAATTAATGGCTCAAGAGGTGCTGCTTCTGACAGGG

Alignment

ORF - retro_btau_1364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.07 %
• Parental protein coverage: 60.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GVRGFRSAAVAMAP-IKVGDAI-PSVEVFEKEPG-NKVNLAELFKGKKGVLFGLPGAFTPGCSKT-HLPG
          G..GFRSA.V...P.IKVG.AI.PSV.V.E.EPG.NK.NLAE.FKGK..V.FG..GAFT.....T.H.PG
Retrocopy GISGFRSAPVSVVP<IKVGAAIQPSVVVCEGEPG<NKLNLAE-FKGKEEVQFGVLGAFTLSTT*T>HFPG

Parental  FVEQADALKAKG-IQVVACLTVNDVFVTEEWARAHKAEGKVRLLADPSGTFGKETDLLLDDSLLFLFG
          F..Q..A.K..G..Q..A.L.VNDVFVTEE...AH.A.GK..L.ADP.G.FG.....L.....L.L.G
Retrocopy FAGQLGAPKVEG<VQILAGLRVNDVFVTEERG*AHNAKGKGGLPADPTGDFGVPVWELMAQEVLLLTG

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
ERP005899_liver	0.00 RPM	23.72 RPM
ERP005899_muscle	0.00 RPM	69.05 RPM
SRP017611_brain	0.00 RPM	30.38 RPM
SRP017611_kidney	0.00 RPM	67.45 RPM
SRP017611_liver	0.00 RPM	101.11 RPM
SRP030211_testis	0.00 RPM	102.48 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1364 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1364 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_1041
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,