RetrogeneDB ID: retro_ecab_823

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:98050475..98050955(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX5
• Ensembl ID: ENSECAG00000017747
• Aliases: None
• Description: peroxiredoxin 5 [Source:HGNC Symbol;Acc:9355]

Sequence

>retro_ecab_823
CCCCTGATTGAGGAGGGAGATGCCATCCTATCAGTGTTGGCATTTGAATGGGAGCCCGGTAACAAGGTGACCCTGGTAGA
GTTCAAGGACAAGAAGGGAGGGCTGTTTGGGGTCCCTGGAGCCTTTATCCCCAACTGTTTCTGGACCCACCTGCGGAGGT
CTGTGCAGCAGGCTGGGGCTCTGAAGGCCTGGGTGATCCAAGTGGCGGCAGTTAGGAGTGTCAATGATGTCCTTGTGACT
GAAGAGTGGGGACCAGCCCATAACGTAGAAGGCAAGGCTTGGCTCTCAGCTGACCCCACGGGGGCATTTGGGAAGGAGAC
AGATTTGTTACTAGATGATTCCTTGGTGTCCCTCTTTGGGAACTGATGGCTCAAGAGGTTCTGCATGGTGATAGAGGATG
GCAGAGTGAAGTCCCTGAATGGGGAGCTGGATGGCACAGGCCTCACCTGCAGCCTGGTCTCCAGCATCCTCTGCCTGCTC

Alignment

ORF - retro_ecab_823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.94 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPIKVGDAIPSVVVFEGDPANKVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFVEQAAALKAKGVEVV
          P.I..GDAI.SV..FE..P.NKV.L.E.FK.KKG.LFGVPGAF.P.C..THL...V.QA.ALKA....V.
Retrocopy PLIEEGDAILSVLAFEWEPGNKVTLVE-FKDKKGGLFGVPGAFIPNCFWTHLRRSVQQAGALKAWVIQVA

Parental  ACLTVNDVFVTEEWGRAHNTKGKVRLLADPTGAFGKETDLLLDDSLVSLFGNRRLKRFSMVIEDGIVKSL
          A...VNDV.VTEEWG.AHN..GK..L.ADPTGAFGKETDLLLDDSLVSLFGN..LKRF.MVIEDG.VKSL
Retrocopy AVRSVNDVLVTEEWGPAHNVEGKAWLSADPTGAFGKETDLLLDDSLVSLFGN*WLKRFCMVIEDGRVKSL

Parental  NVEPDGTGLTCSLAPNIISQL
          N.E.DGTGLTCSL...I...L
Retrocopy NGELDGTGLTCSLVSSILCLL

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
SRP021940_articular_cartilage	0.00 RPM	87.36 RPM
SRP021940_cerebellum	0.05 RPM	169.09 RPM
SRP021940_embryo	0.00 RPM	79.28 RPM
SRP021940_placental_villous	0.10 RPM	264.18 RPM
SRP021940_synovial_membrane	0.03 RPM	56.99 RPM
SRP021940_testis	0.13 RPM	147.96 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_823 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_823 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_823 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1364
Sus scrofa	retro_sscr_1041

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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,