RetrogeneDB ID: retro_btau_1359

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:89213081..89213884(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000022880
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPA2
• Ensembl ID: ENSBTAG00000006225
• Aliases: None
• Description: replication protein A 32 kDa subunit [Source:RefSeq peptide;Acc:NP_001039449]

Sequence

>retro_btau_1359
CACAGTGGATTTGAAAGCTATAGCACCTCCTCTGTCGGGGGAGCCGGCAGCTACACACGGTCCCCTGGGGGCTTTGGATC
TCCGACAGCTTCCCAGGCCGAAAAGAAATCCAGACCTCGAGCTCAGCACATTTTACCCTGTACCATATCTCAGCTGCTTT
CTGCTACTCTGGTTGATGAAGTATTCAGAATTGGAAATGTTGAGATTTCACAGGTCACTATTGTGCGGATTATCAGAAAT
GCAGAGAAGGCTGCAACCAACATTGTTTACAAGATAGATGACATGACAGCTGCACCCATGGATGTTCGCCAGTGGGTTGA
CACAGATGATGCCAGTGGTGAAAACACTGTGGTCCCTCCAGAAACATATGTGAAAGTGGCTGGTCATCTGAGATCTTTCC
AGAACAAGAAAAGCCTGGTAGCCTTTAAGATCATGCCCTGGAGGATATGAATGAGTTCACCACACATACTCTGGAAGTAG
TCAATGCACACATGATGCTGAGCAAATCGAACAGCCAGCCTTCAACAGGGAGAGCGCCTATCAGCAATCCAGGAATGGGT
GAAGCTGGGAACTTCGGTGGGAACAACTTCATACCAGCAAATGGCCTCACTGTGGCCCAGAACCAGGTGCTGAATTTGTT
CAAGGCTTGCCCAAGACCTGAAGGATTGAACTTTCAGGATCTCAAGAACCAACTCCAGCACATGTCCGTAGCCTCAACCA
AGCTAGCTGTGGATTTTCTAAGCAACGAGGGACACATCTATTCCACCGTGGATGATGATCATTTTAAATCCACAGATGCA
GAA

Alignment

ORF - retro_btau_1359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.8 %
• Parental protein coverage: 99.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NSGFESYSTSSFGGAGGYTQSPGGFGSPTASQAEKKSRARAQHIVPCTISQLLSATLVDEVFRIGNVEIS
          .SGFESYSTSS.GGAG.YT.SPGGFGSPTASQAEKKSR.RAQHI.PCTISQLLSATLVDEVFRIGNVEIS
Retrocopy HSGFESYSTSSVGGAGSYTRSPGGFGSPTASQAEKKSRPRAQHILPCTISQLLSATLVDEVFRIGNVEIS

Parental  QVTIVGIIRNAEKAATNIVYKIDDMTAAPMDVRQWVDTDDASSENTVVPPETYVKVAGHLRSFQNKKSLV
          QVTIV.IIRNAEKAATNIVYKIDDMTAAPMDVRQWVDTDDAS.ENTVVPPETYVKVAGHLRSFQNKKSLV
Retrocopy QVTIVRIIRNAEKAATNIVYKIDDMTAAPMDVRQWVDTDDASGENTVVPPETYVKVAGHLRSFQNKKSLV

Parental  AFKIIP-LEDMNEFTTHILEVVNAHMMLSKSNSQPSAGRAPISNPGMGEAGNFGGNNFIPANGLTVAQNQ
          AFKI.P.LEDMNEFTTH.LEVVNAHMMLSKSNSQPS.GRAPISNPGMGEAGNFGGNNFIPANGLTVAQNQ
Retrocopy AFKIMP<LEDMNEFTTHTLEVVNAHMMLSKSNSQPSTGRAPISNPGMGEAGNFGGNNFIPANGLTVAQNQ

Parental  VLNLIKACPRPEGLNFQDLKNQLQHMSVASIKLAVDFLSNEGHIYSTVDDDHFKSTDAE
          VLNL.KACPRPEGLNFQDLKNQLQHMSVAS.KLAVDFLSNEGHIYSTVDDDHFKSTDAE
Retrocopy VLNLFKACPRPEGLNFQDLKNQLQHMSVASTKLAVDFLSNEGHIYSTVDDDHFKSTDAE

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	0.14 RPM	9.52 RPM
ERP005899_muscle	0.00 RPM	14.09 RPM
SRP017611_brain	0.05 RPM	11.42 RPM
SRP017611_kidney	0.00 RPM	15.11 RPM
SRP017611_liver	0.00 RPM	6.27 RPM
SRP030211_testis	0.00 RPM	51.42 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1359 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1359 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006225	5 retrocopies	retro_btau_1093, retro_btau_1228, retro_btau_1359 , retro_btau_406, retro_btau_633,
Callithrix jacchus	ENSCJAG00000009473	1 retrocopy	retro_cjac_225,
Homo sapiens	ENSG00000117748	2 retrocopies	retro_hsap_704, retro_hsap_815,
Gorilla gorilla	ENSGGOG00000015287	2 retrocopies	retro_ggor_599, retro_ggor_668,
Loxodonta africana	ENSLAFG00000014387	1 retrocopy	retro_lafr_519,
Macaca mulatta	ENSMMUG00000018172	2 retrocopies	retro_mmul_1081, retro_mmul_2172,
Nomascus leucogenys	ENSNLEG00000009702	3 retrocopies	retro_nleu_1409, retro_nleu_250, retro_nleu_2511,
Oryctolagus cuniculus	ENSOCUG00000016194	1 retrocopy	retro_ocun_1180,
Otolemur garnettii	ENSOGAG00000015583	2 retrocopies	retro_ogar_1838, retro_ogar_2066,
Pongo abelii	ENSPPYG00000001651	2 retrocopies	retro_pabe_523, retro_pabe_728,
Pan troglodytes	ENSPTRG00000000420	1 retrocopy	retro_ptro_566,
Pteropus vampyrus	ENSPVAG00000001449	1 retrocopy	retro_pvam_166,
Ictidomys tridecemlineatus	ENSSTOG00000004433	2 retrocopies	retro_itri_1257, retro_itri_773,
Tarsius syrichta	ENSTSYG00000010706	2 retrocopies	retro_tsyr_1184, retro_tsyr_1806,
Tursiops truncatus	ENSTTRG00000007507	1 retrocopy	retro_ttru_873,