RetrogeneDB ID: retro_mmul_1081

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:98983341..98984148(+)
• Located in intron of: ENSMMUG00000016737

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9948
• Ensembl ID: ENSMMUG00000018172
• Aliases: None
• Description: replication protein A 32 kDa subunit [Source:RefSeq peptide;Acc:NP_001247563]

Sequence

>retro_mmul_1081
ATGTGGGACAGTGGATTTGAAAGCTATGGCAGCTCCTCATAGGGGAGTCAGCGAATACACGCAGTTCCCGGGAGGCTTTG
GATCGTGGACACCTTCTTAAGCAGAAAAGAAATCAAGAGCCCGAGTACAGCACATTGAACCCCACACTGTATCTCCGATG
CTTTCTGTCACTTTGGTTGATGAAGTGTTCAAAATTGGCAGTGTTGAGATTTCACAAGTCGCTCTTGTGGGGATCATCAG
ACATGCAGAGAAGGCTTCAACCAACATTGTTTACAAAATAGATGACATGACAGCTACACCCATGGATGTTCGCCAGTGGG
TTGACACAGATGACACCAGCAGTGAAAACACTGTAGTTCCTCCAGAAACATATGTGAAAGTGGCAGGCCACCTGAGATCT
TTTCAGAACAAAAAGAGCCTGGTAGCTTTAAGATCATGTCCCTGGAGGATATGAATGAGTTCACCATACATATTCTGGAA
GTGATCAATGCACACATGATACTAAGCAAAGCGAACAGCCAGCCCTCAGCAGGGAGAGCACCTATCAGCAATCCAGGGAA
GAGTGAAGCAGGGTACTTTGGTGGGAATAGCTTCATGCCAGCAAATGGCCTCACTGTGGCCCAAAACCAGGTGTTGAATT
TGATTAAGGCTTGCCCAAGACCTGAAGGATTGAACTTTCAGGATCTCAAGAACCAGATCAAATGCATGTCTGTATCCTCA
ATCAAGCAAGCTATGGATTTTCTGAGCAATAAGGGGCACATCTATTCTACTGTGGATGATGGTCATTTTAAATCCACAGA
TGCAGAA

Alignment

ORF - retro_mmul_1081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MWNSGFESYGSSS-YGGAGGYTQSPGGFGSPAPSQAEKKSRARAQHIVPCTISQLLSATLVDEVFRIGNV
          MW.SGFESYG.SS...G...YTQ.PGGFGS..PS.AEKKSRAR.QHI.P.T.S..LS.TLVDEVF.IG.V
Retrocopy MWDSGFESYG-SS>HRGVSEYTQFPGGFGSWTPS*AEKKSRARVQHIEPHTVSPMLSVTLVDEVFKIGSV

Parental  EISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDASSENTVVPPETYVKVAGHLRSFQNKK
          EISQV..VGIIRHAEKA.TNIVYKIDDMTA.PMDVRQWVDTDD.SSENTVVPPETYVKVAGHLRSFQNKK
Retrocopy EISQVALVGIIRHAEKASTNIVYKIDDMTATPMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKK

Parental  SLVA-FKIMPLEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPGMSEAGNFGGNSFLPANGLTVA
          SLVA.FKIM.LEDMNEFT.HILEVINAHM.LSKANSQPSAGRAPISNPG.SEAG.FGGNSF.PANGLTVA
Retrocopy SLVA<FKIMSLEDMNEFTIHILEVINAHMILSKANSQPSAGRAPISNPGKSEAGYFGGNSFMPANGLTVA

Parental  QNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDHFKSTDAE
          QNQVLNLIKACPRPEGLNFQDLKNQ.K.MSVSSIKQA.DFLSN.GHIYSTVDD.HFKSTDAE
Retrocopy QNQVLNLIKACPRPEGLNFQDLKNQIKCMSVSSIKQAMDFLSNKGHIYSTVDDGHFKSTDAE

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	0.00 RPM	11.21 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.25 RPM
SRP007412_cerebellum	0.00 RPM	15.76 RPM
SRP007412_heart	0.00 RPM	9.95 RPM
SRP007412_kidney	0.00 RPM	15.02 RPM
SRP007412_liver	0.04 RPM	7.76 RPM
SRP007412_testis	0.00 RPM	41.16 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1081 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1081 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1081 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_815
Pan troglodytes	retro_ptro_566
Gorilla gorilla	retro_ggor_668
Pongo abelii	retro_pabe_728

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 26 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,
Tursiops truncatus	ENSTTRG00000007507	1 retrocopy	retro_ttru_873,