RetrogeneDB ID: retro_mmul_2636

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:128942929..128943251(-)
• Located in intron of: ENSMMUG00000013162

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.13094
• Ensembl ID: ENSMMUG00000001613
• Aliases: None
• Description: thioredoxin-like protein 4A [Source:RefSeq peptide;Acc:NP_001247795]

Sequence

>retro_mmul_2636
CAAAAAGACAGAGGCATCATCATTTGGTTTGGACATAACTGAGACCCTGCTTTTATGAATATGAATTAGTTCTATATTGT
ATAGCTGAAAAGGTTAAAAATGTTTTAGTTATTTATCTTGATATTACAGAAGTACTTTACTTCAACAAAAATGTATGAGT
TTTTATGATCTATGTATTGTCATATTTTTCTCTGGGAACAAGCACATCATGATTTTGACTTGAGTACTGGCAACAACAAG
ATTAACTGGGCCACAGAAGGACAAACAGGAGATGGTCAACGTAATAGAGACTGTGTATTGAGGTCCCCGCAAAGAACGAG
GT

Alignment

ORF - retro_mmul_2636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.76 %
• Parental protein coverage: 76.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEDRVVVIRFGHDWDPTCMKM-DEVLYSIAEKVKNFAVIYLVDITEVPDFNK-MYEL-YDPCTVMFFFRN
          ..DR...I.FGH..DP..M.M...VLY.IAEKVKN..VIYL.DITEV..FNK.MYE..YD.C.V.FF..N
Retrocopy QKDRGIIIWFGHN*DPAFMNM<ELVLYCIAEKVKNVLVIYL-DITEVLYFNK>MYEF>YDLCIVIFFSGN

Parental  KHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRG
          KHIMI...............DKQEMV..IETVY.G.RK.RG
Retrocopy KHIMILT*VLATTRLTGPQKDKQEMVNVIETVY*GPRKERG

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	19.16 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	36.10 RPM
SRP007412_cerebellum	0.00 RPM	16.14 RPM
SRP007412_heart	0.00 RPM	11.19 RPM
SRP007412_kidney	0.00 RPM	17.02 RPM
SRP007412_liver	0.00 RPM	13.10 RPM
SRP007412_testis	0.00 RPM	10.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2636 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2636 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4900
Gorilla gorilla	retro_ggor_3060

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010130	2 retrocopies	retro_cjac_2805, retro_cjac_3659,
Homo sapiens	ENSG00000141759	2 retrocopies	retro_hsap_2185, retro_hsap_4900,
Gorilla gorilla	ENSGGOG00000005285	2 retrocopies	retro_ggor_1731, retro_ggor_3060,
Loxodonta africana	ENSLAFG00000003190	1 retrocopy	retro_lafr_198,
Myotis lucifugus	ENSMLUG00000009188	1 retrocopy	retro_mluc_562,
Macaca mulatta	ENSMMUG00000001613	2 retrocopies	retro_mmul_2636 , retro_mmul_913,
Nomascus leucogenys	ENSNLEG00000008378	2 retrocopies	retro_nleu_1268, retro_nleu_314,
Otolemur garnettii	ENSOGAG00000034753	1 retrocopy	retro_ogar_1751,
Pan troglodytes	ENSPTRG00000010136	1 retrocopy	retro_ptro_1663,
Rattus norvegicus	ENSRNOG00000017596	2 retrocopies	retro_rnor_1358, retro_rnor_2458,
Ictidomys tridecemlineatus	ENSSTOG00000022277	1 retrocopy	retro_itri_1063,
Tarsius syrichta	ENSTSYG00000009428	1 retrocopy	retro_tsyr_240,