RetrogeneDB ID: retro_mmul_1062

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:53428319..53428752(+)
• Located in intron of: ENSMMUG00000014615

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1627
• Ensembl ID: ENSMMUG00000009381
• Aliases: None
• Description: WW domain-binding protein 2 [Source:RefSeq peptide;Acc:NP_001245028]

Sequence

>retro_mmul_1062
ACCTTTACAGCAGGGAGGACCATTGAGTTTGGACAATGGGTGCTACAGGTGGCATGTTAAGCCTCCAGAGGTAAGCCCCC
AGTGGAGGCTATAGATACTCTTACGTTCCTGGTGGGGCCTGTGCATCCCATCACCAGTTGCAATGGAATGCACTCCTGCC
CTTCTGTACTCCTATCTACCACCTCCACCTGAGTTCTATCTAGGACCTCCCATCATGGATAGGGCCATAAAACAGGTGCA
GCCCCATGGCACTGCCCTATCCTGGAGTTCTGGAACCTCCCATCAGAAGCACCAAAATTCACTCCATTCCTGCAGCCAAG
GCCAAGCAGCAGCTGCCAGAGCCTATTACAACCTGGGCAACTCACACAACATCTACATGCACATGTACCAGCCTCCACCA
CCCGCATACTACCCTCCCTGGTCTTGGAAGACT

Alignment

ORF - retro_mmul_1062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.89 %
• Parental protein coverage: 56.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TFTAGGAIEFGQRMLQVASQASRGE-APNGAYGYSYMPSGAYV-YPPPVANGMYPCPPGYPYPPPPPEFY
          TFTAG..IEFGQ..LQVA..ASRG..AP.G.Y.YSY.P.GA....P.PVA....P....Y.Y.PPPPEFY
Retrocopy TFTAGRTIEFGQWVLQVAC*ASRGK<APSGGYRYSYVPGGACA<IPSPVAMECTPALL-YSYLPPPPEFY

Parental  PGPPMMDGAMGYVQPPPP-PYPGPMEPPVSGPDVPSTPAAEAK-AAEAAASAYYNPGNPHNVYMPTSQPP
          .GPP.MD.A...VQP....PYPG..EPP.......S.PAA.AK.AA.A...AYYN.GN.HN.YM...QPP
Retrocopy LGPPIMDRAIKQVQPHGT>PYPGVLEPPIRSTKIHSIPAAKAK<AAAA--RAYYNLGNSHNIYMHMYQPP

Parental  PPPYYPPEDKKT
          PP.YYPP...KT
Retrocopy PPAYYPPWSWKT

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	152.84 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	354.68 RPM
SRP007412_cerebellum	0.06 RPM	152.98 RPM
SRP007412_heart	0.06 RPM	69.37 RPM
SRP007412_kidney	0.00 RPM	119.95 RPM
SRP007412_liver	0.04 RPM	122.79 RPM
SRP007412_testis	3.13 RPM	209.01 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1062 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1062 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1062 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_693

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004946	1 retrocopy	retro_cfam_1038,
Callithrix jacchus	ENSCJAG00000037619	1 retrocopy	retro_cjac_575,
Felis catus	ENSFCAG00000005760	1 retrocopy	retro_fcat_1454,
Homo sapiens	ENSG00000132471	1 retrocopy	retro_hsap_1926,
Gorilla gorilla	ENSGGOG00000009241	2 retrocopies	retro_ggor_1404, retro_ggor_698,
Macropus eugenii	ENSMEUG00000000070	1 retrocopy	retro_meug_579,
Macaca mulatta	ENSMMUG00000009381	2 retrocopies	retro_mmul_1062 , retro_mmul_854,
Monodelphis domestica	ENSMODG00000007725	3 retrocopies	retro_mdom_1410, retro_mdom_1847, retro_mdom_375,
Mustela putorius furo	ENSMPUG00000013775	1 retrocopy	retro_mputfur_645,
Nomascus leucogenys	ENSNLEG00000001625	1 retrocopy	retro_nleu_1214,
Ochotona princeps	ENSOPRG00000006045	2 retrocopies	retro_opri_301, retro_opri_851,
Pongo abelii	ENSPPYG00000008640	3 retrocopies	retro_pabe_693, retro_pabe_75, retro_pabe_913,
Pan troglodytes	ENSPTRG00000009660	1 retrocopy	retro_ptro_15,
Ictidomys tridecemlineatus	ENSSTOG00000021421	2 retrocopies	retro_itri_1585, retro_itri_660,