RetrogeneDB ID: retro_mmul_1650

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:179982440..179982749(+)
• Located in intron of: ENSMMUG00000011188

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC5L
• Ensembl ID: ENSMMUG00000020628
• Aliases: None
• Description: Actin-related protein 2/3 complex subunit 5 [Source:UniProtKB/TrEMBL;Acc:F7BM58]

Sequence

>retro_mmul_1650
GGAAACATGACAGCTGCCCTACAGGCAGCTCTGAAGAACCTCCCCATCAACACCAAGAGTCAGGCCGTGAAGGACCGGGC
AGGCAGCATTGTGTTGAAGGTGCTCATCTCTTTTAAAGCTAATGATATTGAAAAGGCAGTTCAATCTCTGGACAAGAATG
GTGTGGATCTCCTAATGAAGTGTATTTATAAAGGATTTGGGAGCCCCTCTGACAATAGCAGTGCTGTGTTACTGCAATGG
CATGAAAAGTCACTTGCTGCTGGAGGAGTAGGGTCCATTGTTCGTGTCTTGACTGCAAGAAAAACCGTG

Alignment

ORF - retro_mmul_1650 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.84 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDMLRAFHAALRNSPVNTKNQAVKERAQGVVLKVLTNFKSSEIEQAVQSLDRNGVDLLMKYIYKGFEKPT
          G.M..A..AAL.N.P.NTK.QAVK.RA...VLKVL..FK...IE.AVQSLD.NGVDLLMK.IYKGF..P.
Retrocopy GNMTAALQAALKNLPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKCIYKGFGSPS

Parental  ENSSAVLLQWHEKALAVGGLGSIIRVLTARKTV
          .NSSAVLLQWHEK.LA.GG.GSI.RVLTARKTV
Retrocopy DNSSAVLLQWHEKSLAAGGVGSIVRVLTARKTV

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	3.14 RPM	43.48 RPM
SRP007412_brain_prefrontal_cortex	5.39 RPM	44.82 RPM
SRP007412_cerebellum	1.61 RPM	23.44 RPM
SRP007412_heart	2.30 RPM	22.67 RPM
SRP007412_kidney	4.11 RPM	16.55 RPM
SRP007412_liver	3.76 RPM	9.46 RPM
SRP007412_testis	1.77 RPM	119.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1650 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1650 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1650 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016540	1 retrocopy	retro_amel_1798,
Callithrix jacchus	ENSCJAG00000006730	4 retrocopies	retro_cjac_1282, retro_cjac_1725, retro_cjac_2744, retro_cjac_3941,
Felis catus	ENSFCAG00000028753	1 retrocopy	retro_fcat_1316,
Macaca mulatta	ENSMMUG00000020628	2 retrocopies	retro_mmul_1650 , retro_mmul_623,
Mustela putorius furo	ENSMPUG00000013924	1 retrocopy	retro_mputfur_1532,
Oryctolagus cuniculus	ENSOCUG00000002997	1 retrocopy	retro_ocun_518,
Procavia capensis	ENSPCAG00000013936	1 retrocopy	retro_pcap_274,
Pan troglodytes	ENSPTRG00000021362	1 retrocopy	retro_ptro_2185,
Rattus norvegicus	ENSRNOG00000014317	1 retrocopy	retro_rnor_2730,
Ictidomys tridecemlineatus	ENSSTOG00000007907	2 retrocopies	retro_itri_275, retro_itri_767,
Tupaia belangeri	ENSTBEG00000008398	1 retrocopy	retro_tbel_442,