RetrogeneDB ID: retro_mmul_557

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:170281791..170282325(-)
• Located in intron of: ENSMMUG00000015915

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM58A
• Ensembl ID: ENSMMUG00000011480
• Aliases: None
• Description: cyclin-related protein FAM58A [Source:RefSeq peptide;Acc:NP_001248137]

Sequence

>retro_mmul_557
TACCTGATTGCCATGTCTTCCACTTACTTGGCCGGCAAAGTGGAAGAGCAGCGCCTGCGGACTCGTGACATCATCAATGT
GTCCAACAGGTACTTCAACCCAAGCGGTGAGCCCCTGGAATTGGACTCCCACTTCTGGGAGCTCCGGGACAGCATTGTGC
AGTGTGAGCTTCTCATACTGAGAAGTATGCACTTCCAGGTCTTCCAGCATCCACACAAGTACCTGCTCCACTACCTGGTT
TCCCTCAGGAATTGGCTGAACCACCACAGCTGGCAGCAGACCCCCGTTGCCGTCACTGTCTGGGCCCTGCTGCAGGACAG
CTACCACCGGGGGCTGTGCCTCCGCTTCCAGGCCCAGCACATCGCCGTGGCGGTGCTCTACCTGGCCCTGCAGGCCTGTG
GAGTCGAGGTGCCTGCCGAGGTCGAGGCTGAGAAGCCGTGGTGGCAGGTGTTTAGTGACGACCTTACCAGGCCAATCATT
GATAATATTGTGTCTGATCTCATTCAGATTTATACTATAGACACAGAGATTCCC

Alignment

ORF - retro_mmul_557 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.94 %
• Parental protein coverage: 72.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YLIAMSSIYLAGKVEEQHLRTRDIINVSNRYFNPSGEPLELDSRFWELRDSIVQCELLMLRVLRFQVSFQ
          YLIAMSS.YLAGKVEEQ.LRTRDIINVSNRYFNPSGEPLELDS.FWELRDSIVQCELL.LR...FQV.FQ
Retrocopy YLIAMSSTYLAGKVEEQRLRTRDIINVSNRYFNPSGEPLELDSHFWELRDSIVQCELLILRSMHFQV-FQ

Parental  HPHKYLLHYLVSLKNWLNRHSWQRTPVAVTAWALLRDSYHGGLCLRFQAQHIAVAVLYLALQVYGVEVPA
          HPHKYLLHYLVSL.NWLN.HSWQ.TPVAVT.WALL.DSYH.GLCLRFQAQHIAVAVLYLALQ..GVEVPA
Retrocopy HPHKYLLHYLVSLRNWLNHHSWQQTPVAVTVWALLQDSYHRGLCLRFQAQHIAVAVLYLALQACGVEVPA

Parental  EVEAEKPWWQVFSDDLTKPIIDNIVSDLIQIYTMDTEIP
          EVEAEKPWWQVFSDDLT.PIIDNIVSDLIQIYT.DTEIP
Retrocopy EVEAEKPWWQVFSDDLTRPIIDNIVSDLIQIYTIDTEIP

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	13.22 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	30.54 RPM
SRP007412_cerebellum	0.00 RPM	11.95 RPM
SRP007412_heart	0.00 RPM	10.36 RPM
SRP007412_kidney	0.00 RPM	17.61 RPM
SRP007412_liver	0.00 RPM	23.12 RPM
SRP007412_testis	0.15 RPM	2.15 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_557 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_557 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_286

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011407	1 retrocopy	retro_cjac_1814,
Dipodomys ordii	ENSDORG00000012846	1 retrocopy	retro_dord_420,
Gorilla gorilla	ENSGGOG00000027073	2 retrocopies	retro_ggor_2302, retro_ggor_911,
Macaca mulatta	ENSMMUG00000011480	1 retrocopy	retro_mmul_557 ,
Nomascus leucogenys	ENSNLEG00000013298	2 retrocopies	retro_nleu_1493, retro_nleu_2416,
Otolemur garnettii	ENSOGAG00000033279	1 retrocopy	retro_ogar_70,