RetrogeneDB ID: retro_mmul_858

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:38993168..38993510(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM173B
• Ensembl ID: ENSMMUG00000020111
• Aliases: None
• Description: None

Sequence

>retro_mmul_858
CTGTATGCTGTAGCTATGCCATTTATAGCACCAATCCTCTGAGAAGTCTGTTTGCCTTTTGTACCTGCAACTACAAAGCA
GATCAAAAATGTGAAAATGTTGCTATGCAGAGGAGGATCCCTGGTAGACATTGGTAATGGCGATGGACACATTAATAACA
CAGTAATAGCAGCTGCAAAGCAAAGATTCACAGCAGTTGGTTGTGAATTAAATCAGTGGCTAGTTTGGTATTCCAAGTAT
CATGCTTGGCAAGAAAGTGTGCATGACTCTGCCAAATTTTATATTTCAGATTTGTGGGCAGTTACTTTTTCATAGTACTC
AAACACTGTTATTTTTGGTGTG

Alignment

ORF - retro_mmul_858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.52 %
• Parental protein coverage: 50.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VYAVATPFITPALRKVCLPFVPATTKQIENVVKMLQCRRGSLVDIGSGDGRI---VIAAAKEGFTAVGYE
          .YAVA.PFI.P.L..VCLPFVPATTKQI.NV.KML.CR.GSLVDIG.GDG.I...VIAAAK..FTAVG.E
Retrocopy LYAVAMPFIAPIL*EVCLPFVPATTKQIKNV-KMLLCRGGSLVDIGNGDGHINNTVIAAAKQRFTAVGCE

Parental  LNPWLVWYSRYRAWREGVHGSAKFYISDLWKVTFSQYSNVVIFGV
          LN.WLVWYS.Y.AW.E.VH.SAKFYISDLW.VTFS.YSN.VIFGV
Retrocopy LNQWLVWYSKYHAWQESVHDSAKFYISDLWAVTFS*YSNTVIFGV

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	3.36 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.13 RPM
SRP007412_cerebellum	0.00 RPM	2.91 RPM
SRP007412_heart	0.00 RPM	1.88 RPM
SRP007412_kidney	0.00 RPM	1.41 RPM
SRP007412_liver	0.00 RPM	1.43 RPM
SRP007412_testis	0.00 RPM	3.69 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_858 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_858 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_858 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002277	1 retrocopy	retro_dnov_1076,
Homo sapiens	ENSG00000150756	1 retrocopy	retro_hsap_1105,
Macaca mulatta	ENSMMUG00000020111	1 retrocopy	retro_mmul_858 ,
Nomascus leucogenys	ENSNLEG00000011587	1 retrocopy	retro_nleu_198,
Oryctolagus cuniculus	ENSOCUG00000025588	1 retrocopy	retro_ocun_1244,
Pan troglodytes	ENSPTRG00000016724	1 retrocopy	retro_ptro_692,