RetrogeneDB ID: retro_mmul_648

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:79825653..79826238(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000020813
• Aliases: None
• Description: None

Sequence

>retro_mmul_648
GGTGGACGTTCCTCAGTCAGTGGGATTGTGGCCACTGTGTTTGGAGCAACAGGATTCCTGGGCCAATGTGTTGTCAACCA
CCTTGGACGTATGGGGTCACAGGTGATCATTCCCTATCGGTGTGATACGTATGACATCATGCACCTTCGTCCCATGGGTG
ACCTGGGCTAGCTTCTGTTTCTGGAATGGGACGCGAGAGATAAAGATTCTATCCGACGAGTAGTGGAACACAGCAATGTG
GTCATCAATCTTGTTGGATGAGACTGGGAAATCAAAAACTTTGATTTTGAGGATGTTTTTGTGAAGATCCCCCAAGCAAT
TGCTCAGGTGTCCAAGGAAGTCGAAGTTGGAAAATTCATTCATGTTTCGCATCTGAATGCGAATATTAAAAGCTCTTCTA
GGTATTTGAGAAATAAGGCTGTTGGAGAGAAAGCAGTGAGAGATGCATTTCCAGAAGCCATTATCATAAAGCTGTTGGAC
ATCTTTGGAAGAGAGGATAGATTCCTTAATTATTTTGCAAATATGTGTTGGTTTGGTGCTATACCCCTTGTTTCCTTGGG
CTGGAAGGCAGTTAAACAACCGCTA

Alignment

ORF - retro_mmul_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.1 %
• Parental protein coverage: 51.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGRSSVSGIVATVFGATGFLGRYVVNHLGRIGSQVIIPHRCDIYDTMHLRPMGDLGQLLFLEWDARDKDS
          GGRSSVSGIVATVFGATGFLG..VVNHLGR.GSQVIIP.RCD.YD.MHLRPMGDLG.LLFLEWDARDKDS
Retrocopy GGRSSVSGIVATVFGATGFLGQCVVNHLGRMGSQVIIPYRCDTYDIMHLRPMGDLG*LLFLEWDARDKDS

Parental  IRRAVEHSNVVINLIGRDWETKNFDFDDVYVKIPQAIAQVSKEAGVEKFIHVSHLNANIKSSSRYLRNKA
          IRR.VEHSNVVINL.G.DWE.KNFDF.DV.VKIPQAIAQVSKE..V.KFIHVSHLNANIKSSSRYLRNKA
Retrocopy IRRVVEHSNVVINLVG*DWEIKNFDFEDVFVKIPQAIAQVSKEVEVGKFIHVSHLNANIKSSSRYLRNKA

Parental  VGEKAVRDAFPEAIIIKPSDIFGREDRFLNSFAHLRQFVLTPLGSLSWTTVKQPV
          VGEKAVRDAFPEAIIIK..DIFGREDRFLN.FA....F...PL.SL.W..VKQP.
Retrocopy VGEKAVRDAFPEAIIIKLLDIFGREDRFLNYFANMCWFGAIPLVSLGWKAVKQPL

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	0.45 RPM	49.41 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	57.28 RPM
SRP007412_cerebellum	0.71 RPM	35.84 RPM
SRP007412_heart	0.18 RPM	86.03 RPM
SRP007412_kidney	0.12 RPM	67.02 RPM
SRP007412_liver	0.04 RPM	54.39 RPM
SRP007412_testis	0.04 RPM	37.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_648 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_648 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2585
Pan troglodytes	retro_ptro_1511
Gorilla gorilla	retro_ggor_1618
Pongo abelii	retro_pabe_1905

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000009588	1 retrocopy	retro_acar_16,
Danio rerio	ENSDARG00000070723	1 retrocopy	retro_drer_1,
Homo sapiens	ENSG00000139180	1 retrocopy	retro_hsap_2585,
Gorilla gorilla	ENSGGOG00000006076	1 retrocopy	retro_ggor_1618,
Macaca mulatta	ENSMMUG00000020813	1 retrocopy	retro_mmul_648 ,
Monodelphis domestica	ENSMODG00000018283	1 retrocopy	retro_mdom_209,
Nomascus leucogenys	ENSNLEG00000003252	1 retrocopy	retro_nleu_1520,
Otolemur garnettii	ENSOGAG00000005225	1 retrocopy	retro_ogar_2244,
Pongo abelii	ENSPPYG00000004171	1 retrocopy	retro_pabe_1905,
Pan troglodytes	ENSPTRG00000004557	1 retrocopy	retro_ptro_1511,
Ictidomys tridecemlineatus	ENSSTOG00000006504	1 retrocopy	retro_itri_543,