RetrogeneDB ID: retro_mmul_1992

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:176663001..176663565(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAR1
• Ensembl ID: ENSMMUG00000021225
• Aliases: None
• Description: GAR1 ribonucleoprotein homolog (yeast) [Source:HGNC Symbol;Acc:14264]

Sequence

>retro_mmul_1992
ATGTCTTTTCAGGGCGGGGATCGTGGAGGCTTTGATCCAGGTGGTGGAAGTGGCGGTTTCCACCGCGGTGGCAGCAGCAA
CCGCTTCTGAGGTGGAGGCAGCGGAAATATCAGAGGTGGCGACAGGGGAGGATTTGGACGAGGGGGTGGCCGCAGAGGCT
TTACCAGAGGCCAAGACCAAGGACCGCCAGAACGTGTAGTCTTATTAGGAGAGTTCCTGCATCCCTGGGGAGATGACATA
GTTTGTAAACGTACTACAGAAGAAAATAAGGTGCCTTATTTCAATGCTCCTTTTTACTTAGAAAAGAAAGAACAAATTGG
AAAAGTGGATGAAATATTTGGACAACTTAGAGATTTTTATTTTTCAGTTAAAATGTCAGAAAATGGGAAGGCGTCATCCT
TTAAGAAACTATAGAAGTTTTATGTAGACCCATATAAGCTGCTGCCACTGCAGAGGTTTTTACCTCGACCTCCAGGTGAG
AAAGGACCTCCAAGATGTGGTGGCAGGGGAGGCCGAGGAGGAAGAAGGGGAGGTGGCAGAGGTGGTGGCAGAAGTGGTGG
TTTT

Alignment

ORF - retro_mmul_1992 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.38 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFRGGGRGGFNRGGGGGGFNRGGSSNHFRGGSGGGGGGNFRGGGRGGFGRGGGRGGFNKGQDQGPPERV
          MSF.GG.RGGF..GGG.GGF.RGGSSN.F.GG....G.GN.RGG.RGGFGRGGGR.GF..GQDQGPPERV
Retrocopy MSFQGGDRGGFDPGGGSGGFHRGGSSNRF*GG----GSGNIRGGDRGGFGRGGGRRGFTRGQDQGPPERV

Parental  VLLGEFLH-CEDDIICKCTTHENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVKLSENMKASSFKK
          VLLGEFLH...DDI.CK.TT.ENKVPYFNAP.YLE.KEQIGKVDEIFGQLRDFYFSVK.SEN.KASSFKK
Retrocopy VLLGEFLHPWGDDIVCKRTTEENKVPYFNAPFYLEKKEQIGKVDEIFGQLRDFYFSVKMSENGKASSFKK

Parental  LQKFYIDPYKLLPLQRFLPRPPGEKGPPRGGGRGGRGGGRGGGGRGGGRGGGF
          L.KFY.DPYKLLPLQRFLPRPPGEKGPPR.GGRGGR.GGR.GGGRGGGR.GGF
Retrocopy L*KFYVDPYKLLPLQRFLPRPPGEKGPPRCGGRGGR-GGRRGGGRGGGRSGGF

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	5.49 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.25 RPM
SRP007412_cerebellum	0.00 RPM	4.13 RPM
SRP007412_heart	0.00 RPM	5.06 RPM
SRP007412_kidney	0.00 RPM	4.11 RPM
SRP007412_liver	0.00 RPM	1.98 RPM
SRP007412_testis	0.04 RPM	16.96 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1992 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1992 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1992 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004605	2 retrocopies	retro_amel_1932, retro_amel_682,
Homo sapiens	ENSG00000109534	1 retrocopy	retro_hsap_3130,
Gorilla gorilla	ENSGGOG00000008681	1 retrocopy	retro_ggor_2144,
Myotis lucifugus	ENSMLUG00000003776	1 retrocopy	retro_mluc_1866,
Macaca mulatta	ENSMMUG00000021225	1 retrocopy	retro_mmul_1992 ,
Mustela putorius furo	ENSMPUG00000008615	2 retrocopies	retro_mputfur_1491, retro_mputfur_689,
Mus musculus	ENSMUSG00000028010	1 retrocopy	retro_mmus_2012,
Nomascus leucogenys	ENSNLEG00000016578	1 retrocopy	retro_nleu_2251,
Oryctolagus cuniculus	ENSOCUG00000003901	1 retrocopy	retro_ocun_414,
Otolemur garnettii	ENSOGAG00000004693	1 retrocopy	retro_ogar_1017,
Ochotona princeps	ENSOPRG00000012089	1 retrocopy	retro_opri_1168,
Pongo abelii	ENSPPYG00000014996	1 retrocopy	retro_pabe_2586,
Pan troglodytes	ENSPTRG00000016364	1 retrocopy	retro_ptro_2119,
Tarsius syrichta	ENSTSYG00000013668	2 retrocopies	retro_tsyr_355, retro_tsyr_613,
Tursiops truncatus	ENSTTRG00000016318	1 retrocopy	retro_ttru_1539,