RetrogeneDB ID: retro_mmul_675

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214275152:8..830(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.310
• Ensembl ID: ENSMMUG00000008330
• Aliases: None
• Description: glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1 [Source:RefSeq peptide;Acc:NP_001244430]

Sequence

>retro_mmul_675
CCCTGGAGTTATTCAAAACAATATAGAGAAAAGAGGAAGTAGAATCTCCACTTTGAGAATGAAGATTCAGACTGGCTGAT
AACTGGAAGAAGCTCAGGTGGGAGTGCAGTTGCCGTATCGGCATTCACATGCTATGCGGCTTTAGGATCATATACAGGAG
GACTGATCAGAAATCCTGCTGCCTACTGTGGGCTTGTTGGTTTCAAACCAAGCTGTGGCTTAGTTTTCCATCATGGTCTC
ATTTCCCCGGAGAATTTGATGGATGTGCAAGGACTCTTAACCAGATATGTGGATGATGCAGCAATTGTCTTGGGTGTACT
GGCTGGACACGACCCTAAGGATTCTACCACAGTACAGGATCCTGTTAAACCATTCATGCTTCCCAGTTTGACAAATGTGA
GCAAACTATGTATAGGAATTCCAAAGGAATATCTTGTACTGGAATTATCAAGTGAAGAACCGTCTCTTTGGTCCAAAGCT
GCTGACCTCTTTGAGTCTGAGGGGATCAAAGTAACTGAAGTATCCTTTTCTCACTTCACTTATTCAATTGTCTGCTACCA
TCTATTGTGCATATCAGAAGCAGCATCAAGTATAGCAAGATTTGATGGGCTACAATATGGTCACAGATGTGACATTGATG
TGTCTACTGAAGCCATGGATGTTGCAACCAGATGAGAAGGGTTCAATGATTTTGTAAGAGGAAGAATTCTCTCAGGAAAT
GTTTTCTTGTTAACATAAAAATATGAAAATTATTTCATCAAAGCACAGAAAGTGAGATGTCTCATTGCTAATGATTTTGT
GAATGCTTTTAACTCTGGAGTA

Alignment

ORF - retro_mmul_675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.73 %
• Parental protein coverage: 52.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PWSYSKQYREKRKQNPHSKNEDSDWLITGGSSGGSAAAVSAFTCYAALGSDTGGSTRNPAAHCGLVGFKP
          PWSYSKQYREKRK.N.H..NEDSDWLITG.SSGGSA.AVSAFTCYAALGS.TGG..RNPAA.CGLVGFKP
Retrocopy PWSYSKQYREKRK*NLHFENEDSDWLITGRSSGGSAVAVSAFTCYAALGSYTGGLIRNPAAYCGLVGFKP

Parental  SYGLVSRHGLIPLVNSMDVPGILTRCVDDAAIVLGALAGPDPKDSTTVHDPINKPFMLPSLADVSKLCIG
          S.GLV..HGLI...N.MDV.G.LTR.VDDAAIVLG.LAG.DPKDSTTV.DP..KPFMLPSL..VSKLCIG
Retrocopy SCGLVFHHGLISPENLMDVQGLLTRYVDDAAIVLGVLAGHDPKDSTTVQDPV-KPFMLPSLTNVSKLCIG

Parental  IPKEYLIPELSSEVRSLWSKAADLFESEGAKVLEVSLPHTSYSIVCYHVLCTSEVASNMARFDGLQYGHR
          IPKEYL..ELSSE..SLWSKAADLFESEG.KV.EVS..H..YSIVCYH.LC.SE.AS..ARFDGLQYGHR
Retrocopy IPKEYLVLELSSEEPSLWSKAADLFESEGIKVTEVSFSHFTYSIVCYHLLCISEAASSIARFDGLQYGHR

Parental  CDINVSTEAMYAATRREGFNDVVRGRILSGNFFLLKENYENYFVKAQKVRRLIANDFVNAFNSGV
          CDI.VSTEAM..ATR.EGFND.VRGRILSGN.FLL...YENYF.KAQKVR.LIANDFVNAFNSGV
Retrocopy CDIDVSTEAMDVATR*EGFNDFVRGRILSGNVFLLT*KYENYFIKAQKVRCLIANDFVNAFNSGV

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	0.22 RPM	15.80 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	16.34 RPM
SRP007412_cerebellum	0.13 RPM	14.46 RPM
SRP007412_heart	0.00 RPM	18.08 RPM
SRP007412_kidney	0.12 RPM	32.04 RPM
SRP007412_liver	0.00 RPM	14.73 RPM
SRP007412_testis	0.00 RPM	6.37 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_675 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_675 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017557	3 retrocopies	retro_btau_476, retro_btau_493, retro_btau_616,
Choloepus hoffmanni	ENSCHOG00000001036	1 retrocopy	retro_chof_2382,
Callithrix jacchus	ENSCJAG00000006200	4 retrocopies	retro_cjac_1421, retro_cjac_3781, retro_cjac_3919, retro_cjac_692,
Cavia porcellus	ENSCPOG00000021670	1 retrocopy	retro_cpor_179,
Homo sapiens	ENSG00000130348	3 retrocopies	retro_hsap_1321, retro_hsap_466, retro_hsap_514,
Gorilla gorilla	ENSGGOG00000008261	3 retrocopies	retro_ggor_1031, retro_ggor_445, retro_ggor_474,
Macaca mulatta	ENSMMUG00000008330	2 retrocopies	retro_mmul_429, retro_mmul_675 ,
Nomascus leucogenys	ENSNLEG00000013383	2 retrocopies	retro_nleu_1403, retro_nleu_1550,
Pongo abelii	ENSPPYG00000016883	3 retrocopies	retro_pabe_1100, retro_pabe_230, retro_pabe_268,
Pan troglodytes	ENSPTRG00000018462	2 retrocopies	retro_ptro_351, retro_ptro_902,