RetrogeneDB ID: retro_mmul_376

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:58071330..58071906(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GYG1
• Ensembl ID: ENSMMUG00000005521
• Aliases: None
• Description: None

Sequence

>retro_mmul_376
ATTTATCAGCCTTCAGTTGAAACATATAATCAGCTGTTGCATCTTGCTTCTGAGCAAGGTAGTTTTGATGGTGGGGGAAC
AAAGCATACAGAACACGTTTTTTAACAGCTGGGCAACAACAGATATCAGAAAACACCTGCTGTTTATTTATAGCCTAAGT
CGCATCTCTATATATTCCTGCCTCCCAGCATTTAAAGTGTTTGGCGGAAGTGCCAAAGTTGTGCATTTCCTGGGATGAGG
CAAACCATGGAATTATGATCCCAAAACAAAAAGTGTCAAGTGAGTCCCACCATCACAACATGACTCATTCAGAGTTTCTC
ATCCTGGTGGAACATCTTTACCACCATCATTTTACCTCTACTTCAACAATTTGGCCTTGTCAAAGGCAACTGCTCATACA
TAAATGTGGAAGATGTCTCAGGAGCCATATCACATCTCTCTCAGGGAGATCCCCACTATGGCCCAGCTTTTGTATGCTCA
GAAGAATGGAAGGAGCAGTGGGAACAGGGCCAGGCTGATTACATGGGAGCAGATTCCTTTGGCAACATGGAGAGGATACT
TGACACTTACCTCCAG

Alignment

ORF - retro_mmul_376 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.38 %
• Parental protein coverage: 58.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VYQPSVETYNQLLRLASEQGSFDGG-DQGILNTFFSSWATRDIRKHLPFIYNLSSISIYSYLPAFKVFGA
          .YQPSVETYNQLL.LASEQGSFDGG..Q.I.NTFF.SWAT.DIRKHL.FIY.LS.ISIYS.LPAFKVFG.
Retrocopy IYQPSVETYNQLLHLASEQGSFDGG>EQSIQNTFFNSWATTDIRKHLLFIYSLSRISIYSCLPAFKVFGG

Parental  SAKVVHFLGRVKPWNYTYDP-KTKSVKSEAHDPNMTHPEFLIL-WWNIFTTNVLPLLQQFGLVKDTCSYV
          SAKVVHFLG..KPWN..YDP.K.K.V.SE.H..NMTH.EFLIL.W.NIFTT..LPLLQQFGLVK..CSY.
Retrocopy SAKVVHFLG*GKPWN--YDP>KQK-VSSESHHHNMTHSEFLIL>W-NIFTTIILPLLQQFGLVKGNCSYI

Parental  NVEDVSGAISHLSLGEIPAMAQPFVSSEERKERWEQGQADYMGADSFDNIKRKLDTYLQ
          NVEDVSGAISHLS.G..P.....FV.SEE.KE.WEQGQADYMGADSF.N..R.LDTYLQ
Retrocopy NVEDVSGAISHLSQGD-PHYGPAFVCSEEWKEQWEQGQADYMGADSFGNMERILDTYLQ

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	35.30 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	30.86 RPM
SRP007412_cerebellum	0.00 RPM	41.20 RPM
SRP007412_heart	0.00 RPM	41.22 RPM
SRP007412_kidney	0.00 RPM	30.52 RPM
SRP007412_liver	0.00 RPM	8.95 RPM
SRP007412_testis	0.00 RPM	51.68 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_376 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_376 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_376 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_159

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001467	2 retrocopies	retro_cjac_1049, retro_cjac_2915,
Danio rerio	ENSDARG00000011934	1 retrocopy	retro_drer_23,
Homo sapiens	ENSG00000163754	2 retrocopies	retro_hsap_1222, retro_hsap_159,
Myotis lucifugus	ENSMLUG00000006382	1 retrocopy	retro_mluc_2351,
Macaca mulatta	ENSMMUG00000005521	2 retrocopies	retro_mmul_1297, retro_mmul_376 ,
Nomascus leucogenys	ENSNLEG00000002557	2 retrocopies	retro_nleu_1556, retro_nleu_693,
Oryctolagus cuniculus	ENSOCUG00000003516	1 retrocopy	retro_ocun_1766,
Pongo abelii	ENSPPYG00000025899	2 retrocopies	retro_pabe_1015, retro_pabe_1080,
Pan troglodytes	ENSPTRG00000015509	1 retrocopy	retro_ptro_836,