RetrogeneDB ID: retro_mmul_1297

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:63312886..63313842(+)
• 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_1297
CACCAAAGGGGTGCCCCGGTCCGGGTCTCACCTCTAAAACAGCACAGGACCACCAGAAGGCTGGCCGTGTTCGCCACCCC
GCAAGTCTCAAACTCCATGAAAAAAGTTTTAGAGACAGTCTTTAATGAAGTCATCATGGTAAATGTCTTAGACAGCAGCG
ATTCTGCTCACCTAACCATAATGAAGAGGCCAGAGTTGGGTGCCATGCTGGCAAAGCTCCATGCCTAGTCACTTACACAG
TATTCAAAATGTGTATTCATGGATGCAGATACTCTGATCCTAGCAAATACTGATGATCTTTTTGAGCAAGAAGAATTGTC
AGCAGCACCCAACCAAGGGTGGCCTAACTGCTTCAATTCCGGAATTTTTGTTTATCAGCCTTCGGTTGAAACATATAATC
AGCTGTTGCATCTTGCTTCTTAGCATGGTAGTTTTGACAGTGGAGACCAAGGCTTACTGAACACATTTTTTAAGCATCTG
GGCAACAACAGACATCAGAAAACACCTGCTGTTCATTTATAACCTAAGCGACATCTCTATATACTCCTACCTCCCAGCAT
TTAAAATGTTTGGTGCAAGTGCCAAAGTTGTGCATTTCCTAGAATGAGCCAAATCATAGAATTATAGTTATGATCCCAAA
ACAAAAAAGTGTCAAAAATGAGTCCCATGATCCCAATGTGACTCATTCAGCATTTCTCATCCTGTGGTGGAGCATCTTTA
CCATGAATGTTTTACCTCTGCTTCAACAATTTGACCTTGTCAAAGACACCTGCTCATATGTAAATGTGGAAGATATCTCA
GGAGGCATATCATATCTGTCCCTTGGGGAGATTCCAGCTATGGCACAGCTTTTTGTATCCTTGGAAGAACAGAAGGAGTG
GTGGGAATAGGGCCAGGCTGATTGTATGGGACAAGATTCCTTTGACATCATGAGGACACGTGACACTTACCTCCAG

Alignment

ORF - retro_mmul_1297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.13 %
• Parental protein coverage: 95.8 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIMVDVLDSGDSAHLTLMKRPELGVTL
          ...GA.V..S.LKQHRTTRRL.V.ATPQVS.SM.KVLETVF.EVIMV.VLDS.DSAHLT.MKRPELG..L
Retrocopy HQRGAPVRVSPLKQHRTTRRLAVFATPQVSNSMKKVLETVFNEVIMVNVLDSSDSAHLTIMKRPELGAML

Parental  TKLHCWSLTQYSKCVFMDADTLVLANIDDLFEREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLRLAS
          .KLH..SLTQYSKCVFMDADTL.LAN.DDLFE.EELSAAP..GWP.CFNSG.FVYQPSVETYNQLL.LAS
Retrocopy AKLHA*SLTQYSKCVFMDADTLILANTDDLFEQEELSAAPNQGWPNCFNSGIFVYQPSVETYNQLLHLAS

Parental  EQGSFDGGDQGILNTFF-SSWATRDIRKHLPFIYNLSSISIYSYLPAFKVFGASAKVVHFLGRVKPWNYT
          ..GSFD.GDQG.LNTFF.S.WAT.DIRKHL.FIYNLS.ISIYSYLPAFK.FGASAKVVHFL...K..NY.
Retrocopy *HGSFDSGDQGLLNTFF>SIWATTDIRKHLLFIYNLSDISIYSYLPAFKMFGASAKVVHFLE*AKS*NYS

Parental  YDPKT-KSVKSEAHDPNMTHPEFLILWWNIFTTNVLPLLQQFGLVKDTCSYVNVEDVSGAISHLSLGEIP
          YDPKT.KSVK.E.HDPN.TH..FLILWW.IFT.NVLPLLQQF.LVKDTCSYVNVED.SG.IS.LSLGEIP
Retrocopy YDPKT>KSVKNESHDPNVTHSAFLILWWSIFTMNVLPLLQQFDLVKDTCSYVNVEDISGGISYLSLGEIP

Parental  AMAQPFVSSEERKERWEQGQADYMGADSFDNIKRKLDTYLQ
          AMAQ.FVS.EE.KE.WE.GQAD.MG.DSFD.I.R..DTYLQ
Retrocopy AMAQLFVSLEEQKEWWE*GQADCMGQDSFD-IMRTRDTYLQ

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	0.00 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	0.04 RPM	51.68 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1297 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1297 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1297 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1222
Pan troglodytes	retro_ptro_836
Pongo abelii	retro_pabe_1015

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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,