RetrogeneDB ID: retro_ptro_836

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:82858037..82858825(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GYG1
• Ensembl ID: ENSPTRG00000015509
• Aliases: None
• Description: glycogenin 1 [Source:HGNC Symbol;Acc:4699]

Sequence

>retro_ptro_836
CACCAAAGGGGTGCCCCGGTCCGGGGCTCACCTCTAAAACAGCACAGGACCACCAGAAGCATGGTTGTATTCACCACCCC
GCAAGTCTCAAACTCCATGAGAAAAGTTTTAGCGACAGTCTTTGATGAAGTCATCATGGTAAATGTCTTGGACAGCAGCG
ATTCTGCTCATCTAACCGTAATGAAGGGGCCAGAGTTGGATGCCACGCTGGCAAAGCTCCACGCCTAGCCACTTACACAG
TATTCAAAATGTGTATTCATGGATGCAGATACTCTGATCCTAGCAAATATTGATGATCTTTTTGAGCGAGAAGAATTGTC
AGCAGCACCAGACTAAGGGTGGCCTAACTGCTCCAATTCCGGAATCTTTGTTTATCAGCCTTCAGTTGAAACATATAATC
AGCTGTTGCATCTTACTTCTGTGCAAGGTAGTTTTGACAGTGGAGACCAAGTCTTACTGAACACATTTTTTAAGCATCTG
GGCAACAACAGATAATCAGAAAACACCTGCTGTTCATTTATAACCTAAGCAACATCACTATATACTCCTACCTCCCAGAA
TTTAAAGTGTTTGGTGCAAATGCCAAAGTTGTGCATTTCCTGGAAGGAGCCAAATCACGGAATTATAGTTATGATCCCAA
AACAAAAAATGTCAAAAGCGAGTCCCATGATCCCAACGTGACTCATCCAGAGTTTCTCATCCTGTGGTGGAGCATCTTTA
CCACCAATGTTTTACCTCTGCGTCAACAATTTGACCTCGTCAAAGACACCTGCTCATATGTAAATGTG

Alignment

ORF - retro_ptro_836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.68 %
• Parental protein coverage: 74.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YAKGALVLGSSLKQHRTTRRLVVLATPQVSNSMRKVLETVFDEVIMVDVLDSGDSAHLTLMKRPELGVTL
          ...GA.V.GS.LKQHRTTR..VV..TPQVSNSMRKVL.TVFDEVIMV.VLDS.DSAHLT.MK.PEL..TL
Retrocopy HQRGAPVRGSPLKQHRTTRSMVVFTTPQVSNSMRKVLATVFDEVIMVNVLDSSDSAHLTVMKGPELDATL

Parental  TKLHCWSLTQYSKCVFMDADTLVLANIDDLFEREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHLAS
          .KLH...LTQYSKCVFMDADTL.LANIDDLFEREELSAAPD.GWP.C.NSG.FVYQPSVETYNQLLHL.S
Retrocopy AKLHA*PLTQYSKCVFMDADTLILANIDDLFEREELSAAPD*GWPNCSNSGIFVYQPSVETYNQLLHLTS

Parental  EQGSFDGGDQGILNTFF-SSWATTD-IRKHLPFIYNLSSISIYSYLPAFKVFGASAKVVHFLGRVKPWNY
          .QGSFD.GDQ..LNTFF.S.WATTD.IRKHL.FIYNLS.I.IYSYLP.FKVFGA.AKVVHFL...K..NY
Retrocopy VQGSFDSGDQVLLNTFF>SIWATTD>IRKHLLFIYNLSNITIYSYLPEFKVFGANAKVVHFLEGAKSRNY

Parental  TYDPKTKSVKSEAHDPNMTHPEFLILWWNIFTTNVLPLLQQFGLVKDTCSYVNV
          .YDPKTK.VKSE.HDPN.THPEFLILWW.IFTTNVLPL.QQF.LVKDTCSYVNV
Retrocopy SYDPKTKNVKSESHDPNVTHPEFLILWWSIFTTNVLPLRQQFDLVKDTCSYVNV

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_prefrontal_cortex	0.00 RPM	24.17 RPM
SRP007412_cerebellum	0.00 RPM	19.14 RPM
SRP007412_heart	0.00 RPM	80.24 RPM
SRP007412_kidney	0.00 RPM	23.93 RPM
SRP007412_liver	0.00 RPM	14.40 RPM
SRP007412_testis	0.53 RPM	281.58 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_836 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_836 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1222
Pongo abelii	retro_pabe_1015
Macaca mulatta	retro_mmul_1297

---

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 ,