RetrogeneDB ID: retro_pabe_1015

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:84397492..84398183(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GYG1
• Ensembl ID: ENSPPYG00000025899
• Aliases: None
• Description: glycogenin 1 [Source:HGNC Symbol;Acc:4699]

Sequence

>retro_pabe_1015
ATGAGAAAAGTTTTAGAGACAGTCTTTGATGAAGTCATCATGGTAAATGTCTTGGGCAGCAGCGATTCTGCTCATCTAAC
CGTAATGAAGAGGCCAGAGTTGGATGCCACGCTGGCAAAGCTCCACGCCTAGCCACTTACACAGTATTCAAAATGTGTAT
TCATGGAAGCAGATACTCTGATCCTAGCAAATATTGATGATCTTTTTGAGCAAGAAGAATTGTCAGCAGCACCAGACTAA
GGGTGGCCTAACTACTTCAATTTCAGAATCTTTGTTTATCAGCCTTCAGTTGAAACATGTAATCAGCTGTTGCATCTTAC
TTCTGAGCAAGGTAGTTTTGACAGTGGAGACCAAGGCTTACTGAATACATTTTTTAAGCATCTGGGCAACAACAGATATC
AGAAAACACCTGCTGTTCATTTATAACCTAAGCAACATCACTATATACTCCTACCTCCCAGCATTTAAAATGTTTGGTGC
AAATGCCAAAGTTGTGCATTTCCTGGAATGAGCCAAATCATGGAATTATAGTTATGATCCCAAAACAAAAAATGTCAAAA
GCGAGTCCCATGATCCCAACGTGACTCATCCAGAGTTTCTCATCCTGTGGTGGAGCATCTTTACCACCAATGTTTTACCT
CTGCTTCAACAATTTGACCTTGTCAAAGACACCTGCTCATATGTAAATGTG

Alignment

ORF - retro_pabe_1015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.68 %
• Parental protein coverage: 75.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRKVLETVFDEVIMVDVLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFE
          MRKVLETVFDEVIMV.VL.S.DSAHLT.MKRPEL..TL.KLH...LTQYSKCVFM.ADTL.LANIDDLFE
Retrocopy MRKVLETVFDEVIMVNVLGSSDSAHLTVMKRPELDATLAKLHA*PLTQYSKCVFMEADTLILANIDDLFE

Parental  REELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHLASEQGSFDGGDQGILNTFF-SSWATTDIRKHLPF
          .EELSAAPD.GWP..FN...FVYQPSVET.NQLLHL.SEQGSFD.GDQG.LNTFF.S.WATTDIRKHL.F
Retrocopy QEELSAAPD*GWPNYFNFRIFVYQPSVETCNQLLHLTSEQGSFDSGDQGLLNTFF>SIWATTDIRKHLLF

Parental  IYNLSSISIYSYLPAFKVFGASAKVVHFLGRVKPWNYTYDPKTKNIKSEAHDPNMTHPEFLILWWNIFTT
          IYNLS.I.IYSYLPAFK.FGA.AKVVHFL...K.WNY.YDPKTKN.KSE.HDPN.THPEFLILWW.IFTT
Retrocopy IYNLSNITIYSYLPAFKMFGANAKVVHFLE*AKSWNYSYDPKTKNVKSESHDPNVTHPEFLILWWSIFTT

Parental  NVLPLLQQFGLVKDTCSYVNV
          NVLPLLQQF.LVKDTCSYVNV
Retrocopy NVLPLLQQFDLVKDTCSYVNV

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	16.64 RPM
SRP007412_cerebellum	0.00 RPM	14.11 RPM
SRP007412_heart	0.00 RPM	27.79 RPM
SRP007412_kidney	0.00 RPM	7.23 RPM
SRP007412_liver	0.00 RPM	15.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1015 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1015 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1015 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1222
Pan troglodytes	retro_ptro_836
Macaca mulatta	retro_mmul_1297

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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,