RetrogeneDB ID: retro_hsap_1222

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:83397583..83398275(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000237099
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GYG1
• Ensembl ID: ENSG00000163754
• Aliases: GYG1, GSD15, GYG
• Description: glycogenin 1 [Source:HGNC Symbol;Acc:4699]

Sequence

>retro_hsap_1222
TCAGATACTCTGATCCTAGCAAATATTGATGATCTTTTTGAGCGAGAAGAATTGTCAGCAGCACCAGACTAAGGGTGGCC
TAACTGCTCCAATTCCGGAATCTTTGTTTATCAGCCTTCAGTTGAAACATATAATCAGCTGTTGCATCTTACTTCTGTGC
AAGGTAGTTTTGACAGTGGAGACCAAGTCTTACTGAACACATTTTTTAAGCATCTGGGCAACAACAGATAATCAGAAAAC
ACCTGCTGTTCATTTATAACCTAAGCAACATCACTATATACTCCTACCTCCCAGAATTTAAAGTGTTTGGTGCAAATGCC
AAAGTTGTGCATTTCCTGGAAGGAGCCAAATCATGGAATTATAGTTATGATCCCAAAACAAAAAATGTCAAAAGCGAGTC
CCATGATCCCAAAGTGACTTATCCAGCGTTTCTCATCCTGTGGTGGAGCATCTTTACCACCAATGTTTTACCTCTGCGTC
AACAATTTGACCTTGTCAAAGACACCTGCTCATATGTAAATGTGGAAGATATCTCAGGAGGCATATCACATCTGTCCCTT
GGGGAGATTCCAGCTATGGCACAGCCTTTTGTATCCTTGGAAGAACAGAAGAAGTGGTGGGAATAGGGCCAGGTTGATTA
TATGGGACCAGATTCCTTTGACATCAAGAGGACACGTGACACTTACCTCCAG

Alignment

ORF - retro_hsap_1222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.26 %
• Parental protein coverage: 69.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ADTLVLANIDDLFDREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHLASEQGSFDGGDQGILNTFF-
          .DTL.LANIDDLF.REELSAAPD.GWP.C.NSG.FVYQPSVETYNQLLHL.S.QGSFD.GDQ..LNTFF.
Retrocopy SDTLILANIDDLFEREELSAAPD*GWPNCSNSGIFVYQPSVETYNQLLHLTSVQGSFDSGDQVLLNTFF>

Parental  SSWATTD-IRKHLPFIYNLSSISIYSYLPAFKVFGASAKVVHFLGRVKPWNYTYDPKTKSVKSEAHDPNM
          S.WATTD.IRKHL.FIYNLS.I.IYSYLP.FKVFGA.AKVVHFL...K.WNY.YDPKTK.VKSE.HDP..
Retrocopy SIWATTD>IRKHLLFIYNLSNITIYSYLPEFKVFGANAKVVHFLEGAKSWNYSYDPKTKNVKSESHDPKV

Parental  THPEFLILWWNIFTTNVLPLLQQFGLVKDTCSYVNVEDVSGAISHLSLGEIPAMAQPFVSSEERKERWEQ
          T.P.FLILWW.IFTTNVLPL.QQF.LVKDTCSYVNVED.SG.ISHLSLGEIPAMAQPFVS.EE.K..WE.
Retrocopy TYPAFLILWWSIFTTNVLPLRQQFDLVKDTCSYVNVEDISGGISHLSLGEIPAMAQPFVSLEEQKKWWE*

Parental  GQADYMGADSFDNIKRKLDTYLQ
          GQ.DYMG.DSFD.IKR..DTYLQ
Retrocopy GQVDYMGPDSFD-IKRTRDTYLQ

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
bodymap2_adipose	0.00 RPM	60.79 RPM
bodymap2_adrenal	0.00 RPM	72.05 RPM
bodymap2_brain	0.00 RPM	52.25 RPM
bodymap2_breast	0.00 RPM	43.58 RPM
bodymap2_colon	0.00 RPM	206.41 RPM
bodymap2_heart	0.00 RPM	134.67 RPM
bodymap2_kidney	0.00 RPM	46.88 RPM
bodymap2_liver	0.00 RPM	14.93 RPM
bodymap2_lung	0.00 RPM	61.18 RPM
bodymap2_lymph_node	0.00 RPM	56.85 RPM
bodymap2_ovary	0.00 RPM	87.69 RPM
bodymap2_prostate	0.00 RPM	171.62 RPM
bodymap2_skeletal_muscle	0.00 RPM	548.82 RPM
bodymap2_testis	0.00 RPM	214.42 RPM
bodymap2_thyroid	0.00 RPM	115.87 RPM
bodymap2_white_blood_cells	0.00 RPM	85.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1222 was not detected

EST

No EST(s) were mapped for retro_hsap_1222 retrocopy.

TSS

No TSS is located nearby retro_hsap_1222 retrocopy 5' end.

Lab

retro_hsap_1222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1222 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_836
Pongo abelii	retro_pabe_1015
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).