RetrogeneDB ID:

retro_hsap_159

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:55688455..55689042(+)
Located in intron of:ENSG00000231090
Retrocopy
information
Ensembl ID:ENSG00000231095
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GYG1
Ensembl ID:ENSG00000163754
Aliases:GYG1, GSD15, GYG
Description:glycogenin 1 [Source:HGNC Symbol;Acc:4699]


Retrocopy-Parental alignment summary:






>retro_hsap_159
ATTTATCAGCCTTCAGTTGAAACATATAATCAGCTGTTGCATCTTGCTTCTGAGCAAGGTAGTTTTGATGGTGGAGAACA
AGGCATACGGAACACATTTTTTCGCAGCTGGGCAACAACAGATATCAGAAAACACCTGCCATTTATTTATAGCCTAAGCT
GCATCTCTATATAGTCCTACCTCCCAGCATTTAAAGTGTTTGGTGCAAGTGCCAAAGTTGTGCATTTCCTGGGACAAGTC
AAACCATGGAATTATACTTATGATCCCAAAACAAAAAGTGTCAAAAATGAGTCCCACCATCCCAACGTGACTCATCCAGA
GTTTCTCATCCTATGGTGGAACATCTTTACCACCACCGTTTTACCTCTGCTTCAACAATTTGGCCTTGTCAAAGACACCT
TCTCATACGTAAATGTGGAAAATGTCTCAGGAGCCATATCACATCTGTCCCTTGGGGGGATCCCAGCTATGGCACAGTCT
GTGTATCCTCAGAAGAATGGAAGGAGCGGTGGGAACAGGGCTAGACCGATTATATGGGAGCAGATTCCTTTGACAACATC
AAGAGGAAGCTTGACACTTACCTCCAG

ORF - retro_hsap_159 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.83 %
Parental protein coverage: 58.86 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVYQPSVETYNQLLHLASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSISIYSYLPAFKVFGAS
.YQPSVETYNQLLHLASEQGSFDGG.QGI.NTFF.SWATTDIRKHLPFIY.LS.ISI.SYLPAFKVFGAS
RetrocopyIYQPSVETYNQLLHLASEQGSFDGGEQGIRNTFFRSWATTDIRKHLPFIYSLSCISI*SYLPAFKVFGAS
ParentalAKVVHFLGRVKPWNYTYDPKTKSVKSEAHDPNMTHPEFLILWWNIFTTNVLPLLQQFGLVKDTCSYVNVE
AKVVHFLG.VKPWNYTYDPKTKSVK.E.H.PN.THPEFLILWWNIFTT.VLPLLQQFGLVKDT.SYVNVE
RetrocopyAKVVHFLGQVKPWNYTYDPKTKSVKNESHHPNVTHPEFLILWWNIFTTTVLPLLQQFGLVKDTFSYVNVE
ParentalDVSGAISHLSLGEIPAMAQPF-VSSEERKERWEQGQADYMGADSFDNIKRKLDTYLQ
.VSGAISHLSLG.IPAMAQ...VSSEE.KERWEQG..DYMGADSFDNIKRKLDTYLQ
RetrocopyNVSGAISHLSLGGIPAMAQSV<VSSEEWKERWEQG*TDYMGADSFDNIKRKLDTYLQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 .02 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 - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_159 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_159 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_159 retrocopy 5' end.

Lab - click to see more details

retro_hsap_159 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_159 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_376
Parental genes homology:
Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000014672 retrocopies
retro_cjac_1049, retro_cjac_2915,
Danio rerio ENSDARG000000119341 retrocopy
retro_drer_23,
Homo sapiens ENSG00000163754 2 retrocopies
retro_hsap_1222, retro_hsap_159 ,
Myotis lucifugus ENSMLUG000000063821 retrocopy
retro_mluc_2351,
Macaca mulatta ENSMMUG000000055212 retrocopies
retro_mmul_1297, retro_mmul_376,
Nomascus leucogenys ENSNLEG000000025572 retrocopies
retro_nleu_1556, retro_nleu_693,
Oryctolagus cuniculus ENSOCUG000000035161 retrocopy
retro_ocun_1766,
Pongo abelii ENSPPYG000000258992 retrocopies
retro_pabe_1015, retro_pabe_1080,
Pan troglodytes ENSPTRG000000155091 retrocopy
retro_ptro_836,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.03 RPM Legend:


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 .02 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 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



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