Human Gene GYG2 (uc010ndc.1)
  Description: Homo sapiens glycogenin 2 (GYG2), transcript variant 3, mRNA.
RefSeq Summary (NM_001184704): This gene encodes a member of the the glycogenin family. Glycogenin is a self-glucosylating protein involved in the initiation reactions of glycogen biosynthesis. A gene on chromosome 3 encodes the muscle glycogenin and this X-linked gene encodes the glycogenin mainly present in liver; both are involved in blood glucose homeostasis. This gene has a short version on chromosome Y, which is 3' truncated and can not make a functional protein. Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, May 2010].
Transcript (Including UTRs)
   Position: hg19 chrX:2,773,034-2,800,861 Size: 27,828 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chrX:2,773,175-2,799,254 Size: 26,080 Coding Exon Count: 6 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:2,773,034-2,800,861)mRNA (may differ from genome)Protein (279 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMalacardsMGIOMIMPubMed
ReactomeTreefamUniProtKBBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: GYG2
Diseases sorted by gene-association score: glycogen storage disease type 0 (20), retinitis pigmentosa 36 (13), retinitis pigmentosa 30 (10)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 38.05 RPKM in Adipose - Subcutaneous
Total median expression: 202.11 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -48.45141-0.344 Picture PostScript Text
3' UTR -525.161607-0.327 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF01501 - Glycosyl transferase family 8

SCOP Domains:
53448 - Nucleotide-diphospho-sugar transferases

ModBase Predicted Comparative 3D Structure on O15488-6
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  U94362 - Homo sapiens glycogenin-2 alpha (glycogenin-2) mRNA, complete cds.
AK292496 - Homo sapiens cDNA FLJ77514 complete cds, highly similar to Homo sapiens glycogenin 2, mRNA.
AK098046 - Homo sapiens cDNA FLJ40727 fis, clone TKIDN2000127, highly similar to Glycogenin-2 (EC 2.4.1.186).
U94363 - Homo sapiens glycogenin-2 beta (glycogenin-2) mRNA, complete cds.
BC023152 - Homo sapiens glycogenin 2, mRNA (cDNA clone MGC:9153 IMAGE:3923041), complete cds.
U94364 - Homo sapiens glycogenin-2 gamma (glycogenin-2) mRNA, complete cds.
DQ424901 - Homo sapiens clone FG060304 glycogenin 2 mRNA, complete cds, alternatively spliced.
DQ894287 - Synthetic construct Homo sapiens clone IMAGE:100008747; FLH169377.01L; RZPDo839B0995D glycogenin 2 (GYG2) gene, encodes complete protein.
KJ897935 - Synthetic construct Homo sapiens clone ccsbBroadEn_07329 GYG2 gene, encodes complete protein.
DQ891106 - Synthetic construct clone IMAGE:100003736; FLH169381.01X; RZPDo839B0996D glycogenin 2 (GYG2) gene, encodes complete protein.
U94360 - Homo sapiens glycogenin-2 delta (glycogenin-2) mRNA, partial cds.
U94358 - Homo sapiens glycogenin-2 epsilon (glycogenin-2) mRNA, partial cds.
U94361 - Homo sapiens glycogenin-2 (glycogenin-2) mRNA, partial cds.
U94357 - Homo sapiens glycogenin-2 delta (glycogenin-2) mRNA, partial cds.
JD283585 - Sequence 264609 from Patent EP1572962.
JD137190 - Sequence 118214 from Patent EP1572962.
JD380297 - Sequence 361321 from Patent EP1572962.
JD298761 - Sequence 279785 from Patent EP1572962.
JD237716 - Sequence 218740 from Patent EP1572962.
JD174298 - Sequence 155322 from Patent EP1572962.
JD126616 - Sequence 107640 from Patent EP1572962.
JD091149 - Sequence 72173 from Patent EP1572962.
JD037002 - Sequence 18026 from Patent EP1572962.
JD322132 - Sequence 303156 from Patent EP1572962.
DQ586918 - Homo sapiens piRNA piR-54030, complete sequence.
JD435904 - Sequence 416928 from Patent EP1572962.
JD206945 - Sequence 187969 from Patent EP1572962.
JD375325 - Sequence 356349 from Patent EP1572962.
JD561139 - Sequence 542163 from Patent EP1572962.
JD294973 - Sequence 275997 from Patent EP1572962.
JD412187 - Sequence 393211 from Patent EP1572962.
JD456341 - Sequence 437365 from Patent EP1572962.
JD514616 - Sequence 495640 from Patent EP1572962.
JD073597 - Sequence 54621 from Patent EP1572962.
JD224119 - Sequence 205143 from Patent EP1572962.
JD445967 - Sequence 426991 from Patent EP1572962.
JD341137 - Sequence 322161 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O15488 (Reactome details) participates in the following event(s):

R-HSA-71590 glycogen-glycogenin-2 + n orthophosphate => limit dextrin-glycogenin-2 + n D-glucose 1-phosphate [PYGL]
R-HSA-3780997 PPP1R3C binds to glycogen:GYG2:GYS2
R-HSA-3322016 GBE1 catalyzes branch formation in polyGlc-GYG2 complexed with GYS2-a
R-HSA-3780994 GYS2 catalyzes the incorporation of phosphoglucose into glycogen-GYG2
R-HSA-3781011 EPM2A dimer dephosphorylates phosphoglycogen-GYG2
R-HSA-453339 poly((1,4)-alpha-glucosyl) glycogenin-2 + n orthophosphate => glycogenin-2 + n D-glucose 1-phosphate [PYGL]
R-HSA-3322009 GYS2 catalyzes the polyglucosylation of oligoGlc-GYG2
R-HSA-3322014 Autoglucosylation of GYG2 complexed with GYS2-a
R-HSA-3322019 Autoglucosylation of GYG2 complexed with GYS2-b
R-HSA-3781021 EPM2A dimer binds PPP1R3C:phosphoglycogen-GYG2 complex
R-HSA-71552 limit dextrin-glycogenin => ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl) glycogenin
R-HSA-71593 ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin => poly{(1,4)-alpha-glucosyl} glycogenin + alpha-D-glucose
R-HSA-70221 Glycogen breakdown (glycogenolysis)
R-HSA-3322077 Glycogen synthesis
R-HSA-3785653 Myoclonic epilepsy of Lafora
R-HSA-3878781 Glycogen storage disease type IV (GBE1)
R-HSA-3858516 Glycogen storage disease type 0 (liver GYS2)
R-HSA-8982491 Glycogen metabolism
R-HSA-3229121 Glycogen storage diseases
R-HSA-71387 Metabolism of carbohydrates
R-HSA-5663084 Diseases of carbohydrate metabolism
R-HSA-1430728 Metabolism
R-HSA-5668914 Diseases of metabolism
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001184704, NP_001171633, O15488-6, U94361
UCSC ID: uc010ndc.1
RefSeq Accession: NM_001184704
Protein: O15488-6, splice isoform of O15488

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: U94361.1
exon count: 6CDS single in 3' UTR: no RNA size: 740
ORF size: 840CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1537.00frame shift in genome: no % Coverage: 98.78
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.