Human Gene PYGL (ENST00000216392.8_7) from GENCODE V47lift37
  Description: glycogen phosphorylase L, transcript variant 1 (from RefSeq NM_002863.5)
Gencode Transcript: ENST00000216392.8_7
Gencode Gene: ENSG00000100504.17_9
Transcript (Including UTRs)
   Position: hg19 chr14:51,371,935-51,411,201 Size: 39,267 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr14:51,372,110-51,411,121 Size: 39,012 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:51,371,935-51,411,201)mRNA (may differ from genome)Protein (847 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PYGL_HUMAN
DESCRIPTION: RecName: Full=Glycogen phosphorylase, liver form; EC=2.4.1.1;
FUNCTION: Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
CATALYTIC ACTIVITY: (1,4-alpha-D-glucosyl)(n) + phosphate = (1,4- alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate.
COFACTOR: Pyridoxal phosphate.
ENZYME REGULATION: Activity of phosphorylase is controlled both by allosteric means (through the noncovalent binding of metabolites) and by covalent modification. Thus AMP allosterically activates, whereas ATP, ADP, and glucose-6-phosphate allosterically inhibit, phosphorylase B.
SUBUNIT: Homodimer. Dimers associate into a tetramer to form the enzymatically active phosphorylase A. Interacts with PPP1R3B (By similarity).
PTM: Phosphorylation of Ser-15 converts phosphorylase B (unphosphorylated) to phosphorylase A.
DISEASE: Defects in PYGL are the cause of glycogen storage disease type 6 (GSD6) [MIM:232700]. A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected.
SIMILARITY: Belongs to the glycogen phosphorylase family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PYGL";

-  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: PYGL
Diseases sorted by gene-association score: glycogen storage disease vi* (1688), glycogen storage disease (24), glycogen storage disease ix (18), glycogen storage disease iiia (8), glycogen storage disease iv (5), glycogen storage disease ia (5)
* = Manually curated disease association

-  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: 170.51 RPKM in Whole Blood
Total median expression: 810.69 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 -22.9080-0.286 Picture PostScript Text
3' UTR -30.10175-0.172 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
  InterPro Domains: Graphical view of domain structure
IPR011833 - Glycg_phsphrylas
IPR000811 - Glyco_trans_35

Pfam Domains:
PF00343 - Carbohydrate phosphorylase

SCOP Domains:
53756 - UDP-Glycosyltransferase/glycogen phosphorylase

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1EM6 - X-ray MuPIT 1EXV - X-ray MuPIT 1FA9 - X-ray MuPIT 1FC0 - X-ray MuPIT 1L5Q - X-ray MuPIT 1L5R - X-ray MuPIT 1L5S - X-ray MuPIT 1L7X - X-ray MuPIT 1XOI - X-ray MuPIT 2ATI - X-ray MuPIT 2QLL - X-ray MuPIT 2ZB2 - X-ray MuPIT 3CEH - X-ray MuPIT 3CEJ - X-ray MuPIT 3CEM - X-ray MuPIT 3DD1 - X-ray MuPIT 3DDS - X-ray MuPIT 3DDW - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P06737
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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 orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details   Gene Details
Gene SorterGene Sorter   Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0002060 purine nucleobase binding
GO:0003824 catalytic activity
GO:0004645 phosphorylase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005536 glucose binding
GO:0008144 drug binding
GO:0008184 glycogen phosphorylase activity
GO:0016208 AMP binding
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups
GO:0019842 vitamin binding
GO:0030170 pyridoxal phosphate binding
GO:0030246 carbohydrate binding
GO:0032052 bile acid binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0005975 carbohydrate metabolic process
GO:0005977 glycogen metabolic process
GO:0005980 glycogen catabolic process
GO:0006015 5-phosphoribose 1-diphosphate biosynthetic process
GO:0008152 metabolic process
GO:0042593 glucose homeostasis
GO:0043312 neutrophil degranulation
GO:0070266 necroptotic process

Cellular Component:
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen


-  Descriptions from all associated GenBank mRNAs
  AK309333 - Homo sapiens cDNA, FLJ99374.
LP895952 - Sequence 816 from Patent EP3253886.
M36807 - Human liver glycogen phosphorylase type IV mRNA, 3' end.
AK300580 - Homo sapiens cDNA FLJ50225 complete cds, highly similar to Glycogen phosphorylase, liver form (EC 2.4.1.1).
BC110791 - Homo sapiens phosphorylase, glycogen, liver, mRNA (cDNA clone MGC:131632 IMAGE:6051020), complete cds.
BC009895 - Homo sapiens phosphorylase, glycogen, liver, mRNA (cDNA clone MGC:2000 IMAGE:2967205), complete cds.
AK225904 - Homo sapiens mRNA for glycogen phosphorylase, liver variant, clone: FCC120A08.
BC095850 - Homo sapiens phosphorylase, glycogen, liver, mRNA (cDNA clone MGC:112938 IMAGE:30343100), complete cds.
LP895300 - Sequence 164 from Patent EP3253886.
BC082229 - Homo sapiens phosphorylase, glycogen, liver, mRNA (cDNA clone MGC:99671 IMAGE:4053354), complete cds.
M14636 - Human liver glycogen phosphorylase mRNA, complete cds.
Y15233 - Homo sapiens mRNA for liver glycogen phosphorylase.
AF046785 - Homo sapiens liver glycogen phosphorylase (PYGL) mRNA, complete cds.
AF066858 - Homo sapiens liver glycogen phosphorylase (PYGL) mRNA, complete cds.
AK313206 - Homo sapiens cDNA, FLJ93707, highly similar to Homo sapiens phosphorylase, glycogen; liver (Hers disease, glycogenstorage disease type VI) (PYGL), mRNA.
KJ891961 - Synthetic construct Homo sapiens clone ccsbBroadEn_01355 PYGL gene, encodes complete protein.
KR711740 - Synthetic construct Homo sapiens clone CCSBHm_00030086 PYGL (PYGL) mRNA, encodes complete protein.
KR711741 - Synthetic construct Homo sapiens clone CCSBHm_00030087 PYGL (PYGL) mRNA, encodes complete protein.
JD258612 - Sequence 239636 from Patent EP1572962.
JD548195 - Sequence 529219 from Patent EP1572962.
AY429567 - Homo sapiens PYGLv_1 mRNA sequence; alternatively spliced.
BC065011 - Homo sapiens phosphorylase, glycogen, liver, mRNA (cDNA clone IMAGE:6166871), partial cds.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-5941 - glycogenolysis

Reactome (by CSHL, EBI, and GO)

Protein P06737 (Reactome details) participates in the following event(s):

R-HSA-71588 glycogen phosphorylase (PYGL) dimer b + 2 ATP => glycogen phosphorylase (PYGL) dimer a + 2 ADP
R-HSA-6800434 Exocytosis of ficolin-rich granule lumen proteins
R-HSA-6798748 Exocytosis of secretory granule lumen proteins
R-HSA-71590 glycogen-glycogenin-2 + n orthophosphate => limit dextrin-glycogenin-2 + n D-glucose 1-phosphate [PYGL]
R-HSA-453339 poly((1,4)-alpha-glucosyl) glycogenin-2 + n orthophosphate => glycogenin-2 + n D-glucose 1-phosphate [PYGL]
R-HSA-70221 Glycogen breakdown (glycogenolysis)
R-HSA-6798695 Neutrophil degranulation
R-HSA-8982491 Glycogen metabolism
R-HSA-168249 Innate Immune System
R-HSA-71387 Metabolism of carbohydrates
R-HSA-168256 Immune System
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A6NDQ4, B4DUB7, ENST00000216392.1, ENST00000216392.2, ENST00000216392.3, ENST00000216392.4, ENST00000216392.5, ENST00000216392.6, ENST00000216392.7, F5H816, NM_002863, O60567, O60752, O60913, P06737, PYGL , PYGL_HUMAN, Q501V9, Q641R5, Q96G82, uc317cql.1, uc317cql.2
UCSC ID: ENST00000216392.8_7
RefSeq Accession: NM_002863.5
Protein: P06737 (aka PYGL_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PYGL:
gsd6 (Glycogen Storage Disease Type VI)

-  Gene Model Information
  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.