Human Gene GPD2 (ENST00000438166.7_4) from GENCODE V47lift37
  Description: glycerol-3-phosphate dehydrogenase 2, transcript variant 2 (from RefSeq NM_000408.5)
Gencode Transcript: ENST00000438166.7_4
Gencode Gene: ENSG00000115159.17_9
Transcript (Including UTRs)
   Position: hg19 chr2:157,292,891-157,442,915 Size: 150,025 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr2:157,332,618-157,439,430 Size: 106,813 Coding Exon Count: 16 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:157,292,891-157,442,915)mRNA (may differ from genome)Protein (727 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GPDM_HUMAN
DESCRIPTION: RecName: Full=Glycerol-3-phosphate dehydrogenase, mitochondrial; Short=GPD-M; Short=GPDH-M; EC=1.1.5.3; AltName: Full=mtGPD; Flags: Precursor;
CATALYTIC ACTIVITY: sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol.
COFACTOR: FAD.
ENZYME REGULATION: Calcium-binding enhance the activity of the enzyme.
PATHWAY: Polyol metabolism; glycerol degradation via glycerol kinase pathway; glycerone phosphate from sn-glycerol 3-phosphate (anaerobic route): step 1/1.
SUBCELLULAR LOCATION: Mitochondrion.
SIMILARITY: Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family.
SIMILARITY: Contains 2 EF-hand domains.
SEQUENCE CAUTION: Sequence=BAD92636.1; Type=Erroneous initiation;

-  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: GPD2
Diseases sorted by gene-association score: diabetes mellitus, noninsulin-dependent* (321), griscelli syndrome, type 3 (5), methylmalonic acidemia (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: 13.28 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 290.49 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 -64.50143-0.451 Picture PostScript Text
3' UTR -802.303485-0.230 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
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR018249 - EF_HAND_2
IPR002048 - EF_hand_Ca-bd
IPR006076 - FAD-dep_OxRdtase
IPR000447 - G3P_DH_FAD-dep

Pfam Domains:
PF00890 - FAD binding domain
PF01266 - FAD dependent oxidoreductase
PF13202 - EF hand
PF13499 - EF-hand domain pair
PF13833 - EF-hand domain pair
PF16901 - C-terminal domain of alpha-glycerophosphate oxidase

SCOP Domains:
47473 - EF-hand
51735 - NAD(P)-binding Rossmann-fold domains
51905 - FAD/NAD(P)-binding domain
52440 - PreATP-grasp domain
51971 - Nucleotide-binding domain
51984 - MurCD N-terminal domain
54373 - FAD-linked reductases, C-terminal domain

ModBase Predicted Comparative 3D Structure on P43304
FrontTopSide
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 orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004368 glycerol-3-phosphate dehydrogenase activity
GO:0005509 calcium ion binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0052590 sn-glycerol-3-phosphate:ubiquinone oxidoreductase activity
GO:0052591 sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity

Biological Process:
GO:0006072 glycerol-3-phosphate metabolic process
GO:0006094 gluconeogenesis
GO:0006127 glycerophosphate shuttle
GO:0019563 glycerol catabolic process
GO:0035264 multicellular organism growth
GO:0043010 camera-type eye development
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0009331 glycerol-3-phosphate dehydrogenase complex


-  Descriptions from all associated GenBank mRNAs
  LF205698 - JP 2014500723-A/13201: Polycomb-Associated Non-Coding RNAs.
MA441275 - JP 2018138019-A/13201: Polycomb-Associated Non-Coding RNAs.
AK291065 - Homo sapiens cDNA FLJ75492 complete cds, highly similar to Homo sapiens glycerol-3-phosphate dehydrogenase 2 (mitochondrial) (GPD2), mRNA.
U79250 - Human glycerol-3-phosphate dehydrogenase mRNA, complete cds.
AK290057 - Homo sapiens cDNA FLJ78475 complete cds, highly similar to Homo sapiens glycerol-3-phosphate dehydrogenase 2 (mitochondrial) (GPD2), mRNA.
AB209399 - Homo sapiens mRNA for glycerol-3-phosphate dehydrogenase 2 (mitochondrial) variant protein.
U36310 - Human glycerol-3-phosphate dehydrogenase mRNA, nuclear gene encoding mitochondrial protein, complete cds.
AK299645 - Homo sapiens cDNA FLJ57187 complete cds, highly similar to Glycerol-3-phosphate dehydrogenase, mitochondrial precursor (EC 1.1.99.5).
AK292817 - Homo sapiens cDNA FLJ78257 complete cds, highly similar to Homo sapiens glycerol-3-phosphate dehydrogenase 2 (mitochondrial) (GPD2), mRNA.
U12424 - Human mitochondrial glycerol-3-phosphate dehydrogenase mRNA, complete cds.
HM005389 - Homo sapiens clone HTL-T-76 testicular tissue protein Li 76 mRNA, complete cds.
BC019874 - Homo sapiens glycerol-3-phosphate dehydrogenase 2 (mitochondrial), mRNA (cDNA clone MGC:30027 IMAGE:4521072), complete cds.
AF311325 - Homo sapiens glycerol-3-phosphate dehydrogenase 3 mRNA, complete cds; nuclear gene for mitochondrial product.
AK093198 - Homo sapiens cDNA FLJ35879 fis, clone TESTI2008595, highly similar to Glycerol-3-phosphate dehydrogenase, mitochondrial precursor (EC 1.1.99.5).
KJ901462 - Synthetic construct Homo sapiens clone ccsbBroadEn_10856 GPD2 gene, encodes complete protein.
KR710638 - Synthetic construct Homo sapiens clone CCSBHm_00014966 GPD2 (GPD2) mRNA, encodes complete protein.
LF205699 - JP 2014500723-A/13202: Polycomb-Associated Non-Coding RNAs.
JD137872 - Sequence 118896 from Patent EP1572962.
KU178099 - Homo sapiens glycerol-3-phosphate dehydrogenase 2 isoform 1 (GPD2) mRNA, partial cds, alternatively spliced.
KU178100 - Homo sapiens glycerol-3-phosphate dehydrogenase 2 isoform 2 (GPD2) mRNA, partial cds, alternatively spliced.
DL491395 - Novel nucleic acids.
MA441276 - JP 2018138019-A/13202: Polycomb-Associated Non-Coding RNAs.
LF347278 - JP 2014500723-A/154781: Polycomb-Associated Non-Coding RNAs.
LF347282 - JP 2014500723-A/154785: Polycomb-Associated Non-Coding RNAs.
JD093155 - Sequence 74179 from Patent EP1572962.
JD503326 - Sequence 484350 from Patent EP1572962.
JD040870 - Sequence 21894 from Patent EP1572962.
JD319034 - Sequence 300058 from Patent EP1572962.
JD284344 - Sequence 265368 from Patent EP1572962.
JD263187 - Sequence 244211 from Patent EP1572962.
AK123563 - Homo sapiens cDNA FLJ41569 fis, clone CTONG2003298.
AK022596 - Homo sapiens cDNA FLJ12534 fis, clone NT2RM4000244.
LF347283 - JP 2014500723-A/154786: Polycomb-Associated Non-Coding RNAs.
AK027840 - Homo sapiens cDNA FLJ14934 fis, clone PLACE1009888.
LF347284 - JP 2014500723-A/154787: Polycomb-Associated Non-Coding RNAs.
LF347285 - JP 2014500723-A/154788: Polycomb-Associated Non-Coding RNAs.
LF347286 - JP 2014500723-A/154789: Polycomb-Associated Non-Coding RNAs.
MA582855 - JP 2018138019-A/154781: Polycomb-Associated Non-Coding RNAs.
MA582859 - JP 2018138019-A/154785: Polycomb-Associated Non-Coding RNAs.
MA582860 - JP 2018138019-A/154786: Polycomb-Associated Non-Coding RNAs.
MA582861 - JP 2018138019-A/154787: Polycomb-Associated Non-Coding RNAs.
MA582862 - JP 2018138019-A/154788: Polycomb-Associated Non-Coding RNAs.
MA582863 - JP 2018138019-A/154789: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_etcPathway - Electron Transport Reaction in Mitochondria

Reactome (by CSHL, EBI, and GO)

Protein P43304 (Reactome details) participates in the following event(s):

R-HSA-188467 Gly-3-P+FAD->DHAP+FADH2 (catalyzed by mitochondrial Gly-Phos dehydrogenase)
R-HSA-163560 Triglyceride catabolism
R-HSA-1483166 Synthesis of PA
R-HSA-8979227 Triglyceride metabolism
R-HSA-1483206 Glycerophospholipid biosynthesis
R-HSA-556833 Metabolism of lipids
R-HSA-1483257 Phospholipid metabolism
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A8K4V0, B3KSA9, ENST00000438166.1, ENST00000438166.2, ENST00000438166.3, ENST00000438166.4, ENST00000438166.5, ENST00000438166.6, GPD2 , GPDM_HUMAN, NM_000408, P43304, Q59FR1, Q9HAP9, uc320gks.1, uc320gks.2
UCSC ID: ENST00000438166.7_4
RefSeq Accession: NM_000408.5
Protein: P43304 (aka GPDM_HUMAN)

-  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.