Human Gene DPH3 (ENST00000383775.4) from GENCODE V44
  Description: Homo sapiens diphthamide biosynthesis 3 (DPH3), transcript variant 2, mRNA. (from RefSeq NM_001047434)
RefSeq Summary (NM_001047434): This gene encodes a CSL zinc finger-containing protein that is required for dipthamide biosynthesis. The encoded protein is necessary for the initial step in the modification of a histidine residue in elongation factor-2 to diphthamide. This modified residue is a target for ADP ribosylation by the bacterial toxins diphtheria toxin and Pseudomonas exotoxin A. Alternative splicing results in multiple transcript variants that encode the same isoform. [provided by RefSeq, Feb 2009].
Gencode Transcript: ENST00000383775.4
Gencode Gene: ENSG00000154813.10
Transcript (Including UTRs)
   Position: hg38 chr3:16,257,979-16,264,969 Size: 6,991 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg38 chr3:16,260,764-16,264,876 Size: 4,113 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:16,257,979-16,264,969)mRNA (may differ from genome)Protein (57 aa)
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HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DPH3_HUMAN
DESCRIPTION: RecName: Full=DPH3 homolog; AltName: Full=CSL-type zinc finger-containing protein 2; AltName: Full=DelGEF-interacting protein 1; Short=DelGIP1;
FUNCTION: Essential for the first step in the synthesis of diphthamide, a post-translational modification of histidine which occurs in elongation factor 2 and which can be ADP-ribosylated by diphtheria toxin and by Pseudomonas exotoxin A (By similarity).
FUNCTION: Down-regulation increases extracellular release of proteoglycans, indicating a possible role in the secretion process. Stimulates binding of GNEFR to SEC5.
INTERACTION: Q9UGK8:SERGEF; NbExp=3; IntAct=EBI-465363, EBI-465368;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Widely expressed with highest levels in small intestine, spleen, thymus, heart, liver and lung.
SIMILARITY: Belongs to the DPH3 family.
SIMILARITY: Contains 1 DPH-type zinc finger.

-  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: DPH3
Diseases sorted by gene-association score: diphtheria (11)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.98 RPKM in Cells - Cultured fibroblasts
Total median expression: 328.37 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -39.8093-0.428 Picture PostScript Text
3' UTR -712.802785-0.256 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
IPR007872 - Znf_DHP

Pfam Domains:
PF05207 - CSL zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2JR7 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q96FX2
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0017183 peptidyl-diphthamide biosynthetic process from peptidyl-histidine
GO:0050709 negative regulation of protein secretion
GO:0051099 positive regulation of binding

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK022970 - Homo sapiens cDNA FLJ12908 fis, clone NT2RP2004399.
LP895459 - Sequence 323 from Patent EP3253886.
BC094863 - Homo sapiens cDNA clone IMAGE:4843485.
BC073931 - Homo sapiens cDNA clone IMAGE:5200193, partial cds.
AK023203 - Homo sapiens cDNA FLJ13141 fis, clone NT2RP3003210.
AK092040 - Homo sapiens cDNA FLJ34721 fis, clone MESAN2005766.
JD142583 - Sequence 123607 from Patent EP1572962.
JD222941 - Sequence 203965 from Patent EP1572962.
JD497890 - Sequence 478914 from Patent EP1572962.
AK311618 - Homo sapiens cDNA, FLJ18660.
BC010181 - Homo sapiens DPH3, KTI11 homolog (S. cerevisiae), mRNA (cDNA clone MGC:20197 IMAGE:4543414), complete cds.
JF432467 - Synthetic construct Homo sapiens clone IMAGE:100073686 DPH3, KTI11 homolog (S. cerevisiae) (DPH3) gene, encodes complete protein.
KJ896002 - Synthetic construct Homo sapiens clone ccsbBroadEn_05396 DPH3 gene, encodes complete protein.

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

Protein Q96FX2 (Reactome details) participates in the following event(s):

R-HSA-5358494 DPH2 transfers a 3-amino-3-carboxypropyl group from AdoMet to residue 715 of nascent EEF2
R-HSA-5358493 Synthesis of diphthamide-EEF2
R-HSA-163841 Gamma carboxylation, hypusine formation and arylsulfatase activation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: DESR1, DPH3_HUMAN, ENST00000383775.1, ENST00000383775.2, ENST00000383775.3, NM_001047434, Q96FX2, uc003cav.1, uc003cav.2, uc003cav.3, uc003cav.4, ZCSL2
UCSC ID: ENST00000383775.4
RefSeq Accession: NM_001047434
Protein: Q96FX2 (aka DPH3_HUMAN)
CCDS: CCDS43058.1

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