Human Gene HDGF (ENST00000357325.10_7) from GENCODE V47lift37
  Description: heparin binding growth factor, transcript variant 1 (from RefSeq NM_004494.3)
Gencode Transcript: ENST00000357325.10_7
Gencode Gene: ENSG00000143321.19_9
Transcript (Including UTRs)
   Position: hg19 chr1:156,711,901-156,721,467 Size: 9,567 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr1:156,713,241-156,721,221 Size: 7,981 Coding Exon Count: 6 

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 (chr1:156,711,901-156,721,467)mRNA (may differ from genome)Protein (240 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HDGF_HUMAN
DESCRIPTION: RecName: Full=Hepatoma-derived growth factor; Short=HDGF; AltName: Full=High mobility group protein 1-like 2; Short=HMG-1L2;
FUNCTION: Heparin-binding protein, with mitogenic activity for fibroblasts. Acts as a transcriptional repressor.
SUBUNIT: Monomer, and domain-swapped homodimer.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Ubiquitous.
DOMAIN: The PWWP domain harbors the heparin-binding sites and is responsible for DNA-binding, while the C-terminal region is essentially unstructured.
PTM: Sumoylated with SUMO1. Sumoylation prevents binding to chromatin.
SIMILARITY: Belongs to the HDGF family.
SIMILARITY: Contains 1 PWWP domain.

-  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: HDGF
Diseases sorted by gene-association score: lung cancer (2), hepatocellular carcinoma (2), retinitis pigmentosa, y-linked (1)

-  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: 72.88 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2269.78 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 -137.30246-0.558 Picture PostScript Text
3' UTR -454.201340-0.339 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
IPR000313 - PWWP

Pfam Domains:
PF00855 - PWWP domain

SCOP Domains:
63748 - Tudor/PWWP/MBT

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1RI0 - NMR MuPIT 2NLU - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P51858
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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0001106 RNA polymerase II transcription corepressor activity
GO:0001222 transcription corepressor binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0008083 growth factor activity
GO:0008201 heparin binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007165 signal transduction
GO:0008283 cell proliferation
GO:0009987 cellular process
GO:0010469 regulation of receptor activity
GO:0036498 IRE1-mediated unfolded protein response

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0017053 transcriptional repressor complex
GO:0031012 extracellular matrix


-  Descriptions from all associated GenBank mRNAs
  BC018991 - Homo sapiens hepatoma-derived growth factor (high-mobility group protein 1-like), mRNA (cDNA clone MGC:20061 IMAGE:3503321), complete cds.
GQ891516 - Homo sapiens clone HEL-S-237 epididymis secretory sperm binding protein mRNA, complete cds.
L24521 - Human transformation-related protein mRNA, 3' end.
D16431 - Homo sapiens mRNA for hepatoma-derived growth factor, complete cds.
E08546 - DNA encoding human Hepatoma-derived Growth Factor.
AK096411 - Homo sapiens cDNA FLJ39092 fis, clone NT2RP7019835, highly similar to HEPATOMA-DERIVED GROWTH FACTOR.
JD081699 - Sequence 62723 from Patent EP1572962.
JD263043 - Sequence 244067 from Patent EP1572962.
JD055655 - Sequence 36679 from Patent EP1572962.
JD192492 - Sequence 173516 from Patent EP1572962.
JD266331 - Sequence 247355 from Patent EP1572962.
JD381512 - Sequence 362536 from Patent EP1572962.
JD260574 - Sequence 241598 from Patent EP1572962.
JD191098 - Sequence 172122 from Patent EP1572962.
JD083745 - Sequence 64769 from Patent EP1572962.
JD500473 - Sequence 481497 from Patent EP1572962.
AL833592 - Homo sapiens mRNA; cDNA DKFZp686J1764 (from clone DKFZp686J1764).
JD525089 - Sequence 506113 from Patent EP1572962.
JD561169 - Sequence 542193 from Patent EP1572962.
JD177324 - Sequence 158348 from Patent EP1572962.
JD173002 - Sequence 154026 from Patent EP1572962.
JD216214 - Sequence 197238 from Patent EP1572962.
JD047308 - Sequence 28332 from Patent EP1572962.
AK292325 - Homo sapiens cDNA FLJ75113 complete cds.
JD498726 - Sequence 479750 from Patent EP1572962.
JD206784 - Sequence 187808 from Patent EP1572962.
JD415426 - Sequence 396450 from Patent EP1572962.
JD051086 - Sequence 32110 from Patent EP1572962.
JD160106 - Sequence 141130 from Patent EP1572962.
JD368312 - Sequence 349336 from Patent EP1572962.
JD171835 - Sequence 152859 from Patent EP1572962.
JD205354 - Sequence 186378 from Patent EP1572962.
AK304468 - Homo sapiens cDNA FLJ53700 complete cds, highly similar to Hepatoma-derived growth factor.
JD381365 - Sequence 362389 from Patent EP1572962.
JD037495 - Sequence 18519 from Patent EP1572962.
JD065138 - Sequence 46162 from Patent EP1572962.
AK298342 - Homo sapiens cDNA FLJ55039 complete cds, moderately similar to Hepatoma-derived growth factor.
E08545 - DNA encoding human Hepatoma-derived Growth Factor.
DQ893406 - Synthetic construct clone IMAGE:100006036; FLH199482.01X; RZPDo839D0282D hepatoma-derived growth factor (high-mobility group protein 1-like) (HDGF) gene, encodes complete protein.
DQ896724 - Synthetic construct Homo sapiens clone IMAGE:100011184; FLH199388.01L; RZPDo839D0281D hepatoma-derived growth factor (high-mobility group protein 1-like) (HDGF) gene, encodes complete protein.
KJ896964 - Synthetic construct Homo sapiens clone ccsbBroadEn_06358 HDGF gene, encodes complete protein.
AK315514 - Homo sapiens cDNA, FLJ96580, highly similar to Homo sapiens hepatoma-derived growth factor (high-mobility group protein 1-like) (HDGF), mRNA.
CU676350 - Synthetic construct Homo sapiens gateway clone IMAGE:100018596 5' read HDGF mRNA.
JD407233 - Sequence 388257 from Patent EP1572962.
JD216879 - Sequence 197903 from Patent EP1572962.
JD408985 - Sequence 390009 from Patent EP1572962.
JD465000 - Sequence 446024 from Patent EP1572962.

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

Protein P51858 (Reactome details) participates in the following event(s):

R-HSA-381038 XBP1(S) activates chaperone genes
R-HSA-381070 IRE1alpha activates chaperones
R-HSA-381119 Unfolded Protein Response (UPR)
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B3KU21, D3DVC9, ENST00000357325.1, ENST00000357325.2, ENST00000357325.3, ENST00000357325.4, ENST00000357325.5, ENST00000357325.6, ENST00000357325.7, ENST00000357325.8, ENST00000357325.9, HDGF_HUMAN, HMG1L2, NM_004494, P51858, Q5SZ07, Q5SZ08, Q5SZ09, uc317zzg.1, uc317zzg.2
UCSC ID: ENST00000357325.10_7
RefSeq Accession: NM_004494.3
Protein: P51858 (aka HDGF_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.