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Aliases for HDGF Gene

Aliases for HDGF Gene

  • Heparin Binding Growth Factor 2 3 5
  • High Mobility Group Protein 1-Like 2 3 4
  • Hepatoma Derived Growth Factor 2 3
  • HMG1L2 3 4
  • Hepatoma-Derived Growth Factor (High-Mobility Group Protein 1-Like) 2
  • High-Mobility Group Protein 1-Like 2
  • Hepatoma-Derived Growth Factor 3
  • HMG-1L2 4

External Ids for HDGF Gene

Previous GeneCards Identifiers for HDGF Gene

  • GC01M154581
  • GC01M152477
  • GC01M153489
  • GC01M153928
  • GC01M153524
  • GC01M154978
  • GC01M156711
  • GC01M128069

Summaries for HDGF Gene

Entrez Gene Summary for HDGF Gene

  • This gene encodes a member of the hepatoma-derived growth factor family. The encoded protein has mitogenic and DNA-binding activity and may play a role in cellular proliferation and differentiation. High levels of expression of this gene enhance the growth of many tumors. This gene was thought initially to be located on chromosome X; however, that location has been determined to correspond to a related pseudogene. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jan 2016]

GeneCards Summary for HDGF Gene

HDGF (Heparin Binding Growth Factor) is a Protein Coding gene. Diseases associated with HDGF include Lung Cancer and Retinitis Pigmentosa, Y-Linked. Among its related pathways are ERK Signaling and Akt Signaling. Gene Ontology (GO) annotations related to this gene include growth factor activity. An important paralog of this gene is HDGFL1.

UniProtKB/Swiss-Prot for HDGF Gene

  • Heparin-binding protein, with mitogenic activity for fibroblasts. Acts as a transcriptional repressor.

Gene Wiki entry for HDGF Gene

Additional gene information for HDGF Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HDGF Gene

Genomics for HDGF Gene

GeneHancer (GH) Regulatory Elements for HDGF Gene

Promoters and enhancers for HDGF Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J156740 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 662.6 +20.1 20063 13.6 CLOCK MLX DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF263 SP3 HDGF MRPL24 KHDC4 GON4L RRNAD1 PRCC LOC246784 CCT3 SYT11 ISG20L2
GH01J156765 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 661.7 -1.0 -1021 4.5 CLOCK ZFP64 FEZF1 DMAP1 YY1 ZNF213 ZNF143 SP3 MEF2D NBN HDGF PRCC RRNAD1 GON4L KHDC4 LOC246784 ISG20L2 CCT3 MRPL24 LRRC71
GH01J156725 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 12.4 +39.1 39138 5.1 CLOCK DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 GLIS1 NBN RRNAD1 ISG20L2 CRABP2 HDGF MRPL24 GC01M156724 PIR61627
GH01J156456 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.2 +309.5 309549 2.7 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 ZNF416 ZNF143 C1orf61 ENSG00000236947 KHDC4 GON4L ENSG00000271267 RRNAD1 LOC246784 LMNA ASH1L MSTO2P
GH01J156689 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.7 +74.9 74925 6 HDGF PKNOX1 ARNT ARID4B NEUROD1 SIN3A ZBTB7B SLC30A9 POLR2B ZNF766 RRNAD1 ENSG00000237588 KHDC4 GON4L MSTO2P PRCC LOC246784 CCT3 LOC105371453 BCAN
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HDGF on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HDGF gene promoter:
  • E2F-3a
  • E2F-2
  • E2F-1
  • E2F

Genomic Locations for HDGF Gene

Genomic Locations for HDGF Gene
chr1:156,742,107-156,766,925
(GRCh38/hg38)
Size:
24,819 bases
Orientation:
Minus strand
chr1:156,711,899-156,736,717
(GRCh37/hg19)
Size:
24,819 bases
Orientation:
Minus strand

Genomic View for HDGF Gene

Genes around HDGF on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HDGF Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HDGF Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HDGF Gene

Proteins for HDGF Gene

  • Protein details for HDGF Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P51858-HDGF_HUMAN
    Recommended name:
    Hepatoma-derived growth factor
    Protein Accession:
    P51858
    Secondary Accessions:
    • B3KU21
    • D3DVC9
    • Q5SZ07
    • Q5SZ08
    • Q5SZ09

    Protein attributes for HDGF Gene

    Size:
    240 amino acids
    Molecular mass:
    26788 Da
    Quaternary structure:
    • Monomer, and domain-swapped homodimer.

    Three dimensional structures from OCA and Proteopedia for HDGF Gene

    Alternative splice isoforms for HDGF Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HDGF Gene

Post-translational modifications for HDGF Gene

  • Sumoylated with SUMO1. Sumoylation prevents binding to chromatin.
  • Ubiquitination at Lys80 and Lys11
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HDGF Gene

Domains & Families for HDGF Gene

Gene Families for HDGF Gene

Protein Domains for HDGF Gene

Blocks:
InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

P51858

UniProtKB/Swiss-Prot:

HDGF_HUMAN :
  • The PWWP domain harbors the heparin-binding sites and is responsible for DNA-binding, while the C-terminal region is essentially unstructured.
  • Belongs to the HDGF family.
Domain:
  • The PWWP domain harbors the heparin-binding sites and is responsible for DNA-binding, while the C-terminal region is essentially unstructured.
Family:
  • Belongs to the HDGF family.
genes like me logo Genes that share domains with HDGF: view

Function for HDGF Gene

Molecular function for HDGF Gene

UniProtKB/Swiss-Prot Function:
Heparin-binding protein, with mitogenic activity for fibroblasts. Acts as a transcriptional repressor.
GENATLAS Biochemistry:
hepatoma-derived growth factor,with mitogenic activity for fibroblasts,expressed (in mice) predominantly in testis and skeletal muscle,to intermediate extents in heart,brain,lung,liver,kidney

Phenotypes From GWAS Catalog for HDGF Gene

Gene Ontology (GO) - Molecular Function for HDGF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0001222 transcription corepressor binding IPI 19162039
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding HDA 22658674
GO:0008083 growth factor activity IEA --
genes like me logo Genes that share ontologies with HDGF: view
genes like me logo Genes that share phenotypes with HDGF: view

Animal Models for HDGF Gene

MGI Knock Outs for HDGF:
  • Hdgf Hdgf<tm1Sefr>

Animal Model Products

miRNA for HDGF Gene

miRTarBase miRNAs that target HDGF

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HDGF Gene

Localization for HDGF Gene

Subcellular locations from UniProtKB/Swiss-Prot for HDGF Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HDGF gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 2
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HDGF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IDA 27068509
GO:0005615 extracellular space TAS,HDA 20551380
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,TAS --
genes like me logo Genes that share ontologies with HDGF: view

Pathways & Interactions for HDGF Gene

genes like me logo Genes that share pathways with HDGF: view

Gene Ontology (GO) - Biological Process for HDGF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 19162039
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007165 signal transduction NAS 7929202
GO:0008283 cell proliferation TAS 7929202
genes like me logo Genes that share ontologies with HDGF: view

No data available for SIGNOR curated interactions for HDGF Gene

Drugs & Compounds for HDGF Gene

(3) Drugs for HDGF Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Copper Approved, Investigational Pharma Target 202
Heparin Approved, Investigational Pharma Antagonist 905

(2) Additional Compounds for HDGF Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HDGF: view

Transcripts for HDGF Gene

Unigene Clusters for HDGF Gene

Hepatoma-derived growth factor:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HDGF Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7
SP1: - -
SP2: - -
SP3:
SP4: -
SP5: -

Relevant External Links for HDGF Gene

GeneLoc Exon Structure for
HDGF
ECgene alternative splicing isoforms for
HDGF

Expression for HDGF Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HDGF Gene

Protein differential expression in normal tissues from HIPED for HDGF Gene

This gene is overexpressed in Nasal epithelium (7.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HDGF Gene



Protein tissue co-expression partners for HDGF Gene

NURSA nuclear receptor signaling pathways regulating expression of HDGF Gene:

HDGF

SOURCE GeneReport for Unigene cluster for HDGF Gene:

Hs.743948

mRNA Expression by UniProt/SwissProt for HDGF Gene:

P51858-HDGF_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for HDGF Gene

  • Nervous system(4.8)
  • Liver(4.5)
  • Blood(4.2)
  • Lung(4.1)
  • Intestine(3.7)
  • Eye(2.7)
  • Muscle(2.6)
  • Pancreas(2.5)
  • Heart(2.4)
  • Kidney(2.3)
  • Lymph node(2.3)
  • Bone marrow(2.2)
  • Skin(2.2)
genes like me logo Genes that share expression patterns with HDGF: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for HDGF Gene

Orthologs for HDGF Gene

This gene was present in the common ancestor of animals.

Orthologs for HDGF Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HDGF 34 33
  • 98.75 (n)
OneToOne
cow
(Bos Taurus)
Mammalia HDGF 34 33
  • 91.63 (n)
OneToOne
dog
(Canis familiaris)
Mammalia HDGF 34 33
  • 89.9 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hdgf 33
  • 87.62 (n)
mouse
(Mus musculus)
Mammalia Hdgf 16 34 33
  • 86.78 (n)
oppossum
(Monodelphis domestica)
Mammalia HDGF 34
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 9 (a)
ManyToMany
chicken
(Gallus gallus)
Aves HDGF 33
  • 77.89 (n)
-- 34
  • 63 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 60 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia hdgf 33
  • 65.87 (n)
zebrafish
(Danio rerio)
Actinopterygii si:ch211-116m6.3 34
  • 4 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta CG7946 34
  • 12 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea C06A5.3 34
  • 7 (a)
OneToMany
Species where no ortholog for HDGF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HDGF Gene

ENSEMBL:
Gene Tree for HDGF (if available)
TreeFam:
Gene Tree for HDGF (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HDGF: view image

Paralogs for HDGF Gene

Paralogs for HDGF Gene

(4) SIMAP similar genes for HDGF Gene using alignment to 4 proteins:

  • HDGF_HUMAN
  • A8K8G0_HUMAN
  • Q7Z4S4_HUMAN
  • Q7Z4S5_HUMAN

Pseudogenes.org Pseudogenes for HDGF Gene

genes like me logo Genes that share paralogs with HDGF: view

Variants for HDGF Gene

Sequence variations from dbSNP and Humsavar for HDGF Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000015286 -- 156,754,306(-) A/G upstream_transcript_variant
rs1000309873 -- 156,748,671(-) G/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000713410 -- 156,744,009(-) C/T intron_variant
rs1000930740 -- 156,750,127(-) T/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1001253444 -- 156,750,412(-) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HDGF Gene

Variant ID Type Subtype PubMed ID
nsv819403 CNV loss 19587683
nsv831648 CNV loss 17160897

Variation tolerance for HDGF Gene

Residual Variation Intolerance Score: 43.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.29; 81.34% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HDGF Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HDGF

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HDGF Gene

Disorders for HDGF Gene

MalaCards: The human disease database

(3) MalaCards diseases for HDGF Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
lung cancer
  • lung cancer, susceptibility to
retinitis pigmentosa, y-linked
  • rpy
cholangiocarcinoma
  • cholangiocarcinoma, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search HDGF in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HDGF

genes like me logo Genes that share disorders with HDGF: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HDGF Gene

Publications for HDGF Gene

  1. Hepatoma-derived growth factor binds DNA through the N-terminal PWWP domain. (PMID: 17974029) Yang J … Everett AD (BMC molecular biology 2007) 3 4 22 58
  2. Hepatoma-derived growth factor stimulates cell growth after translocation to the nucleus by nuclear localization signals. (PMID: 11751870) Kishima Y … Nakamura H (The Journal of biological chemistry 2002) 3 4 22 58
  3. Mapping of the gene encoding the human hepatoma-derived growth factor (HDGF) with homology to the high-mobility group (HMG)-1 protein to Xq25. (PMID: 8833162) Wanschura S … Bullerdiek J (Genomics 1996) 2 3 22 58
  4. Molecular cloning of complementary DNA for a novel human hepatoma-derived growth factor. Its homology with high mobility group-1 protein. (PMID: 7929202) Nakamura H … Kishimoto T (The Journal of biological chemistry 1994) 3 4 22 58
  5. Two new isoforms of the human hepatoma-derived growth factor interact with components of the cytoskeleton. (PMID: 26845719) Nüße J … Dietz F (Biological chemistry 2016) 2 3 58

Products for HDGF Gene