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HDGF heparin binding growth factor [ Homo sapiens (human) ]

Gene ID: 3068, updated on 3-Apr-2024

Summary

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Official Symbol
HDGFprovided by HGNC
Official Full Name
heparin binding growth factorprovided by HGNC
Primary source
HGNC:HGNC:4856
See related
Ensembl:ENSG00000143321 MIM:600339; AllianceGenome:HGNC:4856
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HMG1L2
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 90.4), liver (RPKM 48.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1q23.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (156742107..156767366, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155878940..155904217, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (156711899..156722240, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156674429-156674930 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156676520-156677196 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156677875-156678551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156682885-156683400 Neighboring gene cellular retinoic acid binding protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1434 Neighboring gene interferon stimulated exonuclease gene 20 like 2 Neighboring gene methyltransferase like 25B Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:156711011-156711988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1878 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156717051-156717748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156717749-156718446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156718447-156719143 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156721068-156721842 Neighboring gene mitochondrial ribosomal protein L24 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156729657-156730190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156730191-156730723 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156736100-156736726 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:156736727-156737352 Neighboring gene proline rich mitotic checkpoint control factor Neighboring gene Sharpr-MPRA regulatory region 3718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156774267-156774768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156778787-156779288 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156783176-156783722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1438 Neighboring gene SH2 domain containing 2A Neighboring gene neurotrophic receptor tyrosine kinase 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Extracellular vesicle proteomic analysis leads to the discovery of HDGF as a new factor in multiple myeloma biology. Hoelzinger DB, et al. Blood Adv, 2022 Jun 14. PMID 35395072, Free PMC Article
  2. miR-4323 targets hepatoma-derived growth factor (HDGF) to suppress colorectal cancer cell proliferation. Xia C, et al. Pathol Res Pract, 2021 Sep. PMID 34314948
  3. Hepatoma-Derived Growth Factor: An Overview and Its Role as a Potential Therapeutic Target Molecule for Digestive Malignancies. Enomoto H, et al. Int J Mol Sci, 2020 Jun 13. PMID 32545762, Free PMC Article
  4. Hepatoma-derived growth factor participates in Helicobacter Pylori-induced neutrophils recruitment, gastritis and gastric carcinogenesis. Chu TH, et al. Oncogene, 2019 Sep. PMID 31332288
  5. Hepatoma-derived growth factor supports the antiapoptosis and profibrosis of pancreatic stellate cells. Chen YT, et al. Cancer Lett, 2019 Aug 10. PMID 31078734

See all (156) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. [miR-29a-3p Targets Hepatoma-Derived Growth Factor to Inhibit the Proliferation and Promote the Apoptosis of E6-1 Cells].
    Title: [miR-29a-3p Targets Hepatoma-Derived Growth Factor to Inhibit the Proliferation and Promote the Apoptosis of E6-1 Cells].
  2. Extracellular vesicle proteomic analysis leads to the discovery of HDGF as a new factor in multiple myeloma biology.
    Title: Extracellular vesicle proteomic analysis leads to the discovery of HDGF as a new factor in multiple myeloma biology.
  3. Specificity protein 1-induced serine peptidase inhibitor, Kunitz Type 1 antisense RNA1 regulates colorectal cancer cell proliferation, migration, invasion and apoptosis through targeting heparin binding growth factor via sponging microRNA-214.
    Title: Specificity protein 1-induced serine peptidase inhibitor, Kunitz Type 1 antisense RNA1 regulates colorectal cancer cell proliferation, migration, invasion and apoptosis through targeting heparin binding growth factor via sponging microRNA-214.
  4. miR-4323 targets hepatoma-derived growth factor (HDGF) to suppress colorectal cancer cell proliferation.
    Title: miR-4323 targets hepatoma-derived growth factor (HDGF) to suppress colorectal cancer cell proliferation.
  5. Recurrent co-alteration of HDGF and SETDB1 on chromosome 1q drives cutaneous melanoma progression and poor prognosis.
    Title: Recurrent co-alteration of HDGF and SETDB1 on chromosome 1q drives cutaneous melanoma progression and poor prognosis.
  6. Exosomal lncRNA HEIH promotes cisplatin resistance in tongue squamous cell carcinoma via targeting miR-3619-5p/HDGF axis.
    Title: Exosomal lncRNA HEIH promotes cisplatin resistance in tongue squamous cell carcinoma via targeting miR-3619-5p/HDGF axis.
  7. A novel HDGF-ALCAM axis promotes the metastasis of Ewing sarcoma via regulating the GTPases signaling pathway.
    Title: A novel HDGF-ALCAM axis promotes the metastasis of Ewing sarcoma via regulating the GTPases signaling pathway.
  8. Long intergenic noncoding RNA LINC01232 contributes to esophageal squamous cell carcinoma progression by sequestering microRNA6543p and consequently promoting hepatomaderived growth factor expression.
    Title: Long intergenic non‑coding RNA LINC01232 contributes to esophageal squamous cell carcinoma progression by sequestering microRNA‑654‑3p and consequently promoting hepatoma‑derived growth factor expression.
  9. Long noncoding RNA MKLN1AS aggravates hepatocellular carcinoma progression by functioning as a molecular sponge for miR6543p, thereby promoting hepatomaderived growth factor expression.
    Title: Long non‑coding RNA MKLN1‑AS aggravates hepatocellular carcinoma progression by functioning as a molecular sponge for miR‑654‑3p, thereby promoting hepatoma‑derived growth factor expression.
  10. Hsa_circ_0079480 promotes tumor progression in acute myeloid leukemia via miR-654-3p/HDGF axis.
    Title: Hsa_circ_0079480 promotes tumor progression in acute myeloid leukemia via miR-654-3p/HDGF axis.
Submit: New GeneRIF Correction See all GeneRIFs (79)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of hepatoma-derived growth factor (HDGF) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ96580, DKFZp686J1764

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding HDA PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables growth factor activity IEA
Inferred from Electronic Annotation
more info
  
enables heparin binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription corepressor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in protein localization to nucleus IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in collagen-containing extracellular matrix HDA PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular region HDA PubMed 
located_in extracellular space HDA PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription repressor complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
hepatoma-derived growth factor
Names
epididymis secretory sperm binding protein
hepatoma derived growth factor
high mobility group protein 1-like 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001126050.2 → NP_001119522.1  hepatoma-derived growth factor isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform d.
    Source sequence(s)
    AL590666
    Consensus CDS
    CCDS44247.1
    UniProtKB/TrEMBL
    B7Z958
    Related
    ENSP00000357189.5, ENST00000368206.5
    Conserved Domains (1) summary
    cl02554
    Location:40 → 108
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

  2. NM_001126051.1 → NP_001119523.1  hepatoma-derived growth factor isoform c

    See identical proteins and their annotated locations for NP_001119523.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (c) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform d.
    Source sequence(s)
    AL590666, D16431, DA207052, DA367806, F36780
    Consensus CDS
    CCDS44248.1
    UniProtKB/TrEMBL
    B7Z958
    Related
    ENSP00000357192.5, ENST00000368209.9
    Conserved Domains (1) summary
    cl02554
    Location:21 → 85
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

  3. NM_001319186.2 → NP_001306115.1  hepatoma-derived growth factor isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (d).
    Source sequence(s)
    AL590666
    UniProtKB/TrEMBL
    B7Z958
    Conserved Domains (1) summary
    cl02554
    Location:40 → 108
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

  4. NM_001319187.2 → NP_001306116.1  hepatoma-derived growth factor isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (e) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform d. Variants 5 and 6 both encode the same isoform (e).
    Source sequence(s)
    AL590666
    UniProtKB/TrEMBL
    A8K8G0, B7Z958
    Conserved Domains (1) summary
    cl02554
    Location:7 → 60
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

  5. NM_001319188.2 → NP_001306117.1  hepatoma-derived growth factor isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (e) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform d. Variants 5 and 6 both encode the same isoform (e).
    Source sequence(s)
    AL590666
    UniProtKB/TrEMBL
    A8K8G0, B7Z958
    Conserved Domains (1) summary
    cl02554
    Location:7 → 60
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

  6. NM_004494.3 → NP_004485.1  hepatoma-derived growth factor isoform a

    See identical proteins and their annotated locations for NP_004485.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (a) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform d.
    Source sequence(s)
    AL590666
    Consensus CDS
    CCDS1156.1
    UniProtKB/Swiss-Prot
    B3KU21, D3DVC9, P51858, Q5SZ07, Q5SZ08, Q5SZ09
    UniProtKB/TrEMBL
    A0A384NPW1, B2RDE8
    Related
    ENSP00000349878.5, ENST00000357325.10
    Conserved Domains (1) summary
    cd05834
    Location:8 → 92
    HDGF_related; The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, ...

RNA

  1. NR_135008.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains an alternate exon and uses an alternate splice junction compared to variant 4. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL590666

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    156742107..156767366 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047418832.1 → XP_047274788.1  hepatoma-derived growth factor isoform X1

    UniProtKB/TrEMBL
    A8K8G0

  2. XM_047418831.1 → XP_047274787.1  hepatoma-derived growth factor isoform X1

    UniProtKB/TrEMBL
    A8K8G0
    Related
    ENST00000465180.5

  3. XM_047418833.1 → XP_047274789.1  hepatoma-derived growth factor isoform X1

    UniProtKB/TrEMBL
    A8K8G0

  4. XM_011509455.3 → XP_011507757.1  hepatoma-derived growth factor isoform X1

    See identical proteins and their annotated locations for XP_011507757.1

    UniProtKB/TrEMBL
    A8K8G0, B7Z958
    Conserved Domains (1) summary
    cl02554
    Location:7 → 60
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

  5. XM_011509454.3 → XP_011507756.1  hepatoma-derived growth factor isoform X1

    See identical proteins and their annotated locations for XP_011507756.1

    UniProtKB/TrEMBL
    A8K8G0, B7Z958
    Conserved Domains (1) summary
    cl02554
    Location:7 → 60
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

  6. XM_011509453.3 → XP_011507755.2  hepatoma-derived growth factor isoform X1

    UniProtKB/TrEMBL
    A8K8G0, B7Z958
    Conserved Domains (1) summary
    cl02554
    Location:7 → 60
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    155878940..155904217 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336208.1 → XP_054192183.1  hepatoma-derived growth factor isoform X1

    UniProtKB/TrEMBL
    A8K8G0

  2. XM_054336207.1 → XP_054192182.1  hepatoma-derived growth factor isoform X1

    UniProtKB/TrEMBL
    A8K8G0

  3. XM_054336209.1 → XP_054192184.1  hepatoma-derived growth factor isoform X1

    UniProtKB/TrEMBL
    A8K8G0

  4. XM_054336205.1 → XP_054192180.1  hepatoma-derived growth factor isoform X1

    UniProtKB/TrEMBL
    A8K8G0

  5. XM_054336206.1 → XP_054192181.1  hepatoma-derived growth factor isoform X1

    UniProtKB/TrEMBL
    A8K8G0

  6. XM_054336204.1 → XP_054192179.1  hepatoma-derived growth factor isoform X1

    UniProtKB/TrEMBL
    A8K8G0
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P51858.1 GenPept UniProtKB/Swiss-Prot:P51858

Gene LinkOut

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