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

Gene ID: 3068, updated on 21-Apr-2019

Summary

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
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

Genomic context

See HDGF in Genome Data Viewer
Location:
1q23.1
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (156742107..156752448, complement)
105 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 interferon stimulated exonuclease gene 20 like 2 Neighboring gene ribosomal RNA adenine dimethylase domain containing 1 Neighboring gene mitochondrial ribosomal protein L24 Neighboring gene proline rich mitotic checkpoint control factor Neighboring gene SH2 domain containing 2A Neighboring gene neurotrophic receptor tyrosine kinase 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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 BioSystems

  • IRE1alpha activates chaperones, organism-specific biosystem (from REACTOME)
    IRE1alpha activates chaperones, organism-specific biosystemIRE1-alpha is a single-pass transmembrane protein that resides in the endoplasmic reticulum (ER) membrane. The C-terminus of IRE1-alpha is located in the cytosol; the N-terminus is located in the ER ...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Unfolded Protein Response (UPR), organism-specific biosystem (from REACTOME)
    Unfolded Protein Response (UPR), organism-specific biosystemThe Unfolded Protein Response (UPR) is a regulatory system that protects the Endoplasmic Reticulum (ER) from overload. The UPR is provoked by the accumulation of improperly folded protein in the ER d...
  • XBP1(S) activates chaperone genes, organism-specific biosystem (from REACTOME)
    XBP1(S) activates chaperone genes, organism-specific biosystemXbp-1 (S) binds the sequence CCACG in ER Stress Responsive Elements (ERSE, consensus sequence CCAAT (N)9 CCACG) located upstream from many genes. The ubiquitous transcription factor NF-Y, a heterotri...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ96580, DKFZp686J1764

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA binding HDA PubMed 
growth factor activity IEA
Inferred from Electronic Annotation
more info
 
heparin binding IEA
Inferred from Electronic Annotation
more info
 
nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
IRE1-mediated unfolded protein response TAS
Traceable Author Statement
more info
 
cellular response to interleukin-7 IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
regulation of signaling receptor activity IEA
Inferred from Electronic Annotation
more info
 
signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
collagen-containing extracellular matrix HDA PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
extracellular region HDA PubMed 
extracellular space HDA PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
transcriptional repressor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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_001126050.1NP_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, AU131311, CN392158, D16431, F36780
    Consensus CDS
    CCDS44247.1
    UniProtKB/Swiss-Prot
    P51858
    Related
    ENSP00000357189.5, ENST00000368206.5
    Conserved Domains (1) summary
    cl02554
    Location:40108
    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_001126051.1NP_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/Swiss-Prot
    P51858
    Related
    ENSP00000357192.5, ENST00000368209.9
    Conserved Domains (1) summary
    cl02554
    Location:2185
    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_001319186.1NP_001306115.1  hepatoma-derived growth factor isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (d).
    Source sequence(s)
    AK304468, AL590666, AU131311, D16431, F36780
    UniProtKB/Swiss-Prot
    P51858
    UniProtKB/TrEMBL
    B7Z958
    Conserved Domains (1) summary
    cl02554
    Location:40108
    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_001319187.1NP_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)
    AK292325, D16431, F36780
    UniProtKB/Swiss-Prot
    P51858
    UniProtKB/TrEMBL
    A8K8G0
    Conserved Domains (1) summary
    cl02554
    Location:760
    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_001319188.1NP_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, D16431, DB057555, F36780
    UniProtKB/Swiss-Prot
    P51858
    UniProtKB/TrEMBL
    A8K8G0
    Conserved Domains (1) summary
    cl02554
    Location:760
    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_004494.3NP_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
    P51858
    Related
    ENSP00000349878.5, ENST00000357325.10
    Conserved Domains (1) summary
    cd05834
    Location:892
    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_135008.1 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, AU131311, CA866443, D16431, F36780

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    156742107..156752448 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509455.2XP_011507757.1  hepatoma-derived growth factor isoform X1

    See identical proteins and their annotated locations for XP_011507757.1

    UniProtKB/TrEMBL
    A8K8G0
    Conserved Domains (1) summary
    cl02554
    Location:760
    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. XM_011509454.2XP_011507756.1  hepatoma-derived growth factor isoform X1

    See identical proteins and their annotated locations for XP_011507756.1

    UniProtKB/TrEMBL
    A8K8G0
    Conserved Domains (1) summary
    cl02554
    Location:760
    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. XM_011509453.2XP_011507755.2  hepatoma-derived growth factor isoform X1

    UniProtKB/TrEMBL
    A8K8G0
    Conserved Domains (1) summary
    cl02554
    Location:760
    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 ...

RNA

  1. XR_001737133.1 RNA Sequence

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