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

    Gene ID: 3068, updated on 27-Nov-2024

    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; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HDGF in Genome Data Viewer
    Location:
    1q23.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (156742107..156767366, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155878940..155904217, complement)
    RS_2024_09 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

    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 Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 actin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables growth factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    NOT enables heparin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables heparin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables heparin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription corepressor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription corepressor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables tubulin binding 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)

    NEW Try the new Transcript table

    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_001126050.2NP_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: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/TrEMBL
      B7Z958
      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_001319186.2NP_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: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_001319187.2NP_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: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_001319188.2NP_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: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
      B3KU21, D3DVC9, P51858, Q5SZ07, Q5SZ08, Q5SZ09
      UniProtKB/TrEMBL
      A0A384NPW1, B2RDE8
      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_135008.2 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_2024_08

    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_047418832.1XP_047274788.1  hepatoma-derived growth factor isoform X1

      UniProtKB/TrEMBL
      A8K8G0
    2. XM_047418831.1XP_047274787.1  hepatoma-derived growth factor isoform X1

      UniProtKB/TrEMBL
      A8K8G0
      Related
      ENST00000465180.5
    3. XM_047418833.1XP_047274789.1  hepatoma-derived growth factor isoform X1

      UniProtKB/TrEMBL
      A8K8G0
    4. XM_011509455.3XP_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: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. XM_011509454.3XP_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: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. XM_011509453.3XP_011507755.2  hepatoma-derived growth factor isoform X1

      UniProtKB/TrEMBL
      A8K8G0, B7Z958
      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 ...

    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_054336208.1XP_054192183.1  hepatoma-derived growth factor isoform X1

      UniProtKB/TrEMBL
      A8K8G0
    2. XM_054336207.1XP_054192182.1  hepatoma-derived growth factor isoform X1

      UniProtKB/TrEMBL
      A8K8G0
    3. XM_054336209.1XP_054192184.1  hepatoma-derived growth factor isoform X1

      UniProtKB/TrEMBL
      A8K8G0
    4. XM_054336205.1XP_054192180.1  hepatoma-derived growth factor isoform X1

      UniProtKB/TrEMBL
      A8K8G0
    5. XM_054336206.1XP_054192181.1  hepatoma-derived growth factor isoform X1

      UniProtKB/TrEMBL
      A8K8G0
    6. XM_054336204.1XP_054192179.1  hepatoma-derived growth factor isoform X1

      UniProtKB/TrEMBL
      A8K8G0