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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HMGB4 Gene

protein-coding   GIFtS: 44
GCID: GC01P034326

High Mobility Group Box 4

(Previous name: high-mobility group box 4)
  Search for HMGB4
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
High Mobility Group Box 41 2
High-Mobility Group Box 41
dJ1007G16.52
High Mobility Group Protein B42
HMG2 Like2

External Ids:    HGNC: 249541   Entrez Gene: 1275402   Ensembl: ENSG000001762567   UniProtKB: Q8WW323   

Export aliases for HMGB4 gene to outside databases

Previous GC identifers: GC01P033996 GC01P034098 GC01P032442


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for HMGB4 Gene: 
HMGB4 (high mobility group box 4) is a protein-coding gene. GO annotations related to this gene include DNA binding. An important paralog of this gene is HMGB3.

Gene Wiki entry for HMGB4 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.2  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HMGB4 gene promoter:
         NF-AT2   NF-kappaB1   Cdc5   NF-AT   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): HMGB4 promoter sequence
   Search SABiosciences Chromatin IP Primers for HMGB4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HMGB4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p35.1   Ensembl cytogenetic band:  1p35.1   HGNC cytogenetic band: 1p35.1

HMGB4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HMGB4 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P034326:  view genomic region     (about GC identifiers)

Start:
34,326,076 bp from pter      End:
34,330,392 bp from pter
Size:
4,317 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: HMGB4_HUMAN, Q8WW32 (See protein sequence)
Recommended Name: High mobility group protein B4  
Size: 186 amino acids; 22490 Da
Subcellular location: Nucleus (By similarity). Chromosome (By similarity)
Secondary accessions: B2R4X7 Q0QWA4

Explore the universe of human proteins at neXtProt for HMGB4: NX_Q8WW32

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8WW32

  • HMGB4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --
    REFSEQ proteins: NP_660206.2  
    ENSEMBL proteins: 
     ENSP00000429214   ENSP00000430919  

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    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005694chromosome IEA--

    HMGB4 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    HMG: High-mobility group / Canonical

    1 InterPro protein domain:
     IPR009071 HMG_box_dom

    Graphical View of Domain Structure for InterPro Entry Q8WW32

    ProtoNet protein and cluster: Q8WW32

    1 Blocks protein domain: IPB000135 High mobility group proteins HMG1 and HMG2

    UniProtKB/Swiss-Prot: HMGB4_HUMAN, Q8WW32
    Similarity: Belongs to the HMGB family
    Similarity: Contains 2 HMG box DNA-binding domains


    HMGB4 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
         
    HMGB4 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for HMGB4:
     Decreased Wnt reporter activit  Increased gamma-H2AX phosphory 

    Animal Models:
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HMGB4

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for HMGB4

    Search CenterWatch for drugs/clinical trials and news about HMGB4

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for HMGB4 gene: 
    NM_145205.4  

    Unigene Cluster for HMGB4:

    High mobility group box 4
    Hs.568628  [show with all ESTs]
    Unigene Representative Sequence: NM_145205
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000519684(uc001bxp.3) ENST00000522796 ENST00000458277 ENST00000425537(uc001bxq.3)

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    Additional mRNA sequence: 

    AK097707.1 AK130859.1 AK310465.1 AK311985.1 BC021180.2 BC070148.1 DQ207367.1 NR_033264.1 

    2 DOTS entries:

    DT.95367635  DT.408782 

    24/87 AceView cDNA sequences (see all 87):

    AA629230 AK130859 AI824962 BC070148 AI634070 AK097707 BU567351 AI655836 
    AI917843 BE503338 AI970364 BP371217 BE504819 AI968361 BC021180 BP369500 
    BF057167 BP371157 BU854564 BP368976 BP370698 BP371397 AI982569 AI797725 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    HMGB4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGAAAAGAAA
    HMGB4 Expression
    About this image


    Genevestigator expression for HMGB4

    SOURCE GeneReport for Unigene cluster: Hs.568628
        SABiosciences Custom PCR Arrays for HMGB4
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMGB4

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals and fungi.

    Orthologs for HMGB4 gene from 4/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hmgb41 , 5 high-mobility group box 41, 5 78.97(n)1
    78.57(a)1
      4 (61.97 cM)5
    693171  NM_027036.31  NP_081312.21 
     1282602125 
    fruit fly
    (Drosophila melanogaster)
    Insecta Dsp16
    Dorsal switch protein 1
    15(a)
    possible ortholog
    X(16227645-16234657)
    worm
    (Caenorhabditis elegans)
    Secernentea hmg-1.26
    High mobility group protein 1.2
    23(a)
    possible ortholog
    III(6280383-6283119)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes NHP6B6
    NHP6A6
    High-mobility group (HMG) protein that binds to an...
    High-mobility group (HMG) protein that binds to an...
    32(a)
    31(a)
    many ↔ many
    many ↔ many
    II(426190-426489)
    XVI(665693-665974)


    ENSEMBL Gene Tree for HMGB4 (if available)
    TreeFam Gene Tree for HMGB4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HMGB4 gene
    HMGB32  HMGB12  HMGB22  
    11 SIMAP similar genes for HMGB4 using alignment to 2 protein entries:     HMGB4_HUMAN (see all proteins):
    HMG1    DKFZp779G118    HMGB2    HMGB1    HMGB3    HMGB1P1
    Bbtx1    TOX2    TOX4    SP100    WUGSC

    HMGB4 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for HMGB4
    PGOHUM00000257054


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    3 SNPs in HMGB4 are shown    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0559514
    ----see VAR_0559512 K R mis40--------
    VAR_0674684
    ----see VAR_0674682 Y H mis40--------
    VAR_0674674
    ----see VAR_0674672 E A mis40--------

    HapMap Linkage Disequilibrium report for HMGB4 (34326076 - 34330392 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for HMGB4:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv34112CNV Loss18971310
    nsv871907CNV Loss21882294
    nsv834624CNV Loss17160897

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    HMGB4 for disorders           About MalaCards

    HMGB4 for disorders           About GeneDecksing

    Human Genome Epidemiology (HuGE) Navigator: HMGB4 (1 document)

    Export disorders for HMGB4 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for HMGB4 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with HMGB4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    4. Convergent Animal and Human Evidence Suggests a Role of PPM1A Gene in Response to Antidepressants. (PubMed id 20970119)1 Malki K....Schalkwyk L.C. (2010)
    5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
    6. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (2006)
    7. A transcript finishing initiative for closing gaps in the human transcriptome. (PubMed id 15197164)1 Sogayar M.C....Zanette D.L. (2004)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    9. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 127540 HGNC: 24954 AceView: LOC127540 Ensembl:ENSG00000176256 euGenes: HUgn127540
    ECgene: HMGB4 H-InvDB: HMGB4

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for HMGB4 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for HMGB4 gene:
    Search GeneIP for patents involving HMGB4

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
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