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HMGB1 Gene

protein-coding   GIFtS: 65
GCID: GC13M031032

High Mobility Group Box 1

(Previous names: high-mobility group (nonhistone chromosomal) protein 1,...)
(Previous symbol: HMG1)
  See HMGB1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
High Mobility Group Box 11 2     Sulfoglucuronyl Carbohydrate Binding Protein1 2
HMG11 2 3 5     HMG-12 3
High Mobility Group Protein 11 2 3     HMG32
High-Mobility Group (Nonhistone Chromosomal) Protein 11 2     SBP-12
High-Mobility Group Box 11 2     High Mobility Group Protein B12
Amphoterin1 2     

External Ids:    HGNC: 49831   Entrez Gene: 31462   Ensembl: ENSG000001894037   OMIM: 1639055   UniProtKB: P094293   

Export aliases for HMGB1 gene to outside databases

Previous GC identifers: GC13M029013 GC13M025012 GC13M029963 GC13M028831 GC13M029930 GC13M011850


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for HMGB1 Gene:
HMGB1 (high mobility group box 1) is a protein-coding gene. Diseases associated with HMGB1 include staphylococcal toxic shock syndrome, and malignant peritoneal mesothelioma. GO annotations related to this gene include cytokine activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is HMGB4.

UniProtKB/Swiss-Prot: HMGB1_HUMAN, P09429
Function: DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds
preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex.
Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal
sequences (RSS). Heparin-binding protein that has a role in the extension of neurite-type cytoplasmic processes
in developing cells (By similarity)

Gene Wiki entry for HMGB1 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000013.10  NT_024524.15  NC_018924.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the HMGB1 gene promoter:
         TBP   GATA-3   TFIID   STAT3   GATA-2   GATA-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 4): HMGB1 promoter sequence
   Search Chromatin IP Primers for HMGB1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HMGB1


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

Entrez Gene cytogenetic band: 13q12   Ensembl cytogenetic band:  13q12.3   HGNC cytogenetic band: 13q12

HMGB1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HMGB1 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M031032:  view genomic region     (about GC identifiers)

Start:
31,032,877 bp from pter      End:
31,191,734 bp from pter
Size:
158,858 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: HMGB1_HUMAN, P09429 (See protein sequence)
Recommended Name: High mobility group protein B1  
Size: 215 amino acids; 24894 Da
Subunit: Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or
HMGB2 (By similarity)
2 PDB 3D structures from and Proteopedia for HMGB1:
2LY4 (3D)        2YRQ (3D)    
Secondary accessions: A5D8W9 Q14321 Q5T7C3 Q6IBE1

Explore the universe of human proteins at neXtProt for HMGB1: NX_P09429

Explore proteomics data for HMGB1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys12, Lys43, Lys50, Lys112, Lys114, Lys128, Lys157
  • Modification sites at PhosphoSitePlus

  • See HMGB1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_002119.1  
    ENSEMBL proteins: 
     ENSP00000384678   ENSP00000343040   ENSP00000345347   ENSP00000382412   ENSP00000382417  
     ENSP00000369904   ENSP00000410465  
    Reactome Protein details: P09429

    HMGB1 Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
    R&D Systems Recombinant & Natural Proteins for HMGB1 (HMGB1/HMG-1)
    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Proteins for HMGB1
    OriGene Protein Over-expression Lysate for HMGB1
    OriGene MassSpec for HMGB1
    OriGene Custom Protein Services for HMGB1
    GenScript Purified and Recombinant Proteins for HMGB1
    Novus Biologicals HMGB1 Proteins
    Novus Biologicals HMGB1 Lysate
    Sino Biological Recombinant Protein for HMGB1
    Sino Biological Cell Lysate for HMGB1
    ProSpec Recombinant Protein for HMGB1
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for HMGB1 

     
    antibodies-online proteins for HMGB1 (71 products) 

     
    antibodies-online peptides for HMGB1

    HMGB1 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of HMGB1
    R&D Systems Antibodies for HMGB1 (HMGB1/HMG-1)
    Cell Signaling Technology (CST) Antibodies for HMGB1 
    OriGene Antibodies for HMGB1
    OriGene Custom Antibody Services for HMGB1
    Novus Biologicals HMGB1 Antibodies
    Abcam antibodies for HMGB1 (Q5T7C4, P09429)
    Browse Antibodies at Cloud-Clone Corp.
    ThermoFisher Antibody for HMGB1
    antibodies-online antibodies for HMGB1 (206 products) 

    HMGB1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for HMGB1
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for HMGB1
    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for HMGB1 
    antibodies-online kits for HMGB1 (39 products) 


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

    2 InterPro protein domains:
     IPR009071 HMG_box_dom
     IPR017967 HMG_boxA_CS

    Graphical View of Domain Structure for InterPro Entry P09429

    ProtoNet protein and cluster: P09429

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

    UniProtKB/Swiss-Prot: HMGB1_HUMAN, P09429
    Similarity: Belongs to the HMGB family
    Similarity: Contains 2 HMG box DNA-binding domains


    Find genes that share domains with HMGB1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HMGB1_HUMAN, P09429
    Function: DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds
    preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex.
    Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal
    sequences (RSS). Heparin-binding protein that has a role in the extension of neurite-type cytoplasmic processes
    in developing cells (By similarity)

         Gene Ontology (GO): Selected molecular function terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ----
    GO:0003684damaged DNA binding ISS--
    GO:0003690double-stranded DNA binding ISS--
    GO:0003697single-stranded DNA binding ISS--
    GO:0003700sequence-specific DNA binding transcription factor activity IDA19223331
         
    Find genes that share ontologies with HMGB1           About GenesLikeMe


    Phenotypes:
         7 MGI mutant phenotypes (inferred from 1 allele(MGI details for Hmgb1):
     behavior/neurological  cellular  growth/size/body  homeostasis/metabolism  mortality/aging 
     respiratory system  vision/eye 

    Find genes that share phenotypes with HMGB1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Hmgb1tm1Meb for HMGB1

       genOway: Develop your customized and physiologically relevant rodent model for HMGB1

    miRNA
    Products:
        
    miRTarBase miRNAs that target HMGB1:
    hsa-mir-100-5p (MIRT048569), hsa-mir-193b-3p (MIRT016305), hsa-let-7b-5p (MIRT052166), hsa-mir-148a-3p (MIRT048039), hsa-mir-181d-5p (MIRT041163), hsa-let-7e-5p (MIRT051522), hsa-mir-652-3p (MIRT039473), hsa-mir-92a-3p (MIRT049759), hsa-mir-877-3p (MIRT037020), hsa-mir-328-3p (MIRT043798), hsa-let-7g-5p (MIRT046564), hsa-mir-18a-3p (MIRT040864), hsa-mir-148b-3p (MIRT043587), hsa-mir-26b-5p (MIRT050047), hsa-mir-22-3p (MIRT007157)

    Block miRNA regulation of human, mouse, rat HMGB1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HMGB1 (see all 67):
    hsa-miR-549 hsa-miR-3152-3p hsa-miR-300 hsa-miR-759 hsa-miR-4275 hsa-miR-3613-3p hsa-miR-642b hsa-miR-192*
    SwitchGear 3'UTR luciferase reporter plasmidHMGB1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for HMGB1
    Predesigned siRNA for gene silencing in human, mouse, rat HMGB1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for HMGB1

    Clone
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    OriGene clones in human, mouse for HMGB1 (see all 9)
    OriGene ORF clones in mouse, rat for HMGB1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: HMGB1 (NM_002128)
    Sino Biological Human cDNA Clone for HMGB1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HMGB1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HMGB1
    Addgene plasmids for HMGB1 

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for HMGB1
    Browse ESI BIO Cell Lines and PureStem Progenitors for HMGB1 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMGB1

    Flow Cytometry
    Products:
       

     
    eBioscience FlowRNA Probe Sets ( VA1-12271) for HMGB1 


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    HMGB1_HUMAN, P09429: Nucleus. Chromosome
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    nucleus5
    lysosome2
    plasma membrane2
    vacuole2
    cytoskeleton1
    cytosol1
    endoplasmic reticulum1
    mitochondrion1

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000793condensed chromosome IDA12925773
    GO:0005576extracellular region TAS--
    GO:0005615extracellular space IDA19841752
    GO:0005634nucleus IDA19223331
    GO:0005654nucleoplasm TAS--

    Find genes that share ontologies with HMGB1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for HMGB1 About   (see all 14)  
    See pathways by source

    SuperPathContained pathways About
    1Toll Like Receptor 7/8 (TLR7/8) Cascade
    Toll Like Receptor 9 (TLR9) Cascade0.93
    MyD88 dependent cascade initiated on endosome0.69
    TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation0.93
    MyD88-independent cascade0.69
    Toll Like Receptor 7/8 (TLR7/8) Cascade0.69
    Toll Like Receptor 3 (TLR3) Cascade0.69
    2Cytosolic sensors of pathogen-associated DNA
    RIP-mediated NFkB activation via ZBP10.81
    TAK1 activates NFkB by phosphorylation and activation of IKKs complex0.52
    ZBP1(DAI) mediated induction of type I IFNs0.81
    Cytosolic sensors of pathogen-associated DNA0.38
    TRAF6 mediated NF-kB activation0.55
    DEx/H-box helicases activate type I IFN and inflammatory cytokines production0.00
    3Activation of DNA fragmentation factor
    Activation of DNA fragmentation factor0.32
    Apoptosis induced DNA fragmentation0.00
    4Apoptotic cleavage of cellular proteins
    Apoptotic execution phase0.74
    5Resolution of Abasic Sites (AP sites)
    Base excision repair0.53


    Find genes that share SuperPaths with HMGB1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for HMGB1
        HMGB1 Pathway

    1 Cell Signaling Technology (CST) Pathway for HMGB1
        Chromatin Regulation / Acetylation

    3 BioSystems Pathways for HMGB1
        DNA damage response (only ATM dependent)
    RB in Cancer
    amb2 Integrin signaling


    Selected Reactome Pathways for HMGB1 (see all 6)
        Activation of DNA fragmentation factor
    DEx/H-box helicases activate type I IFN and inflammatory cytokines production
    Advanced glycosylation endproduct receptor signaling
    RIP-mediated NFkB activation via ZBP1
    TAK1 activates NFkB by phosphorylation and activation of IKKs complex


    1 Kegg Pathway  (Kegg details for HMGB1):
        Base excision repair

        Pathway & Disease-focused RT2 Profiler PCR Arrays including HMGB1: 
              Toll-Like Receptor Signaling Pathway in human mouse rat
              Apoptosis 384HT in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for HMGB1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for HMGB1 (P094292, 3 ENSP000003430404) via UniProtKB, MINT, STRING, and/or I2D (see all 217)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DNM2P505702, 3, ENSP000003527214MINT-8254432 I2D: score=2 STRING: ENSP00000352721
    TXNP105992, 3, ENSP000003636414MINT-6795963 I2D: score=1 STRING: ENSP00000363641
    AGERQ151093, ENSP000003642174I2D: score=3 STRING: ENSP00000364217
    ENSG00000235068Q018603, ENSP000004050414I2D: score=2 STRING: ENSP00000405041
    POU5F1Q018603, ENSP000002599154I2D: score=2 STRING: ENSP00000259915
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    Gene Ontology (GO): Selected biological process terms (see all 22):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IMP19158276
    GO:0001773myeloid dendritic cell activation ISS--
    GO:0002407dendritic cell chemotaxis ISS--
    GO:0002437inflammatory response to antigenic stimulus IEP19841752
    GO:0006265DNA topological change ISS--

    Find genes that share ontologies with HMGB1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for HMGB1

    Selected Novoseek inferred chemical compound relationships for HMGB1 gene (see all 53)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hmga 61.7 3 10598102 (1), 12590928 (1)
    endotoxin 56.4 53 10398600 (4), 17339485 (4), 16424112 (3), 19450686 (3) (see all 27)
    cisplatin 51.8 85 9427537 (6), 11245470 (5), 12614161 (5), 17922863 (3) (see all 29)
    glycyrrhizin 49.1 23 16935945 (2), 17462578 (2), 19906009 (1), 20419158 (1) (see all 8)
    neurocan 37.6 5 9507007 (4), 11766883 (1)
    platinum 36.5 7 10460158 (2), 11733188 (1), 10747955 (1), 18777181 (1) (see all 6)
    cholesterol-sulfate 35.3 9 11243881 (4), 14993789 (1)
    anaphylatoxin 32 1 17464119 (1)
    perchloric acid 27.2 1 18682735 (1)
    sb 203580 20.6 5 19726280 (2), 17135572 (1), 18949384 (1), 18402807 (1)



    Find genes that share compounds with HMGB1           About GenesLikeMe



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for HMGB1 gene: 
    NM_002128.4  

    Unigene Clusters for HMGB1:

    High mobility group box 1
    Hs.434102  [show with all ESTs], Hs.593339  [show with all ESTs], Hs.596078  [show with all ESTs]
    Unigene Representative Sequences: AK122825, BG421380, BE963360
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000405805(uc001usv.3 uc001usx.3 uc001usy.3 uc001usz.3)
    ENST00000339872 ENST00000341423(uc001uta.1) ENST00000399489 ENST00000399494
    ENST00000326004 ENST00000490788 ENST00000398908 ENST00000468384
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate HMGB1 (see all 67):
    hsa-miR-549 hsa-miR-3152-3p hsa-miR-300 hsa-miR-759 hsa-miR-4275 hsa-miR-3613-3p hsa-miR-642b hsa-miR-192*
    SwitchGear 3'UTR luciferase reporter plasmidHMGB1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat HMGB1
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    GenScript: all cDNA clones in your preferred vector: HMGB1 (NM_002128)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HMGB1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HMGB1
    Addgene plasmids for HMGB1 
    Primer
    Products:
        
    OriGene qPCR primer pairs and template standards for HMGB1
    OriGene qSTAR qPCR primer pairs in human, mouse for HMGB1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat HMGB1
      QuantiTect SYBR Green Assays in human, mouse, rat HMGB1
      QuantiFast Probe-based Assays in human, mouse, rat HMGB1
    Flow Cytometry
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    eBioscience FlowRNA Probe Sets ( VA1-12271) for HMGB1 

    Additional mRNA sequence: 

    BC066889.1 BC067732.1 D63874.1 X12597.1 

    Selected DOTS entries (see all 91):

    DT.100052897  DT.92071638  DT.100697442  DT.100680078  DT.92071310  DT.92049316  DT.100697450  DT.95377774 
    DT.100697434  DT.414948  DT.95253133  DT.100697429  DT.100697445  DT.92071298  DT.120795160  DT.100697446 
    DT.438329  DT.100712011  DT.95377063  DT.120905298  DT.121044751  DT.40252816  DT.100697454  DT.100857814 

    Selected AceView cDNA sequences (see all 1611):

    AI277824 BU844394 AI735358 AI278561 AI476553 BG776097 CR607900 AI819697 
    CR601960 CR625918 BF692448 AI553646 AA903448 BF435533 BU678237 AK122825 
    BG034466 AW189442 BM463779 AI866044 BX109832 AW135109 BQ787404 AA417986 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    HMGB1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAAATTTAAA
    HMGB1 Expression
    About this image

    HMGB1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HMGB1 Protein Expression

    SOURCE GeneReport for Unigene clusters: Hs.434102 Hs.593339 Hs.596078
        Pathway & Disease-focused RT2 Profiler PCR Arrays including HMGB1: 
              Toll-Like Receptor Signaling Pathway in human mouse rat
              Apoptosis 384HT in human mouse rat

    Primer
    Products:
    OriGene qPCR primer pairs and template standards for HMGB1
    OriGene qSTAR qPCR primer pairs in human, mouse for HMGB1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat HMGB1
    QuantiTect SYBR Green Assays in human, mouse, rat HMGB1
    QuantiFast Probe-based Assays in human, mouse, rat HMGB1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMGB1

    (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

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    This gene was present in the common ancestor of chordates.

    Orthologs for HMGB1 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hmgb15 high mobility group box 1   --   5 (89.18 cM) 149046702 
    chicken
    (Gallus gallus)
    Aves HMGB11 high mobility group box 1 85.8(n)
    94.32(a)
      395724  NM_204902.2  NP_990233.1 
    lizard
    (Anolis carolinensis)
    Reptilia HMGB16
    high mobility group box 1
    87(a)
    1 ↔ 1
    3(184556515-184568685)
    African clawed frog
    (Xenopus laevis)
    Amphibia BC054148.12   -- 88.84(n)    BC054148.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufb23c022 wufb23c02 77.66(n)   321622  AY398358.1 


    ENSEMBL Gene Tree for HMGB1 (if available)
    TreeFam Gene Tree for HMGB1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HMGB1 gene
    HMGB42  HMGB32  HMGB22  
    12 SIMAP similar genes for HMGB1 using alignment to 4 protein entries:     HMGB1_HUMAN (see all proteins):
    HMG1    HMGB1P1    HMGB2    DKFZp779G118    HMGB3    SP100
    HMGB4    Bbtx1    HMG20B    UBTF    PMS1    WUGSC

    Find genes that share paralogs with HMGB1           About GenesLikeMe


    Selected Pseudogenes.org Pseudogenes for HMGB1 (see all 36)
    PGOHUM00000238714 PGOHUM00000238784 PGOHUM00000251277 PGOHUM00000256675 PGOHUM00000242611


    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for HMGB1 (see all 240)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0464524
    Gastric-carcinoma cell line4--see VAR_0464522 A E mis40--------
    VAR_0464544
    Gastric-carcinoma cell line4--see VAR_0464542 D G mis40--------
    VAR_0464514
    Gastric-carcinoma cell line4--see VAR_0464512 G R mis40--------
    rs79933241,2
    C,F,A--31032457(+) CAGTTG/ATCTCT 1 -- ds50015Minor allele frequency- A:0.25NA WA CSA 126
    rs114609411,2
    C--31032468(+) TTTTTT/-GAGAT 1 -- ds50011Minor allele frequency- -:0.00NA 2
    rs1413289521,2
    --31032515(+) AGGCTA/GGAGTG 1 -- ds50010--------
    rs1926421631,2
    --31032634(+) GCTAAC/TTTTTT 1 -- ds50010--------
    rs1853824451,2
    C--31032669(+) CACCAC/TGTTAG 1 -- ds50010--------
    rs1507912421,2
    --31032683(+) GGATGA/GTCTCA 1 -- ds50010--------
    rs561193681,2
    C,F--31032697(+) TCCTGG/ACCTCG 1 -- ds50011Minor allele frequency- A:0.50WA 2

    HapMap Linkage Disequilibrium report for HMGB1 (31032877 - 31191734 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for HMGB1: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HMGB1
    DNA2.0 Custom Variant and Variant Library Synthesis for HMGB1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 163905    OMIM disorders: --

    6 diseases for HMGB1:    
    About MalaCards
    staphylococcal toxic shock syndrome    malignant peritoneal mesothelioma    endophthalmitis    idiopathic neutropenia
    recessive dystrophic epidermolysis bullosa    malaria

    3 diseases from the University of Copenhagen DISEASES database for HMGB1:
    Vascular disease     Arthritis     Cancer

    Find genes that share disorders with HMGB1           About GenesLikeMe

    Selected Novoseek inferred disease relationships for HMGB1 gene (see all 59)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    sepsis 66.6 165 17334246 (6), 17901841 (5), 14620138 (4), 17625012 (4) (see all 70)
    inflammation 62 136 15947118 (3), 16645483 (3), 19679874 (3), 19948257 (3) (see all 90)
    necrosis 50.2 67 19587006 (4), 16855214 (3), 16354107 (3), 17516211 (2) (see all 46)
    systemic inflammatory response syndrome 46.7 8 18577209 (2), 20158885 (1), 17346334 (1), 19819342 (1)
    shock septic 46 19 15753748 (3), 12974876 (2), 18713653 (2), 12297673 (1) (see all 11)
    arthritis 40.6 56 14871458 (5), 18759291 (5), 17203009 (4), 17397533 (3) (see all 22)
    tumors 39.6 130 17667523 (4), 19639200 (4), 18031610 (3), 19876719 (3) (see all 74)
    rheumatoid arthritis 33.9 19 17597834 (2), 18346273 (2), 17172710 (1), 17060363 (1) (see all 17)
    multiple organ failure 31.7 4 19533845 (1), 15877951 (1), 19209785 (1)
    cancer 31.1 51 17611640 (3), 14763124 (3), 19506549 (3), 20044610 (3) (see all 29)

    Genetic Association Database (GAD): HMGB1
    Human Genome Epidemiology (HuGE) Navigator: HMGB1 (5 documents)

    Export disorders for HMGB1 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)
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    PubMed articles for HMGB1 gene, integrated from 10 sources (see all 830):
    (articles sorted by number of sources associating them with HMGB1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The genetic variation of the human HMGB1 gene. (PubMed id 17610420)1, 2, 4, 9 Kornblit B....Garred P. (Tissue Antigens 2007)
    2. The active gene that encodes human high mobility group 1 protein (HMG1) contains introns and maps to chromosome 13. (PubMed id 8661151)1, 2, 3 Ferrari S.... Bianchi M.E. (Genomics 1996)
    3. Association of HMGB1 polymorphisms with outcome in patients with systemic inflammatory response syndrome. (PubMed id 18577209)1, 4, 9 Kornblit B....Garred P. (Crit Care 2008)
    4. Association of HMGB1 polymorphisms with outcome after allogeneic hematopoietic cell transplantation. (PubMed id 19819342)1, 4, 9 Kornblit B....v L. (Biol. Blood Marrow Transplant. 2010)
    5. Expression of high-mobility group-1 mRNA in human gastrointestinal adenocarcinoma and corresponding non-cancerous mucosa. (PubMed id 9036861)1, 2, 9 Xiang Y.-Y.... Sugimura H. (Int. J. Cancer 1997)
    6. Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease. (PubMed id 21116278)1, 4 Furney S.J.... . (Mol. Psychiatry 2011)
    7. The association of innate immune response gene polymorphisms and puerperal group A streptococcal sepsis. (PubMed id 20207250)1, 4 Davis S.M....Silver R.M. (Am. J. Obstet. Gynecol. 2010)
    8. Proteomic analysis of ubiquitinated proteins in normal hepatocyte cell line Chang liver cells. (PubMed id 18655026)1, 2 Tan F.... Peng X. (Proteomics 2008)
    9. 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. (Genome Res. 2004)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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)
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    Entrez Gene: 3146 HGNC: 4983 AceView: HMGB1 Ensembl:ENSG00000189403 euGenes: HUgn3146
    ECgene: HMGB1 Kegg: 3146 H-InvDB: HMGB1

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for HMGB1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for HMGB1 Genetics and Cytogenetics in Oncology and Haematology
    SeattleSNPshttp://pga.gs.washington.edu/data/hmgb1/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HMGB1 gene:
    Search GeneIP for patents involving HMGB1

    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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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