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Aliases for HMGB1 Gene

Aliases for HMGB1 Gene

  • High Mobility Group Box 1 2 3 2
  • High Mobility Group Protein 1 2 3 4
  • HMG1 3 4 6
  • High-Mobility Group (Nonhistone Chromosomal) Protein 1 2 3
  • Sulfoglucuronyl Carbohydrate Binding Protein 2 3
  • High-Mobility Group Box 1 2 3
  • Amphoterin 2 3
  • HMG-1 3 4
  • High Mobility Group Protein B1 3
  • SBP-1 3
  • HMG3 3

External Ids for HMGB1 Gene

Previous Symbols for HMGB1 Gene

  • HMG1

Summaries for HMGB1 Gene

GeneCards Summary for HMGB1 Gene

HMGB1 (High Mobility Group Box 1) is a Protein Coding gene. Diseases associated with HMGB1 include malaria and staphylococcal toxic shock syndrome. Among its related pathways are amb2 Integrin signaling and RB in Cancer. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and cytokine activity. An important paralog of this gene is HMGB4.

UniProtKB/Swiss-Prot for HMGB1 Gene

  • 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

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMGB1 Gene

Genomics for HMGB1 Gene

Genomic Location for HMGB1 Gene

Start:
30,456,704 bp from pter
End:
30,617,597 bp from pter
Size:
160,894 bases
Orientation:
Minus strand

Genomic View for HMGB1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HMGB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMGB1 Gene

Regulatory Elements for HMGB1 Gene

Proteins for HMGB1 Gene

  • Protein details for HMGB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P09429-HMGB1_HUMAN
    Recommended name:
    High mobility group protein B1
    Protein Accession:
    P09429
    Secondary Accessions:
    • A5D8W9
    • Q14321
    • Q5T7C3
    • Q6IBE1

    Protein attributes for HMGB1 Gene

    Size:
    215 amino acids
    Molecular mass:
    24894 Da
    Quaternary structure:
    • Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2.

    Three dimensional structures from OCA and Proteopedia for HMGB1 Gene

neXtProt entry for HMGB1 Gene

Proteomics data for HMGB1 Gene at MOPED

Post-translational modifications for HMGB1 Gene

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

Other Protein References for HMGB1 Gene

No data available for DME Specific Peptides for HMGB1 Gene

Domains for HMGB1 Gene

Gene Families for HMGB1 Gene

HGNC:
  • HMG :High-mobility group / Canonical

Protein Domains for HMGB1 Gene

UniProtKB/Swiss-Prot:

HMGB1_HUMAN
Domain:
  • Contains 2 HMG box DNA-binding domains.:
    • P09429
Family:
  • Belongs to the HMGB family.:
    • P09429
genes like me logo Genes that share domains with HMGB1: view

Function for HMGB1 Gene

Molecular function for HMGB1 Gene

UniProtKB/Swiss-Prot 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) - Molecular Function for HMGB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0003682 chromatin binding IBA --
GO:0003684 damaged DNA binding ISS --
GO:0003690 double-stranded DNA binding ISS --
GO:0003697 single-stranded DNA binding ISS --
genes like me logo Genes that share ontologies with HMGB1: view
genes like me logo Genes that share phenotypes with HMGB1: view

Animal Models for HMGB1 Gene

MGI Knock Outs for HMGB1:

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for HMGB1 Gene

Localization for HMGB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMGB1 Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HMGB1 Gene COMPARTMENTS Subcellular localization image for HMGB1 gene
Compartment Confidence
extracellular 5
nucleus 5
lysosome 2
plasma membrane 2
vacuole 2
cytoskeleton 1
cytosol 1
endoplasmic reticulum 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for HMGB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000793 condensed chromosome IDA 12925773
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IDA 19841752
GO:0005634 nucleus IDA 19223331
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with HMGB1: view

Pathways for HMGB1 Gene

genes like me logo Genes that share pathways with HMGB1: view

Pathways by source for HMGB1 Gene

Gene Ontology (GO) - Biological Process for HMGB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IMP 19158276
GO:0001773 myeloid dendritic cell activation ISS --
GO:0002407 dendritic cell chemotaxis ISS --
GO:0002437 inflammatory response to antigenic stimulus IEP 19841752
GO:0006265 DNA topological change ISS --
genes like me logo Genes that share ontologies with HMGB1: view

Compounds for HMGB1 Gene

(53) Novoseek inferred chemical compound relationships for HMGB1 Gene

Compound -log(P) Hits PubMed IDs
hmga 61.7 2
endotoxin 56.4 45
cisplatin 51.8 61
glycyrrhizin 49.1 10
neurocan 37.6 5
genes like me logo Genes that share compounds with HMGB1: view

Transcripts for HMGB1 Gene

Unigene Clusters for HMGB1 Gene

High mobility group box 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HMGB1 Gene

No ASD Table

Relevant External Links for HMGB1 Gene

GeneLoc Exon Structure for
HMGB1
ECgene alternative splicing isoforms for
HMGB1

Expression for HMGB1 Gene

mRNA expression in normal human tissues for HMGB1 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for HMGB1 Gene

SOURCE GeneReport for Unigene cluster for HMGB1 Gene Hs.434102

genes like me logo Genes that share expressions with HMGB1: view

Orthologs for HMGB1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HMGB1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HMGB1 36
  • 99.69 (n)
  • 99.53 (a)
HMGB1 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia -- 37
  • 98 (a)
OneToMany
HMGB1 36
  • 94.26 (n)
  • 99.53 (a)
HMGB1 37
  • 100 (a)
OneToMany
dog
(Canis familiaris)
Mammalia HMGB1 36
  • 95.19 (n)
  • 100 (a)
HMGB1 37
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hmgb1 16
Hmgb1 37
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 37
  • 80 (a)
OneToMany
-- 37
  • 98 (a)
OneToMany
-- 37
  • 85 (a)
OneToMany
-- 37
  • 83 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia HMGB1 37
  • 62 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia LOC685520 36
  • 90.34 (n)
  • 98.3 (a)
chicken
(Gallus gallus)
Aves HMGB1 36
  • 85.8 (n)
  • 94.32 (a)
HMGB1 37
  • 91 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HMGB1 37
  • 87 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8407 36
zebrafish
(Danio rerio)
Actinopterygii hmgb1a 36
  • 77.51 (n)
  • 87.35 (a)
hmgb1a 37
  • 77 (a)
OneToMany
hmgb1b 37
  • 82 (a)
OneToMany
wufb23c02 36
Species with no ortholog for HMGB1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HMGB1 Gene

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

Paralogs for HMGB1 Gene

Paralogs for HMGB1 Gene

Selected SIMAP similar genes for HMGB1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with HMGB1: view

Variants for HMGB1 Gene

Sequence variations from dbSNP and Humsavar for HMGB1 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type MAF
rs12589 -- 30,458,905(-) CAAAG(A/G)TTGAG utr-variant-3-prime
rs969248 -- 30,463,076(-) TCATA(C/T)TGGTT intron-variant
rs983723 -- 30,463,308(-) GCAAA(A/G)GCGGA reference, synonymous-codon
rs1045411 -- 30,459,095(-) GTGCT(A/G)TGGGG utr-variant-3-prime
rs1056130 -- 30,464,514(+) CCGAG(A/G)AGAGA intron-variant, utr-variant-5-prime

Relevant External Links for HMGB1 Gene

HapMap Linkage Disequilibrium report
HMGB1
Human Gene Mutation Database (HGMD)
HMGB1

No data available for Structural Variations from Database of Genomic Variants (DGV) for HMGB1 Gene

Disorders for HMGB1 Gene

(3) University of Copenhagen DISEASES for HMGB1 Gene

(59) Novoseek inferred disease relationships for HMGB1 Gene

Disease -log(P) Hits PubMed IDs
sepsis 66.6 118
inflammation 62 109
necrosis 50.2 57
systemic inflammatory response syndrome 46.7 5
shock septic 46 15

Relevant External Links for HMGB1

Genetic Association Database (GAD)
HMGB1
Human Genome Epidemiology (HuGE) Navigator
HMGB1
genes like me logo Genes that share disorders with HMGB1: view

No data available for UniProtKB/Swiss-Prot for HMGB1 Gene

Publications for HMGB1 Gene

  1. Expression of high-mobility group-1 mRNA in human gastrointestinal adenocarcinoma and corresponding non-cancerous mucosa. (PMID: 9036861) Xiang Y.-Y. … Sugimura H. (Int. J. Cancer 1997) 3 4 23
  2. Association of HMGB1 polymorphisms with outcome in patients with systemic inflammatory response syndrome. (PMID: 18577209) Kornblit B. … Garred P. (Crit Care 2008) 3 23 49
  3. Association of HMGB1 polymorphisms with outcome after allogeneic hematopoietic cell transplantation. (PMID: 19819342) Kornblit B. … v L. (Biol. Blood Marrow Transplant. 2010) 3 23 49
  4. The genetic variation of the human HMGB1 gene. (PMID: 17610420) Kornblit B. … Garred P. (Tissue Antigens 2007) 3 4 49
  5. The active gene that encodes human high mobility group 1 protein (HMG1) contains introns and maps to chromosome 13. (PMID: 8661151) Ferrari S. … Bianchi M.E. (Genomics 1996) 2 3 4

Products for HMGB1 Gene

  • Addgene plasmids for HMGB1

Sources for HMGB1 Gene

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