Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

HMGB1 (high mobility group box 1)

Identity

Alias_namesHMG1
high-mobility group (nonhistone chromosomal) protein 1
high-mobility group box 1
Alias_symbol (synonym)HMG3
SBP-1
DKFZp686A04236
Other aliasHMG-1
HGNC (Hugo) HMGB1
LocusID (NCBI) 3146
Atlas_Id 40834
Location 13q12.3  [Link to chromosome band 13q12]
Location_base_pair Starts at 31032053 and ends at 31038464 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
AD_1 () / HMGB1 (13q12.3)HMGB1 (13q12.3) / HMGB1 (13q12.3)MRS2 (6p22.3) / HMGB1 (13q12.3)
SYT11 (1q22) / HMGB1 (13q12.3)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)HMGB1   4983
Cards
Entrez_Gene (NCBI)HMGB1  3146  high mobility group box 1
AliasesHMG-1; HMG1; HMG3; SBP-1
GeneCards (Weizmann)HMGB1
Ensembl hg19 (Hinxton)ENSG00000189403 [Gene_View]  chr13:31032053-31038464 [Contig_View]  HMGB1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000189403 [Gene_View]  chr13:31032053-31038464 [Contig_View]  HMGB1 [Vega]
ICGC DataPortalENSG00000189403
TCGA cBioPortalHMGB1
AceView (NCBI)HMGB1
Genatlas (Paris)HMGB1
WikiGenes3146
SOURCE (Princeton)HMGB1
Genetics Home Reference (NIH)HMGB1
Genomic and cartography
GoldenPath hg19 (UCSC)HMGB1  -     chr13:31032053-31038464 -  13q12.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)HMGB1  -     13q12.3   [Description]    (hg38-Dec_2013)
EnsemblHMGB1 - 13q12.3 [CytoView hg19]  HMGB1 - 13q12.3 [CytoView hg38]
Mapping of homologs : NCBIHMGB1 [Mapview hg19]  HMGB1 [Mapview hg38]
OMIM163905   
Gene and transcription
Genbank (Entrez)AA430980 AB208998 AF401215 AK057120 AK122825
RefSeq transcript (Entrez)NM_001313892 NM_001313893 NM_002128
RefSeq genomic (Entrez)NC_000013 NC_018924 NT_024524 NW_004929388
Consensus coding sequences : CCDS (NCBI)HMGB1
Cluster EST : UnigeneHs.596078 [ NCBI ]
CGAP (NCI)Hs.596078
Alternative Splicing GalleryENSG00000189403
Gene ExpressionHMGB1 [ NCBI-GEO ]   HMGB1 [ EBI - ARRAY_EXPRESS ]   HMGB1 [ SEEK ]   HMGB1 [ MEM ]
Gene Expression Viewer (FireBrowse)HMGB1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3146
GTEX Portal (Tissue expression)HMGB1
Protein : pattern, domain, 3D structure
UniProt/SwissProtP09429   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP09429  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP09429
Splice isoforms : SwissVarP09429
PhosPhoSitePlusP09429
Domaine pattern : Prosite (Expaxy)HMG_BOX_1 (PS00353)    HMG_BOX_2 (PS50118)   
Domains : Interpro (EBI)HMG_box_dom    HMG_boxA_CS   
Domain families : Pfam (Sanger)HMG_box (PF00505)    HMG_box_2 (PF09011)   
Domain families : Pfam (NCBI)pfam00505    pfam09011   
Domain families : Smart (EMBL)HMG (SM00398)  
Conserved Domain (NCBI)HMGB1
DMDM Disease mutations3146
Blocks (Seattle)HMGB1
PDB (SRS)2LY4    2RTU    2YRQ   
PDB (PDBSum)2LY4    2RTU    2YRQ   
PDB (IMB)2LY4    2RTU    2YRQ   
PDB (RSDB)2LY4    2RTU    2YRQ   
Structural Biology KnowledgeBase2LY4    2RTU    2YRQ   
SCOP (Structural Classification of Proteins)2LY4    2RTU    2YRQ   
CATH (Classification of proteins structures)2LY4    2RTU    2YRQ   
SuperfamilyP09429
Human Protein AtlasENSG00000189403
Peptide AtlasP09429
HPRD01228
IPIIPI00419258   IPI00645948   IPI00644653   IPI00643746   
Protein Interaction databases
DIP (DOE-UCLA)P09429
IntAct (EBI)P09429
FunCoupENSG00000189403
BioGRIDHMGB1
STRING (EMBL)HMGB1
ZODIACHMGB1
Ontologies - Pathways
QuickGOP09429
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  four-way junction DNA binding  bubble DNA binding  condensed chromosome  lipopolysaccharide binding  eye development  myeloid dendritic cell activation  phosphatidylserine binding  endothelial cell proliferation  activation of innate immune response  plasmacytoid dendritic cell activation  macrophage activation involved in immune response  dendritic cell chemotaxis  inflammatory response to antigenic stimulus  regulation of tolerance induction  regulation of T cell mediated immune response to tumor cell  damaged DNA binding  damaged DNA binding  double-stranded DNA binding  single-stranded DNA binding  transcription factor activity, sequence-specific DNA binding  double-stranded RNA binding  single-stranded RNA binding  cytokine activity  protein binding  extracellular region  extracellular space  nucleus  nucleoplasm  early endosome  endoplasmic reticulum-Golgi intermediate compartment  plasma membrane  DNA topological change  base-excision repair  apoptotic DNA fragmentation  DNA recombination  regulation of transcription from RNA polymerase II promoter  autophagy  inflammatory response  positive regulation of cytosolic calcium ion concentration  transcription factor binding  DNA binding, bending  DNA binding, bending  cell surface  regulation of autophagy  calcium-dependent protein kinase regulator activity  lyase activity  transcriptional repressor complex  negative regulation of RNA polymerase II transcriptional preinitiation complex assembly  C-X-C chemokine binding  protein kinase activator activity  lung development  neuron projection development  chromatin assembly  regulation of restriction endodeoxyribonuclease activity  activation of protein kinase activity  DNA geometric change  positive regulation of mismatch repair  negative regulation of interferon-gamma production  positive regulation of interferon-alpha production  positive regulation of interferon-beta production  positive regulation of interleukin-10 production  positive regulation of interleukin-12 production  positive regulation of tumor necrosis factor production  V(D)J recombination  positive regulation of toll-like receptor 2 signaling pathway  positive regulation of toll-like receptor 4 signaling pathway  positive regulation of toll-like receptor 9 signaling pathway  T-helper 1 cell activation  endothelial cell chemotaxis  chemoattractant activity  positive regulation of activated T cell proliferation  neuron projection  positive regulation of apoptotic process  apoptotic cell clearance  positive regulation of cysteine-type endopeptidase activity involved in apoptotic process  negative regulation of CD4-positive, alpha-beta T cell differentiation  positive regulation of DNA binding  positive regulation of MAPK cascade  negative regulation of blood vessel endothelial cell migration  poly(A) RNA binding  T-helper 1 cell differentiation  innate immune response  positive regulation of myeloid cell differentiation  positive regulation of glycogen catabolic process  positive regulation of transcription from RNA polymerase II promoter  positive regulation of JNK cascade  positive regulation of interleukin-1 secretion  positive regulation of interleukin-1 beta secretion  RAGE receptor binding  positive chemotaxis  DNA ligation involved in DNA repair  positive regulation of DNA ligation  response to glucocorticoid  DNA polymerase binding  positive regulation of ERK1 and ERK2 cascade  repressing transcription factor binding  positive regulation of monocyte chemotaxis  positive regulation of wound healing  supercoiled DNA binding  neutrophil clearance  positive regulation of NIK/NF-kappaB signaling  positive regulation of sprouting angiogenesis  tumor necrosis factor secretion  negative regulation of apoptotic cell clearance  positive regulation of interleukin-6 secretion  regulation of nucleotide-excision repair  positive regulation of dendritic cell differentiation  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  four-way junction DNA binding  bubble DNA binding  condensed chromosome  lipopolysaccharide binding  eye development  myeloid dendritic cell activation  phosphatidylserine binding  endothelial cell proliferation  activation of innate immune response  plasmacytoid dendritic cell activation  macrophage activation involved in immune response  dendritic cell chemotaxis  inflammatory response to antigenic stimulus  regulation of tolerance induction  regulation of T cell mediated immune response to tumor cell  damaged DNA binding  damaged DNA binding  double-stranded DNA binding  single-stranded DNA binding  transcription factor activity, sequence-specific DNA binding  double-stranded RNA binding  single-stranded RNA binding  cytokine activity  protein binding  extracellular region  extracellular space  nucleus  nucleoplasm  early endosome  endoplasmic reticulum-Golgi intermediate compartment  plasma membrane  DNA topological change  base-excision repair  apoptotic DNA fragmentation  DNA recombination  regulation of transcription from RNA polymerase II promoter  autophagy  inflammatory response  positive regulation of cytosolic calcium ion concentration  transcription factor binding  DNA binding, bending  DNA binding, bending  cell surface  regulation of autophagy  calcium-dependent protein kinase regulator activity  lyase activity  transcriptional repressor complex  negative regulation of RNA polymerase II transcriptional preinitiation complex assembly  C-X-C chemokine binding  protein kinase activator activity  lung development  neuron projection development  chromatin assembly  regulation of restriction endodeoxyribonuclease activity  activation of protein kinase activity  DNA geometric change  positive regulation of mismatch repair  negative regulation of interferon-gamma production  positive regulation of interferon-alpha production  positive regulation of interferon-beta production  positive regulation of interleukin-10 production  positive regulation of interleukin-12 production  positive regulation of tumor necrosis factor production  V(D)J recombination  positive regulation of toll-like receptor 2 signaling pathway  positive regulation of toll-like receptor 4 signaling pathway  positive regulation of toll-like receptor 9 signaling pathway  T-helper 1 cell activation  endothelial cell chemotaxis  chemoattractant activity  positive regulation of activated T cell proliferation  neuron projection  positive regulation of apoptotic process  apoptotic cell clearance  positive regulation of cysteine-type endopeptidase activity involved in apoptotic process  negative regulation of CD4-positive, alpha-beta T cell differentiation  positive regulation of DNA binding  positive regulation of MAPK cascade  negative regulation of blood vessel endothelial cell migration  poly(A) RNA binding  T-helper 1 cell differentiation  innate immune response  positive regulation of myeloid cell differentiation  positive regulation of glycogen catabolic process  positive regulation of transcription from RNA polymerase II promoter  positive regulation of JNK cascade  positive regulation of interleukin-1 secretion  positive regulation of interleukin-1 beta secretion  RAGE receptor binding  positive chemotaxis  DNA ligation involved in DNA repair  positive regulation of DNA ligation  response to glucocorticoid  DNA polymerase binding  positive regulation of ERK1 and ERK2 cascade  repressing transcription factor binding  positive regulation of monocyte chemotaxis  positive regulation of wound healing  supercoiled DNA binding  neutrophil clearance  positive regulation of NIK/NF-kappaB signaling  positive regulation of sprouting angiogenesis  tumor necrosis factor secretion  negative regulation of apoptotic cell clearance  positive regulation of interleukin-6 secretion  regulation of nucleotide-excision repair  positive regulation of dendritic cell differentiation  
Pathways : BIOCARTAApoptotic DNA fragmentation and tissue homeostasis [Genes]    The information-processing pathway at the IFN-beta enhancer [Genes]   
Pathways : KEGGBase excision repair   
NDEx NetworkHMGB1
Atlas of Cancer Signalling NetworkHMGB1
Wikipedia pathwaysHMGB1
Orthology - Evolution
OrthoDB3146
GeneTree (enSembl)ENSG00000189403
Phylogenetic Trees/Animal Genes : TreeFamHMGB1
HOVERGENP09429
HOGENOMP09429
Homologs : HomoloGeneHMGB1
Homology/Alignments : Family Browser (UCSC)HMGB1
Gene fusions - Rearrangements
Fusion Cancer (Beijing)AD_1 [HMGB1]  -  13q12.3 [FUSC000512]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHMGB1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HMGB1
dbVarHMGB1
ClinVarHMGB1
1000_GenomesHMGB1 
Exome Variant ServerHMGB1
ExAC (Exome Aggregation Consortium)HMGB1 (select the gene name)
Genetic variants : HAPMAP3146
Genomic Variants (DGV)HMGB1 [DGVbeta]
DECIPHER (Syndromes)13:31032053-31038464  ENSG00000189403
CONAN: Copy Number AnalysisHMGB1 
Mutations
ICGC Data PortalHMGB1 
TCGA Data PortalHMGB1 
Broad Tumor PortalHMGB1
OASIS PortalHMGB1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHMGB1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHMGB1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch HMGB1
DgiDB (Drug Gene Interaction Database)HMGB1
DoCM (Curated mutations)HMGB1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HMGB1 (select a term)
intoGenHMGB1
Cancer3DHMGB1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM163905   
Orphanet
MedgenHMGB1
Genetic Testing Registry HMGB1
NextProtP09429 [Medical]
TSGene3146
GENETestsHMGB1
Huge Navigator HMGB1 [HugePedia]
snp3D : Map Gene to Disease3146
BioCentury BCIQHMGB1
ClinGenHMGB1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3146
Chemical/Pharm GKB GenePA188
Clinical trialHMGB1
Miscellaneous
canSAR (ICR)HMGB1 (select the gene name)
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHMGB1
EVEXHMGB1
GoPubMedHMGB1
iHOPHMGB1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Mar 14 13:09:19 CET 2017

Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.