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HMGB3 (high mobility group box 3)

Identity

Alias_namesHMG4
high-mobility group (nonhistone chromosomal) protein 4
high-mobility group box 3
Alias_symbol (synonym)HMG2A
MGC90319
Other aliasHMG-2a
HMG-4
HGNC (Hugo) HMGB3
LocusID (NCBI) 3149
Atlas_Id 47167
Location Xq28  [Link to chromosome band Xq28]
Location_base_pair Starts at 150983385 and ends at 150990775 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
AGRN (1p36.33) / HMGB3 (Xq28)NUP98 (11p15.4) / HMGB3 (Xq28)SFTPB (2p11.2) / HMGB3 (Xq28)

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

 


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(X;11)(q28;p15) NUP98/HMGB3


External links

Nomenclature
HGNC (Hugo)HMGB3   5004
Cards
Entrez_Gene (NCBI)HMGB3  3149  high mobility group box 3
AliasesHMG-2a; HMG-4; HMG2A; HMG4
GeneCards (Weizmann)HMGB3
Ensembl hg19 (Hinxton)ENSG00000029993 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000029993 [Gene_View]  chrX:150983385-150990775 [Contig_View]  HMGB3 [Vega]
ICGC DataPortalENSG00000029993
TCGA cBioPortalHMGB3
AceView (NCBI)HMGB3
Genatlas (Paris)HMGB3
WikiGenes3149
SOURCE (Princeton)HMGB3
Genetics Home Reference (NIH)HMGB3
Genomic and cartography
GoldenPath hg38 (UCSC)HMGB3  -     chrX:150983385-150990775 +  Xq28   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)HMGB3  -     Xq28   [Description]    (hg19-Feb_2009)
EnsemblHMGB3 - Xq28 [CytoView hg19]  HMGB3 - Xq28 [CytoView hg38]
Mapping of homologs : NCBIHMGB3 [Mapview hg19]  HMGB3 [Mapview hg38]
OMIM300193   300915   
Gene and transcription
Genbank (Entrez)AM393246 AM393784 BC007608 BC010378 BC012370
RefSeq transcript (Entrez)NM_001301228 NM_001301229 NM_001301231 NM_005342
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)HMGB3
Cluster EST : UnigeneHs.19114 [ NCBI ]
CGAP (NCI)Hs.19114
Alternative Splicing GalleryENSG00000029993
Gene ExpressionHMGB3 [ NCBI-GEO ]   HMGB3 [ EBI - ARRAY_EXPRESS ]   HMGB3 [ SEEK ]   HMGB3 [ MEM ]
Gene Expression Viewer (FireBrowse)HMGB3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3149
GTEX Portal (Tissue expression)HMGB3
Human Protein AtlasENSG00000029993-HMGB3 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO15347   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO15347  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO15347
Splice isoforms : SwissVarO15347
PhosPhoSitePlusO15347
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)HMGB3
DMDM Disease mutations3149
Blocks (Seattle)HMGB3
PDB (SRS)2EQZ    2YQI   
PDB (PDBSum)2EQZ    2YQI   
PDB (IMB)2EQZ    2YQI   
PDB (RSDB)2EQZ    2YQI   
Structural Biology KnowledgeBase2EQZ    2YQI   
SCOP (Structural Classification of Proteins)2EQZ    2YQI   
CATH (Classification of proteins structures)2EQZ    2YQI   
SuperfamilyO15347
Human Protein Atlas [tissue]ENSG00000029993-HMGB3 [tissue]
Peptide AtlasO15347
HPRD02181
IPIIPI00217477   IPI00744556   IPI00643317   IPI00640781   IPI00411540   
Protein Interaction databases
DIP (DOE-UCLA)O15347
IntAct (EBI)O15347
FunCoupENSG00000029993
BioGRIDHMGB3
STRING (EMBL)HMGB3
ZODIACHMGB3
Ontologies - Pathways
QuickGOO15347
Ontology : AmiGOfour-way junction DNA binding  double-stranded DNA binding  RNA binding  protein binding  nucleus  chromosome  cytoplasm  DNA recombination  transcription, DNA-templated  regulation of transcription, DNA-templated  multicellular organism development  DNA binding, bending  DNA geometric change  innate immune response  
Ontology : EGO-EBIfour-way junction DNA binding  double-stranded DNA binding  RNA binding  protein binding  nucleus  chromosome  cytoplasm  DNA recombination  transcription, DNA-templated  regulation of transcription, DNA-templated  multicellular organism development  DNA binding, bending  DNA geometric change  innate immune response  
NDEx NetworkHMGB3
Atlas of Cancer Signalling NetworkHMGB3
Wikipedia pathwaysHMGB3
Orthology - Evolution
OrthoDB3149
GeneTree (enSembl)ENSG00000029993
Phylogenetic Trees/Animal Genes : TreeFamHMGB3
HOVERGENO15347
HOGENOMO15347
Homologs : HomoloGeneHMGB3
Homology/Alignments : Family Browser (UCSC)HMGB3
Gene fusions - Rearrangements
Tumor Fusion PortalHMGB3
Fusion Cancer (Beijing)SFTPB [2p11.2]  -  HMGB3 [Xq28]  [FUSC003659]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHMGB3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HMGB3
dbVarHMGB3
ClinVarHMGB3
1000_GenomesHMGB3 
Exome Variant ServerHMGB3
ExAC (Exome Aggregation Consortium)ENSG00000029993
GNOMAD BrowserENSG00000029993
Genetic variants : HAPMAP3149
Genomic Variants (DGV)HMGB3 [DGVbeta]
DECIPHERHMGB3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisHMGB3 
Mutations
ICGC Data PortalHMGB3 
TCGA Data PortalHMGB3 
Broad Tumor PortalHMGB3
OASIS PortalHMGB3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHMGB3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHMGB3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch HMGB3
DgiDB (Drug Gene Interaction Database)HMGB3
DoCM (Curated mutations)HMGB3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HMGB3 (select a term)
intoGenHMGB3
Cancer3DHMGB3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM300193    300915   
Orphanet
DisGeNETHMGB3
MedgenHMGB3
Genetic Testing Registry HMGB3
NextProtO15347 [Medical]
TSGene3149
GENETestsHMGB3
Target ValidationHMGB3
Huge Navigator HMGB3 [HugePedia]
snp3D : Map Gene to Disease3149
BioCentury BCIQHMGB3
ClinGenHMGB3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3149
Chemical/Pharm GKB GenePA35092
Clinical trialHMGB3
Miscellaneous
canSAR (ICR)HMGB3 (select the gene name)
Probes
Litterature
PubMed34 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHMGB3
EVEXHMGB3
GoPubMedHMGB3
iHOPHMGB3
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 Nov 21 14:16:25 CET 2017

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