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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

HMGB1 Gene

protein-coding GIFtS: 64
GCID: GC13M031032

high mobility group box 1

(Previous names: high-mobility group (nonhistone chromosomal) protein 1,...)
(Previous symbol: HMG1)

Explore 114 diseases affiliated with
HMGB1 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
High Mobility Group Box 1¹ ²		High Mobility Group Protein 1² ³
HMG1¹ ² ³ ⁵		HMG-1² ³
HMG3¹ ²		DKFZp686A04236¹
SBP-1¹ ²		Amphoterin²
High-Mobility Group (Nonhistone Chromosomal) Protein 1¹ ²		High Mobility Group Protein B1²
High-Mobility Group Box 1¹ ²		Sulfoglucuronyl Carbohydrate Binding Protein²

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

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

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000013.10 NC_018924.1 NT_024524.14

Regulatory elements:

SABiosciences 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 SABiosciences Chromatin IP Primers for HMGB1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

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)

Subcellular location: Nucleus. Chromosome

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

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_P09429

HMGB1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_002119.1

ENSEMBL proteins:

ENSP00000384678 ENSP00000343040 ENSP00000345347 ENSP00000382412 ENSP00000382417

ENSP00000411269 ENSP00000369904 ENSP00000410465

Reactome Protein details: P09429
Human Recombinant Protein Products for HMGB1:

	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
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	GenScript Purified and Recombinant Proteins for HMGB1
	Novus Biologicals HMGB1 Proteins Novus Biologicals HMGB1 Lysates
	Sino Biological Recombinant Protein for HMGB1
	ProSpec Recombinant Protein for HMGB1
	Uscn Proteins for HMGB1

Gene Ontology (GO): 5/11 cellular component terms (GO ID links to tree view) (see all 11): About this table

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:0005625	soluble fraction	--	--
GO:0005634	nucleus	IDA	19223331

HMGB1 for ontologies About GeneDecksing

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 (see all 3): HMGB1 OriGene Custom Antibody Services for HMGB1
	GenScript Custom Superior Antibodies Services for HMGB1
	Novus Biologicals HMGB1 Antibodies
	Abcam antibodies for HMGB1
	Uscn Antibodies for HMGB1
	ThermoFisher Antibody for HMGB1

Assay Products for HMGB1:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Immunoassay Development Browse OriGene Fluorogenic Cell Assay Kits
	Browse R&D Systems for biochemical assays
	GenScript Custom Assay Services for HMGB1
	Browse Enzo Life Sciences for kits & assays
	Uscn ELISAs and CLIAs for HMGB1

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

HMGB1 for domains About GeneDecksing

2 InterPro domains/families:

IPR009071 HMG_superfamily

IPR017967 HMG_boxA_CS

Graphical View of Domain Structure for InterPro Entry P09429

ProtoNet protein and cluster: P09429

1 Blocks protein family: 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

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

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): 5/22 molecular function terms (GO ID links to tree view) (see all 22): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000401	open form four-way junction DNA binding	--	--
GO:0000402	crossed form four-way junction DNA binding	--	--
GO:0003677	DNA binding	--	--
GO:0003681	bent DNA binding	--	--
GO:0003684	damaged DNA binding	ISS	--

HMGB1 for ontologies About GeneDecksing

Phenotypes:
7 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Hmgb1):

behavior/neurological	cellular	growth/size	homeostasis/metabolism	mortality/aging
respiratory system	vision/eye

HMGB1 for phenotypes About GeneDecksing

Animal Models:
Mouse knock-out Hmgb1^tm1Meb for HMGB1

inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for HMGB1

miRNA Products:		OriGene 3'-UTR Clone: HMGB1 Browse MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat HMGB1
		8/67 QIAGEN miScript miRNA 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 plasmid: HMGB1 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for HMGB1 (see all 4) OriGene shRNA RFP: HMGB1 OriGene siRNA: HMGB1
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat HMGB1
		Sirion Biotech Custom design and validation of potent shRNA sequences against HMGB1

Gene Editing Products:			DNA2.0 Custom Protein Engineering Service for HMGB1
			Sirion Biotech Customized adenovirus for overexpression of HMGB1 Sirion Biotech Customized adenovirus for potent knockdown of HMGB1

Clone Products:		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for HMGB1 (see all 5) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for HMGB1 (see all 2) 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

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for HMGB1
		Search LifeMap BioReagents cell lines for HMGB1
		Sirion Biotech Customized stable knockdown cell line services for HMGB1 Sirion Biotech Customized inducible knockdown cell line services for HMGB1 Sirion Biotech Customized stable overexpressing cell line services for HMGB1 Sirion Biotech Customized inducible overexpressing cell line services for HMGB1

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMGB1

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways - 5/11 super-pathways (see all 11) About this table

See pathways by source

Super-pathway

contained gene-specific pathways

Immune System

Immune System

1.00

Innate Immune System

0.46

Activation of DNA fragmentation factor

Activation of DNA fragmentation factor

1.00

Apoptosis induced DNA fragmentation

1.00

Chromatin Regulation / Acetylation

Chromatin Regulation / Acetylation

1.00

Selected targets of Oct-3/4

Selected targets of Oct-3/4

1.00

amb2 Integrin signaling

amb2 Integrin signaling

1.00

Pathway sources
See GeneCards unified pathways
Show all pathways

1 EMD Millipore Pathway for HMGB1

Selected targets of Oct-3/4

1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for HMGB1

HMGB1 Pathway

1 Cell Signaling Technology (CST) Pathway for HMGB1

Chromatin Regulation / Acetylation

2 BioSystems Pathways for HMGB1

	DNA damage response (only ATM dependent)
	amb2 Integrin signaling

5/7 Reactome Pathways for HMGB1 (see all 7)

	Activation of DNA fragmentation factor
	Advanced glycosylation endproduct receptor signaling
	Apoptosis induced DNA fragmentation
	Apoptotic execution phase
	Apoptosis

1 Kegg Pathway (Kegg details for HMGB1):

Base excision repair

HMGB1 for pathways About GeneDecksing

Interactions:

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for HMGB1

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

5/117 Interacting proteins for HMGB1 (P09429^{2, 3} ENSP00000343040⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 117)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
DNM2	P50570²^,³, ENSP00000352721⁴	MINT-8254432 I2D: score=2 STRING: ENSP00000352721
TXN	P10599²^,³, ENSP00000363641⁴	MINT-6795963 I2D: score=1 STRING: ENSP00000363641
CSNK1A1	P48729²^,³, ENSP00000261798⁴	MINT-14881 MINT-16364 I2D: score=3 STRING: ENSP00000261798
H3F3A	P84243³, ENSP00000355778⁴	I2D: score=1 STRING: ENSP00000355778
TP53	P04637³, ENSP00000269305⁴	I2D: score=6 STRING: ENSP00000269305

About this table

Gene Ontology (GO): 5/51 biological process terms (GO ID links to tree view) (see all 51): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	IMP	19158276
GO:0000902	cell morphogenesis	--	--
GO:0001654	eye development	IEA	--
GO:0001773	myeloid dendritic cell activation	ISS	--
GO:0001934	positive regulation of protein phosphorylation	--	--

HMGB1 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

HMGB1 for compounds About GeneDecksing

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for HMGB1
10/53 Novoseek 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)

Search CenterWatch for drugs/clinical trials and news about HMGB1

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 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,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

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

10 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

ENST00000426225 ENST00000326004 ENST00000490788 ENST00000398908 ENST00000468384

miRNA Products:		OriGene 3'-UTR Clone: HMGB1 Browse OriGene MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat HMGB1
		8/67 QIAGEN miScript miRNA 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 plasmid: HMGB1 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for HMGB1 (see all 4) OriGene shRNA RFP: HMGB1 OriGene siRNA: HMGB1
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat HMGB1
		Sirion Biotech Custom design and validation of potent shRNA sequences against HMGB1

Clone Products:		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for HMGB1 (see all 5) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for HMGB1 (see all 2) OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		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

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for HMGB1 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat HMGB1
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HMGB1
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HMGB1

Additional cDNA sequence:

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

24/91 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.438329

DT.100697446 DT.100712011 DT.95377063 DT.120905298 DT.121044751 DT.40252816 DT.100697454 DT.100857814

24/1611 AceView cDNA sequences (see all 1611):

BX335202 AI375302 AA206166 CR591935 BU580659 BQ778108 AW071524 AA360132

AW074286 H97719 AI383756 AW675575 BX109832 AW162373 CR600442 AI831345

CR625918 AA205334 BQ613950 BF692448 BU075650 AI553646 BG034466 AI628822

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

HMGB1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GAAATTTAAA

About this image

HMGB1 expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

2 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Skeletal Muscle

Hyoid Arch Muscles

Myoblasts

Skeletal Muscle

Mandibular Arch Muscles

Myoblasts

Skeletal Muscle

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See HMGB1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for HMGB1

SOURCE GeneReport for Unigene clusters: Hs.434102 Hs.593339 Hs.596078

SABiosciences Expression via Pathway-Focused PCR Arrays including HMGB1:

Toll-Like Receptor Signaling Pathway in human mouse rat

Apoptosis 384HT in human mouse rat

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for HMGB1 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat HMGB1
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HMGB1
		QIAGEN 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

This gene was present in the common ancestor of eukaryotes.

Orthologs for HMGB1 gene from 8/28 species (see all 28) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	HMGB1¹	high mobility group box 1	85.43(n) 90.7(a)		395724 NM_204902.2 NP_990233.1
lizard (Anolis carolinensis)	Reptilia	HMGB1⁶	--	88(a)	1 ↔ 1	3(184565801-184568685)
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
fruit fly (Drosophila melanogaster)	Insecta	Dsp1¹	Dorsal switch protein 1	55.77(n) 47.12(a)		117294 NM_206762.2 NP_996485.1
worm (Caenorhabditis elegans)	Secernentea	hmg-1.2¹	Protein HMG-1.2	55.69(n) 44.72(a)		175890 NM_065974.6 NP_498375.1
thale cress (Arabidopsis thaliana)	eudicotyledons	NFD⁶	FACT complex subunit SSRP1	8(a)	possible ortholog	3(10784889-10788729)
rice (Oryza sativa)	Liliopsida	-- --	SSRP1-like FACT complex subunit, putative, express... SSRP1-like FACT complex subunit, putative, express...	6(a) 6(a)	possible ortholog possible ortholog	1(4496719-4503407) 5(4965403-4971007)

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)
About This Section

Paralogs for HMGB1 gene

TOX² TOX4² HMGB4² TOX3² HMGB3² TOX2² 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

HMGB1 for paralogs About GeneDecksing

5/36 Pseudogenes.org Pseudogenes for HMGB1 (see all 36)
PGOHUM00000238714 PGOHUM00000238784 PGOHUM00000251277 PGOHUM00000256675 PGOHUM00000242611

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, 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

SNP ID	Valid	Clinical significance	Chr 13 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs7993324^1,2	C,F,A	--	31032457(+)	`CAGTTG/ATCTCT`	1	--	ds500¹		5		NA WA CSA	126
rs66479274^1,2	C	--	31032469(+)	`TTTTTT/-GAGAT`	1	--	ds500¹		1		NA	2
rs141328952^1,2		--	31032515(+)	`AGGCTA/GGAGTG`	1	--	ds500¹		0	--	--	--	--
rs192642163^1,2		--	31032634(+)	`GCTAAC/TTTTTT`	1	--	ds500¹		0	--	--	--	--
rs185382445^1,2		--	31032669(+)	`CACCAC/TGTTAG`	1	--	ds500¹		0	--	--	--	--
rs150791242^1,2		--	31032683(+)	`GGATGA/GTCTCA`	1	--	ds500¹		0	--	--	--	--
rs56119368^1,2	C	--	31032697(+)	`TCCTGG/ACCTCG`	1	--	ds500¹		1		WA	2
rs2039338^1,2	C,F,A,H	--	31032717(-)	`aggccG/Aaggcg`	1	--	ds500¹		2		NA	6
rs188946320^1,2		--	31032732(+)	`AAGTGA/CTGGGA`	1	--	ds500¹		0	--	--	--	--
rs147193792^1,2		--	31032749(+)	`GCGTGA/GGCCAC`	1	--	ds500¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for HMGB1 (31032877 - 31191734 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for HMGB1: --

SABiosciences Cancer Mutation PCR Assays

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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.)
About This Section

HMGB1 for disorders           About GeneDecksing

OMIM gene information: 163905    OMIM disorders: --

20/114 diseases for HMGB1 (see all 114):    About MalaCards

churg-strauss syndrome disseminated intravascular coagulation staphylococcal toxic shock syndrome xeroderma pigmentosum

graft versus host disease non-small cell lung carcinoma thoracic aortic aneurysm toxic shock syndrome

non-hodgkin lymphoma squamous cell carcinoma aortic aneurysm autonomic dysfunction

gastrointestinal stromal tumor chronic obstructive pulmonary disease herpes simplex lupus erythematosus

cutaneous lupus erythematosus laryngeal squamous cell carcinoma immunodysregulation myocardial infarction

1 disease from the University of Copenhagen DISEASES database for HMGB1:

Vascular disease

10/59 Novoseek 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)

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 9 sources (see all 759):
(articles sorted by number of sources associating them with HMGB1)

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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. (1996)
The genetic variation of the human HMGB1 gene. (PubMed id 17610420)^{1, 2, 9} Kornblit B....Garred P. (2007)
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. (1997)
Proteomic analysis of ubiquitinated proteins in normal hepatocyte cell line Chang liver cells. (PubMed id 18655026)^{1, 2} Tan F....Peng X. (2008)
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)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{1, 2} Ota T.... Sugano S. (2004)
Identity of nuclear high-mobility-group protein, HMG-1, and sulfoglucuronyl carbohydrate-binding protein, SBP-1, in brain. (PubMed id 11279268)^{1, 3} Chou D.K....Jungalwala F.B. (2001)
Two-dimensional electrophoretic analysis of human breast carcinoma proteins: mapping of proteins that bind to the SH3 domain of mixed lineage kinase MLK2. (PubMed id 9150946)^{1, 2} Rasmussen R.K.... Dorow D.S. (1997)
A human placental cDNA clone that encodes nonhistone chromosomal protein HMG-1. (PubMed id 2922262)^{1, 2} Wen L.... Reeck G.R. (1989)
Effects of HMGB1 on PMN apoptosis during LPS-induced acute lung injury. (PubMed id 18952078)^{1, 9} Feng Y....Liu Y. (2008)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
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)
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(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

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

Intellectual Property for HMGB1 gene
(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:
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high mobility group box 1

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