Human Gene HMGB1 (ENST00000341423.10_7) from GENCODE V47lift37
  Description: high mobility group box 1, transcript variant 2 (from RefSeq NM_002128.7)
Gencode Transcript: ENST00000341423.10_7
Gencode Gene: ENSG00000189403.15_10
Transcript (Including UTRs)
   Position: hg19 chr13:31,030,841-31,040,073 Size: 9,233 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr13:31,035,494-31,037,817 Size: 2,324 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:31,030,841-31,040,073)mRNA (may differ from genome)Protein (215 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HMGB1_HUMAN
DESCRIPTION: RecName: Full=High mobility group protein B1; AltName: Full=High mobility group protein 1; Short=HMG-1;
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).
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.
SIMILARITY: Belongs to the HMGB family.
SIMILARITY: Contains 2 HMG box DNA-binding domains.
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/hmgb1/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: HMGB1
Diseases sorted by gene-association score: 13q12.3 microdeletion syndrome (18), endophthalmitis (15), adenosquamous gallbladder carcinoma (10), staphylococcal toxic shock syndrome (10), recessive dystrophic epidermolysis bullosa (10), anca-associated vasculitis (9), hand, foot and mouth disease (8), mouth disease (7), toxic shock syndrome (7), thymic hyperplasia (7), macrophage activation syndrome (7), idiopathic neutropenia (5), ariboflavinosis (5), suppurative cholangitis (4), inclusion conjunctivitis (4), systemic lupus erythematosus (4), rheumatoid arthritis (4), rheumatic disease (3), colorectal cancer (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 58.90 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1933.09 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -49.90155-0.322 Picture PostScript Text
3' UTR -1226.644653-0.264 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR017967 - HMG_boxA_CS
IPR009071 - HMG_superfamily

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF09011 - HMG-box domain

SCOP Domains:
48371 - ARM repeat
47095 - HMG-box
46785 - "Winged helix" DNA-binding domain
90250 - Troponin coil-coiled subunits

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2YRQ - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P09429
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000400 four-way junction DNA binding
GO:0000405 bubble DNA binding
GO:0001530 lipopolysaccharide binding
GO:0001786 phosphatidylserine binding
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003690 double-stranded DNA binding
GO:0003697 single-stranded DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003723 RNA binding
GO:0003725 double-stranded RNA binding
GO:0003727 single-stranded RNA binding
GO:0005125 cytokine activity
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0008301 DNA binding, bending
GO:0010858 calcium-dependent protein kinase regulator activity
GO:0016829 lyase activity
GO:0019958 C-X-C chemokine binding
GO:0030295 protein kinase activator activity
GO:0042056 chemoattractant activity
GO:0050786 RAGE receptor binding
GO:0070182 DNA polymerase binding
GO:0070491 repressing transcription factor binding
GO:0097100 supercoiled DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001654 eye development
GO:0001773 myeloid dendritic cell activation
GO:0001934 positive regulation of protein phosphorylation
GO:0001935 endothelial cell proliferation
GO:0002218 activation of innate immune response
GO:0002224 toll-like receptor signaling pathway
GO:0002250 adaptive immune response
GO:0002270 plasmacytoid dendritic cell activation
GO:0002281 macrophage activation involved in immune response
GO:0002376 immune system process
GO:0002407 dendritic cell chemotaxis
GO:0002437 inflammatory response to antigenic stimulus
GO:0002643 regulation of tolerance induction
GO:0002840 regulation of T cell mediated immune response to tumor cell
GO:0006265 DNA topological change
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006309 apoptotic DNA fragmentation
GO:0006310 DNA recombination
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006914 autophagy
GO:0006935 chemotaxis
GO:0006954 inflammatory response
GO:0006974 cellular response to DNA damage stimulus
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0010469 regulation of receptor activity
GO:0010506 regulation of autophagy
GO:0017055 negative regulation of RNA polymerase II transcriptional preinitiation complex assembly
GO:0030324 lung development
GO:0031175 neuron projection development
GO:0031497 chromatin assembly
GO:0032072 regulation of restriction endodeoxyribonuclease activity
GO:0032147 activation of protein kinase activity
GO:0032392 DNA geometric change
GO:0032425 positive regulation of mismatch repair
GO:0032689 negative regulation of interferon-gamma production
GO:0032727 positive regulation of interferon-alpha production
GO:0032728 positive regulation of interferon-beta production
GO:0032733 positive regulation of interleukin-10 production
GO:0032735 positive regulation of interleukin-12 production
GO:0032755 positive regulation of interleukin-6 production
GO:0032760 positive regulation of tumor necrosis factor production
GO:0033151 V(D)J recombination
GO:0034137 positive regulation of toll-like receptor 2 signaling pathway
GO:0034145 positive regulation of toll-like receptor 4 signaling pathway
GO:0034165 positive regulation of toll-like receptor 9 signaling pathway
GO:0035711 T-helper 1 cell activation
GO:0035767 endothelial cell chemotaxis
GO:0042104 positive regulation of activated T cell proliferation
GO:0043065 positive regulation of apoptotic process
GO:0043277 apoptotic cell clearance
GO:0043280 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0043312 neutrophil degranulation
GO:0043371 negative regulation of CD4-positive, alpha-beta T cell differentiation
GO:0043388 positive regulation of DNA binding
GO:0043410 positive regulation of MAPK cascade
GO:0043536 positive regulation of blood vessel endothelial cell migration
GO:0043537 negative regulation of blood vessel endothelial cell migration
GO:0045063 T-helper 1 cell differentiation
GO:0045087 innate immune response
GO:0045089 positive regulation of innate immune response
GO:0045639 positive regulation of myeloid cell differentiation
GO:0045819 positive regulation of glycogen catabolic process
GO:0045859 regulation of protein kinase activity
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046330 positive regulation of JNK cascade
GO:0050716 positive regulation of interleukin-1 secretion
GO:0050718 positive regulation of interleukin-1 beta secretion
GO:0050918 positive chemotaxis
GO:0051103 DNA ligation involved in DNA repair
GO:0051106 positive regulation of DNA ligation
GO:0051384 response to glucocorticoid
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0071639 positive regulation of monocyte chemotactic protein-1 production
GO:0090026 positive regulation of monocyte chemotaxis
GO:0090303 positive regulation of wound healing
GO:0097350 neutrophil clearance
GO:1901224 positive regulation of NIK/NF-kappaB signaling
GO:1903672 positive regulation of sprouting angiogenesis
GO:1905564 positive regulation of vascular endothelial cell proliferation
GO:1990774 tumor necrosis factor secretion
GO:2000426 negative regulation of apoptotic cell clearance
GO:2000778 positive regulation of interleukin-6 secretion
GO:2000819 regulation of nucleotide-excision repair
GO:2001200 positive regulation of dendritic cell differentiation

Cellular Component:
GO:0000793 condensed chromosome
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0034774 secretory granule lumen
GO:0035868 alphav-beta3 integrin-HMGB1 complex
GO:0043005 neuron projection
GO:1904813 ficolin-1-rich granule lumen
GO:0017053 transcriptional repressor complex


-  Descriptions from all associated GenBank mRNAs
  AK122825 - Homo sapiens cDNA FLJ16428 fis, clone BRACE3008066, highly similar to High mobility group protein B1.
CR749614 - Homo sapiens mRNA; cDNA DKFZp686A04236 (from clone DKFZp686A04236).
KJ896987 - Synthetic construct Homo sapiens clone ccsbBroadEn_06381 HMGB1 gene, encodes complete protein.
JD197862 - Sequence 178886 from Patent EP1572962.
JD212485 - Sequence 193509 from Patent EP1572962.
JD112367 - Sequence 93391 from Patent EP1572962.
JD212484 - Sequence 193508 from Patent EP1572962.
JD542605 - Sequence 523629 from Patent EP1572962.
JD222873 - Sequence 203897 from Patent EP1572962.
JD497687 - Sequence 478711 from Patent EP1572962.
JD497688 - Sequence 478712 from Patent EP1572962.
JA482248 - Sequence 231 from Patent WO2011072091.
JE980540 - Sequence 231 from Patent EP2862929.
AL110194 - Homo sapiens mRNA; cDNA DKFZp566M063 (from clone DKFZp566M063).
BC141844 - Homo sapiens high-mobility group box 1, mRNA (cDNA clone MGC:166986 IMAGE:8860319), complete cds.
AK057120 - Homo sapiens cDNA FLJ32558 fis, clone SPLEN1000143, highly similar to High mobility group protein B1.
BC030981 - Homo sapiens high-mobility group box 1, mRNA (cDNA clone MGC:32637 IMAGE:4041682), complete cds.
JD100653 - Sequence 81677 from Patent EP1572962.
JD566758 - Sequence 547782 from Patent EP1572962.
JD228297 - Sequence 209321 from Patent EP1572962.
JD052614 - Sequence 33638 from Patent EP1572962.
JD557206 - Sequence 538230 from Patent EP1572962.
AK291494 - Homo sapiens cDNA FLJ77690 complete cds, highly similar to Homo sapiens high-mobility group box 1 (HMGB1), mRNA.
L13804 - Homo sapiens (clone 06) liver expressed high mobility group 1 protein mRNA, 3' end.
BC067732 - Homo sapiens high-mobility group box 1, mRNA (cDNA clone MGC:86953 IMAGE:4818524), complete cds.
BX647267 - Homo sapiens mRNA; cDNA DKFZp686N1099 (from clone DKFZp686N1099).
D63874 - Homo sapiens FM1 mRNA for HMG-1, complete cds.
AX795278 - Sequence 1 from Patent WO03051383.
BC003378 - Homo sapiens high-mobility group box 1, mRNA (cDNA clone MGC:5223 IMAGE:2901382), complete cds.
JD551355 - Sequence 532379 from Patent EP1572962.
LF337017 - JP 2014500723-A/144520: Polycomb-Associated Non-Coding RNAs.
AF401215 - Homo sapiens HMG1 mRNA, 3' untranslated region.
BC066889 - Homo sapiens high-mobility group box 1, mRNA (cDNA clone MGC:86954 IMAGE:5268698), complete cds.
AB208998 - Homo sapiens mRNA for high-mobility group box 1 variant protein.
AK310975 - Homo sapiens cDNA, FLJ18017.
JD297262 - Sequence 278286 from Patent EP1572962.
X12597 - Human mRNA for high mobility group-1 protein (HMG-1).
LF323756 - JP 2014500723-A/131259: Polycomb-Associated Non-Coding RNAs.
JD307312 - Sequence 288336 from Patent EP1572962.
JD299750 - Sequence 280774 from Patent EP1572962.
L13805 - Homo sapiens (clone 06) high mobility group 1 protein mRNA fragment.
JD283835 - Sequence 264859 from Patent EP1572962.
AY377859 - Homo sapiens high mobility group protein 1 mRNA, complete cds.
CR456863 - Homo sapiens full open reading frame cDNA clone RZPDo834D0816D for gene HMGB1, high-mobility group box 1; complete cds, incl. stopcodon.
BT006940 - Homo sapiens high-mobility group box 1 mRNA, complete cds.
BT020159 - Homo sapiens high-mobility group box 1 mRNA, complete cds.
CU678446 - Synthetic construct Homo sapiens gateway clone IMAGE:100016790 5' read HMGB1 mRNA.
CU688180 - Synthetic construct Homo sapiens gateway clone IMAGE:100021064 5' read HMGB1 mRNA.
BC140013 - Synthetic construct Homo sapiens clone IMAGE:100000676, MGC:167158 high-mobility group box 1 (HMGB1) mRNA, encodes complete protein.
BC140018 - Synthetic construct Homo sapiens clone IMAGE:100013567, MGC:167183 high-mobility group box 1 (HMGB1) mRNA, encodes complete protein.
AB527489 - Synthetic construct DNA, clone: pF1KB7934, Homo sapiens HMGB1 gene for high-mobility group box 1, without stop codon, in Flexi system.
LF317124 - JP 2014500723-A/124627: Polycomb-Associated Non-Coding RNAs.
KX821210 - Homo sapiens isolate THM1 high mobility group box 1 (HMGB1) mRNA, partial cds.
LF343553 - JP 2014500723-A/151056: Polycomb-Associated Non-Coding RNAs.
LF343357 - JP 2014500723-A/150860: Polycomb-Associated Non-Coding RNAs.
LF372070 - JP 2014500723-A/179573: Polycomb-Associated Non-Coding RNAs.
LF361953 - JP 2014500723-A/169456: Polycomb-Associated Non-Coding RNAs.
LF366776 - JP 2014500723-A/174279: Polycomb-Associated Non-Coding RNAs.
LF370158 - JP 2014500723-A/177661: Polycomb-Associated Non-Coding RNAs.
LF371918 - JP 2014500723-A/179421: Polycomb-Associated Non-Coding RNAs.
LF365203 - JP 2014500723-A/172706: Polycomb-Associated Non-Coding RNAs.
LF336970 - JP 2014500723-A/144473: Polycomb-Associated Non-Coding RNAs.
LF343160 - JP 2014500723-A/150663: Polycomb-Associated Non-Coding RNAs.
LF345325 - JP 2014500723-A/152828: Polycomb-Associated Non-Coding RNAs.
LF343393 - JP 2014500723-A/150896: Polycomb-Associated Non-Coding RNAs.
LF331940 - JP 2014500723-A/139443: Polycomb-Associated Non-Coding RNAs.
LF317744 - JP 2014500723-A/125247: Polycomb-Associated Non-Coding RNAs.
LF317125 - JP 2014500723-A/124628: Polycomb-Associated Non-Coding RNAs.
LF325343 - JP 2014500723-A/132846: Polycomb-Associated Non-Coding RNAs.
AK304506 - Homo sapiens cDNA FLJ56337 complete cds, highly similar to High mobility group protein B1.
LF323755 - JP 2014500723-A/131258: Polycomb-Associated Non-Coding RNAs.
LF361954 - JP 2014500723-A/169457: Polycomb-Associated Non-Coding RNAs.
LF366040 - JP 2014500723-A/173543: Polycomb-Associated Non-Coding RNAs.
KX821209 - Homo sapiens isolate CHM1 high mobility group box 1 (HMGB1) mRNA, partial cds.
LF372071 - JP 2014500723-A/179574: Polycomb-Associated Non-Coding RNAs.
LF334605 - JP 2014500723-A/142108: Polycomb-Associated Non-Coding RNAs.
LF375440 - JP 2014500723-A/182943: Polycomb-Associated Non-Coding RNAs.
JD343525 - Sequence 324549 from Patent EP1572962.
JD484349 - Sequence 465373 from Patent EP1572962.
MA559333 - JP 2018138019-A/131259: Polycomb-Associated Non-Coding RNAs.
MA579130 - JP 2018138019-A/151056: Polycomb-Associated Non-Coding RNAs.
MA578934 - JP 2018138019-A/150860: Polycomb-Associated Non-Coding RNAs.
MA607647 - JP 2018138019-A/179573: Polycomb-Associated Non-Coding RNAs.
MA602353 - JP 2018138019-A/174279: Polycomb-Associated Non-Coding RNAs.
MA605735 - JP 2018138019-A/177661: Polycomb-Associated Non-Coding RNAs.
MA607495 - JP 2018138019-A/179421: Polycomb-Associated Non-Coding RNAs.
MA600780 - JP 2018138019-A/172706: Polycomb-Associated Non-Coding RNAs.
MA578737 - JP 2018138019-A/150663: Polycomb-Associated Non-Coding RNAs.
MA580902 - JP 2018138019-A/152828: Polycomb-Associated Non-Coding RNAs.
MA578970 - JP 2018138019-A/150896: Polycomb-Associated Non-Coding RNAs.
MA567517 - JP 2018138019-A/139443: Polycomb-Associated Non-Coding RNAs.
MA560920 - JP 2018138019-A/132846: Polycomb-Associated Non-Coding RNAs.
MA559332 - JP 2018138019-A/131258: Polycomb-Associated Non-Coding RNAs.
MA601617 - JP 2018138019-A/173543: Polycomb-Associated Non-Coding RNAs.
MA607648 - JP 2018138019-A/179574: Polycomb-Associated Non-Coding RNAs.
MA572594 - JP 2018138019-A/144520: Polycomb-Associated Non-Coding RNAs.
MA552701 - JP 2018138019-A/124627: Polycomb-Associated Non-Coding RNAs.
MA597530 - JP 2018138019-A/169456: Polycomb-Associated Non-Coding RNAs.
MA572547 - JP 2018138019-A/144473: Polycomb-Associated Non-Coding RNAs.
MA553321 - JP 2018138019-A/125247: Polycomb-Associated Non-Coding RNAs.
MA552702 - JP 2018138019-A/124628: Polycomb-Associated Non-Coding RNAs.
MA597531 - JP 2018138019-A/169457: Polycomb-Associated Non-Coding RNAs.
MA570182 - JP 2018138019-A/142108: Polycomb-Associated Non-Coding RNAs.
MA611017 - JP 2018138019-A/182943: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_DNAfragmentPathway - Apoptotic DNA fragmentation and tissue homeostasis
h_pcafpathway - The information-processing pathway at the IFN-beta enhancer

Reactome (by CSHL, EBI, and GO)

Protein P09429 (Reactome details) participates in the following event(s):

R-HSA-5432825 HMGB1 binds TLR4:LY96
R-HSA-6804099 HMGB1 binds LTP
R-HSA-6804100 HMGB1 binds LPS
R-HSA-266204 Association of HMGB1/HMGB2 with chromatin
R-HSA-879411 Advanced glycosylation end product-specific receptor (AGER/RAGE) is a multiligand receptor
R-HSA-6800434 Exocytosis of ficolin-rich granule lumen proteins
R-HSA-6798748 Exocytosis of secretory granule lumen proteins
R-HSA-879362 AGER binds ERK1/2
R-NUL-997411 AGER binds rat ERK1/2
R-HSA-5686938 Regulation of TLR by endogenous ligand
R-HSA-211227 Activation of DNA fragmentation factor
R-HSA-168898 Toll-Like Receptors Cascades
R-HSA-879415 Advanced glycosylation endproduct receptor signaling
R-HSA-6798695 Neutrophil degranulation
R-HSA-140342 Apoptosis induced DNA fragmentation
R-HSA-168249 Innate Immune System
R-HSA-75153 Apoptotic execution phase
R-HSA-168256 Immune System
R-HSA-109581 Apoptosis
R-HSA-5357801 Programmed Cell Death

-  Other Names for This Gene
  Alternate Gene Symbols: A5D8W9, ENST00000341423.1, ENST00000341423.2, ENST00000341423.3, ENST00000341423.4, ENST00000341423.5, ENST00000341423.6, ENST00000341423.7, ENST00000341423.8, ENST00000341423.9, HMG1, HMGB1 , HMGB1_HUMAN, NM_002128, P09429, Q14321, Q5T7C3, Q6IBE1, uc317wag.1, uc317wag.2
UCSC ID: ENST00000341423.10_7
RefSeq Accession: NM_002128.7
Protein: P09429 (aka HMGB1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.