Human Gene HMGB1 (uc001usv.3)
  Description: Homo sapiens high mobility group box 1 (HMGB1), mRNA.
RefSeq Summary (NM_002128): This gene encodes a protein that belongs to the High Mobility Group-box superfamily. The encoded non-histone, nuclear DNA-binding protein regulates transcription, and is involved in organization of DNA. This protein plays a role in several cellular processes, including inflammation, cell differentiation and tumor cell migration. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Sep 2015]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Transcript (Including UTRs)
   Position: hg19 chr13:31,032,879-31,038,384 Size: 5,506 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr13:31,035,820-31,037,817 Size: 1,998 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:31,032,879-31,038,384)mRNA (may differ from genome)Protein (158 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMalacardsMGIPubMed
UniProtKBWikipedia

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HMGB1
CDC HuGE Published Literature: HMGB1
Positive Disease Associations: Alzheimer Disease , Lipids
Related Studies:
  1. Alzheimer Disease
    S J Furney et al. Molecular psychiatry 2011, Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease., Molecular psychiatry. [PubMed 21116278]
  2. Lipids
    , , . [PubMed 0]

-  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
  • D004997 Ethinyl Estradiol
  • D006861 Hydrogen Peroxide
  • D008070 Lipopolysaccharides
  • D011794 Quercetin
  • D020849 Raloxifene
  • D014635 Valproic Acid
  • C440499 lipopolysaccharide, Escherichia coli 0111 B4
  • C492600 (2,3,5,6-tetrafluoro-4-methoxymethylphenyl)methyl-2,2-dimethyl-3-(1-propenyl)cyclopropanecarboxylate
  • C049325 1,2-dithiol-3-thione
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
          more ... click here to view the complete list

+  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 -145.26567-0.256 Picture PostScript Text
3' UTR -708.392836-0.250 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
IPR017967 - HMG_boxA_CS
IPR009071 - HMG_superfamily

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

SCOP Domains:
47095 - HMG-box

ModBase Predicted Comparative 3D Structure on Q5T7C4
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:0003677 DNA binding

Cellular Component:
GO:0005634 nucleus


-  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.
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.
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
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03410 - Base excision repair

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

-  Other Names for This Gene
  Alternate Gene Symbols: BX647267, Q5T7C4, Q5T7C4_HUMAN, RP11-550P23.1-003
UCSC ID: uc001usv.3
RefSeq Accession: NM_002128
Protein: Q5T7C4

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BX647267.1
exon count: 5CDS single in 3' UTR: no RNA size: 1782
ORF size: 477CDS single in intron: no Alignment % ID: 99.83
txCdsPredict score: 1019.00frame shift in genome: no % Coverage: 96.75
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 553# strange splices: 0
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.