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HMGB4 Gene

protein-coding   GIFtS: 42
GCID: GC01P034326

High Mobility Group Box 4

(Previous name: high-mobility group box 4)
  Search for HMGB4
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
High Mobility Group Box 41 2
High-Mobility Group Box 41
dJ1007G16.52
High Mobility Group Protein B42
HMG2 Like2

External Ids:    HGNC: 249541   Entrez Gene: 1275402   Ensembl: ENSG000001762567   UniProtKB: Q8WW323   

Export aliases for HMGB4 gene to outside databases

Previous GC identifers: GC01P033996 GC01P034098 GC01P032442


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for HMGB4 Gene:
HMGB4 (high mobility group box 4) is a protein-coding gene. An important paralog of this gene is HMGB3.

Gene Wiki entry for HMGB4 Gene


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000001.11  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the HMGB4 gene promoter:
         NF-AT2   NF-kappaB1   Cdc5   NF-AT   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): HMGB4 promoter sequence
   Search Chromatin IP Primers for HMGB4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HMGB4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p35.1   Ensembl cytogenetic band:  1p35.1   HGNC cytogenetic band: 1p35.1

HMGB4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HMGB4 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P034326:  view genomic region     (about GC identifiers)

Start:
34,326,076 bp from pter      End:
34,330,392 bp from pter
Size:
4,317 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: HMGB4_HUMAN, Q8WW32 (See protein sequence)
Recommended Name: High mobility group protein B4  
Size: 186 amino acids; 22490 Da
Secondary accessions: B2R4X7 Q0QWA4

Explore the universe of human proteins at neXtProt for HMGB4: NX_Q8WW32

REFSEQ proteins: NP_660206.2  
ENSEMBL proteins: 
 ENSP00000429214   ENSP00000430919  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
HMG: High-mobility group / Canonical

1 InterPro protein domain:
 IPR009071 HMG_box_dom

Graphical View of Domain Structure for InterPro Entry Q8WW32

ProtoNet protein and cluster: Q8WW32

1 Blocks protein domain: IPB000135 High mobility group proteins HMG1 and HMG2

UniProtKB/Swiss-Prot: HMGB4_HUMAN, Q8WW32
Similarity: Belongs to the HMGB family
Similarity: Contains 2 HMG box DNA-binding domains


HMGB4 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding IEA--
     
HMGB4 for ontologies           About GeneDecksing


Phenotypes:
     2 GenomeRNAi human phenotypes for HMGB4:
 Decreased Wnt reporter activit  Increased gamma-H2AX phosphory 

Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
HMGB4_HUMAN, Q8WW32: Nucleus (By similarity). Chromosome (By similarity)

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--
GO:0005694chromosome IEA--

HMGB4 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HMGB4
Interactions:

    Search GeneGlobe Interaction Network for HMGB4

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for HMGB4



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for HMGB4 gene: 
NM_145205.5  

Unigene Cluster for HMGB4:

High mobility group box 4
Hs.568628  [show with all ESTs]
Unigene Representative Sequence: NM_145205
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000519684(uc001bxp.3) ENST00000522796 ENST00000458277 ENST00000425537(uc001bxq.3)

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Additional mRNA sequence: 

AK097707.1 AK130859.1 AK310465.1 AK311985.1 BC021180.2 BC070148.1 DQ207367.1 NR_033264.1 

2 DOTS entries:

DT.95367635  DT.408782 

Selected AceView cDNA sequences (see all 87):

AK130859 AA629230 AI205504 BP370698 AI968361 AI970364 BP371463 AI828842 
AI797725 AI867911 BC021180 AI917843 AI655836 BC070148 BP368976 BE504819 
AI634070 AI824962 BF057167 BF223107 BU567351 AA757981 BP371157 BP371217 

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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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HMGB4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGAAAAGAAA
HMGB4 Expression
About this image

HMGB4 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.568628
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMGB4

(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)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for HMGB4 gene from Selected species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Hmgb41 , 5 high-mobility group box 41, 5 78.97(n)1
78.57(a)1
  4 (61.97 cM)5
693171  NM_027036.31  NP_081312.21 
 1282602125 
zebrafish
(Danio rerio)
Actinopterygii hmgb2b6
high-mobility group box 2b
31(a)
many ↔ many
23(45378522-45382172) ENSDARG00000053990
fruit fly
(Drosophila melanogaster)
Insecta Dsp16
Dorsal switch protein 1
15(a)
1 → many
X(16227645-16234657)
worm
(Caenorhabditis elegans)
Secernentea hmg-1.16
Protein HMG-1.1 (hmg-1.1) mRNA, complete cds
32(a)
1 → many
II(14250695-14251448) WBGene00001971
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NHP6A6
NHP6B6
High-mobility group (HMG) protein that binds to an...
High-mobility group (HMG) protein that binds to an...
33(a)
32(a)
many ↔ many
many ↔ many
XVI(665693-665974) YPR052C
II(426190-426489) YBR089C-A


ENSEMBL Gene Tree for HMGB4 (if available)
TreeFam Gene Tree for HMGB4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for HMGB4 gene
HMGB32  HMGB12  HMGB22  
9 SIMAP similar genes for HMGB4 using alignment to 2 protein entries:     HMGB4_HUMAN (see all proteins):
HMG1    DKFZp779G118    HMGB2    HMGB1    HMGB3    HMGB1P1
Bbtx1    SP100    WUGSC

HMGB4 for paralogs           About GeneDecksing


1 Pseudogenes.org Pseudogene for HMGB4
PGOHUM00000257054


(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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3 SNPs for HMGB4    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs115426861,2,4
----see VAR_0559512 mis40--------
rs570689371,2,4
----see VAR_0674682 mis40--------
rs103791,2,4
----see VAR_0674672 mis40--------

HapMap Linkage Disequilibrium report for HMGB4 (34326076 - 34330392 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for HMGB4:    About this table    
Variant IDTypeSubtypePubMed ID
esv34112CNV Loss18971310
nsv871907CNV Loss21882294
nsv834624CNV Loss17160897

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing HMGB4
DNA2.0 Custom Variant and Variant Library Synthesis for HMGB4

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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HMGB4 for disorders           About GeneDecksing

Human Genome Epidemiology (HuGE) Navigator: HMGB4 (1 document)

Export disorders for HMGB4 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 HMGB4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with HMGB4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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. (Genome Res. 2004)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. Convergent animal and human evidence suggests a role of PPM1A gene in response to antidepressants. (PubMed id 20970119)1 Malki K....Schalkwyk L.C. (Biol. Psychiatry 2011)
  4. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
  5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
  6. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)
  7. A transcript finishing initiative for closing gaps in the human transcriptome. (PubMed id 15197164)1 Sogayar M.C....Zanette D.L. (Genome Res. 2004)
  8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  9. (PubMed id )2 

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
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: 127540 HGNC: 24954 AceView: LOC127540 Ensembl:ENSG00000176256 euGenes: HUgn127540
ECgene: HMGB4 H-InvDB: HMGB4

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for HMGB4 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for HMGB4 gene:
Search GeneIP for patents involving HMGB4

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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 LSBio Antibodies in human, mouse, rat for HMGB4
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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