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HMGB2 Gene

protein-coding   GIFtS: 62
GCID: GC04M174252

High Mobility Group Box 2

(Previous names: high-mobility group (nonhistone chromosomal) protein 2,...)
(Previous symbol: HMG2)
  See HMGB2-related disease
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 21 2     High Mobility Group Protein 22 3
HMG21 2 3 5     HMG-22 3
High-Mobility Group (Nonhistone Chromosomal) Protein 21 2     High Mobility Group Protein B22
High-Mobility Group Box 21 2     

External Ids:    HGNC: 50001   Entrez Gene: 31482   Ensembl: ENSG000001641047   OMIM: 1639065   UniProtKB: P265833   

Export aliases for HMGB2 gene to outside databases

Previous GC identifers: GC04M175172 GC04M174790 GC04M174948 GC04M174627 GC04M174489 GC04M170000


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for HMGB2 Gene:
This gene encodes a member of the non-histone chromosomal high mobility group protein family. The proteins of this
family are chromatin-associated and ubiquitously distributed in the nucleus of higher eukaryotic cells. In vitro
studies have demonstrated that this protein is able to efficiently bend DNA and form DNA circles. These studies
suggest a role in facilitating cooperative interactions between cis-acting proteins by promoting DNA flexibility.
This protein was also reported to be involved in the final ligation step in DNA end-joining processes of DNA
double-strand breaks repair and V(D)J recombination. (provided by RefSeq, Jul 2008)

GeneCards Summary for HMGB2 Gene:
HMGB2 (high mobility group box 2) is a protein-coding gene. Diseases associated with HMGB2 include juvenile rheumatoid arthritis. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and protein domain specific binding. An important paralog of this gene is HMGB4.

UniProtKB/Swiss-Prot: HMGB2_HUMAN, P26583
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) (By similarity)

Gene Wiki entry for HMGB2 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 at NCBI GenBank:
NC_000004.11  NC_018915.2  NT_016354.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the HMGB2 gene promoter:
         HFH-3   FOXI1   E2F-1   E2F   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 3): HMGB2 promoter sequence
   Search Chromatin IP Primers for HMGB2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HMGB2


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

Entrez Gene cytogenetic band: 4q31   Ensembl cytogenetic band:  4q34.1   HGNC cytogenetic band: 4q31

HMGB2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HMGB2 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M174252:  view genomic region     (about GC identifiers)

Start:
174,252,527 bp from pter      End:
174,256,276 bp from pter
Size:
3,750 bases      Orientation:
minus 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: HMGB2_HUMAN, P26583 (See protein sequence)
Recommended Name: High mobility group protein B2  
Size: 209 amino acids; 24034 Da
Subunit: Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or
HMGB2 (By similarity). Component of the SET complex, which also contains SET, ANP32A, APEX1 and NME1. Directly
interacts with SET
Secondary accessions: B2R4K8 D3DP37 Q5U072

Explore the universe of human proteins at neXtProt for HMGB2: NX_P26583

Explore proteomics data for HMGB2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys12, Lys50, Lys114, Lys147, Lys157
  • Modification sites at PhosphoSitePlus

  • See HMGB2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001124160.1  NP_001124161.1  NP_002120.1  

    ENSEMBL proteins: 
     ENSP00000296503   ENSP00000404912   ENSP00000393448   ENSP00000423001  
    Reactome Protein details: P26583

    HMGB2 Human Recombinant Protein Products:

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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

    2 InterPro protein domains:
     IPR009071 HMG_box_dom
     IPR017967 HMG_boxA_CS

    Graphical View of Domain Structure for InterPro Entry P26583

    ProtoNet protein and cluster: P26583

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

    UniProtKB/Swiss-Prot: HMGB2_HUMAN, P26583
    Similarity: Belongs to the HMGB family
    Similarity: Contains 2 HMG box DNA-binding domains


    Find genes that share domains with HMGB2           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HMGB2_HUMAN, P26583
    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) (By similarity)

         Gene Ontology (GO): Selected molecular function terms (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IMP11909973
    GO:0003684damaged DNA binding IDA8226934
    GO:0003690double-stranded DNA binding ISS--
    GO:0003697single-stranded DNA binding ISS--
    GO:0003700sequence-specific DNA binding transcription factor activity IDA19223331
         
    Find genes that share ontologies with HMGB2           About GenesLikeMe


    Phenotypes:
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Hmgb2):
     endocrine/exocrine gland  reproductive system 

    Find genes that share phenotypes with HMGB2           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HMGB2
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for HMGB2

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for HMGB2
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for HMGB2

    miRNA
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    miRTarBase miRNAs that target HMGB2:
    hsa-mir-24-3p (MIRT030580), hsa-mir-374a-5p (MIRT044016), hsa-mir-181a-5p (MIRT025152), hsa-mir-33a-5p (MIRT028203)

    Block miRNA regulation of human, mouse, rat HMGB2 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HMGB2 (see all 32):
    hsa-miR-520d-5p hsa-miR-181c hsa-miR-300 hsa-miR-4328 hsa-miR-4272 hsa-let-7a-2* hsa-miR-421 hsa-miR-548l
    SwitchGear 3'UTR luciferase reporter plasmidHMGB2 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for HMGB2
    Predesigned siRNA for gene silencing in human, mouse, rat HMGB2

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 3): HMGB2 (NM_002129)
    Sino Biological Human cDNA Clone for HMGB2
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HMGB2
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HMGB2

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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMGB2


    (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
    HMGB2_HUMAN, P26583: Nucleus. Chromosome
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    nucleus5

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000793condensed chromosome IDA12925773
    GO:0005615extracellular space IDA19811285
    GO:0005634nucleus IDA11909973
    GO:0005654nucleoplasm TAS--
    GO:0005737cytoplasm IDA11909973

    Find genes that share ontologies with HMGB2           About GenesLikeMe


    (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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    SuperPaths for HMGB2 About   (see all 6)  
    See pathways by source

    SuperPathContained pathways About
    1Activation of DNA fragmentation factor
    Activation of DNA fragmentation factor0.32
    Apoptosis induced DNA fragmentation0.00
    Granzyme-A Pathway0.32
    2Apoptotic cleavage of cellular proteins
    Apoptotic execution phase0.74
    3CDK-mediated phosphorylation and removal of Cdc6
    Apoptosis0.38
    4RB in Cancer
    RB in Cancer
    5Granzyme Pathway
    Granzyme Pathway


    Find genes that share SuperPaths with HMGB2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for HMGB2
        Granzyme-A Pathway
    Granzyme Pathway

    1 Cell Signaling Technology (CST) Pathway for HMGB2
        Chromatin Regulation / Acetylation

    1 BioSystems Pathway for HMGB2
        RB in Cancer


    1 Reactome Pathway for HMGB2
        Activation of DNA fragmentation factor


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HMGB2
    Interactions:

        GeneGlobe Interaction Network for HMGB2

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

    Selected Interacting proteins for HMGB2 (P265832, 3 ENSP000002965034) via UniProtKB, MINT, STRING, and/or I2D (see all 128)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000235068Q018603, ENSP000004050414I2D: score=3 STRING: ENSP00000405041
    POU5F1Q018603, ENSP000002599154I2D: score=3 STRING: ENSP00000259915
    ENSG00000206454Q018603I2D: score=3 
    ENSG00000229094Q018603I2D: score=3 
    ENSG00000230336Q018603I2D: score=3 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 28):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001938positive regulation of endothelial cell proliferation IDA19811285
    GO:0006265DNA topological change ISS--
    GO:0006288base-excision repair, DNA ligation IDA9600082
    GO:0006309apoptotic DNA fragmentation TAS--
    GO:0006325chromatin organization NAS11909973

    Find genes that share ontologies with HMGB2           About GenesLikeMe



    (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 HMGB2

    3 Novoseek inferred chemical compound relationships for HMGB2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cisplatin 33 9 1445361 (3), 8975778 (2), 10076573 (1), 8226934 (1)
    estrogen 0.701 1 9671457 (1)
    atp 0 1 8007973 (1)



    Find genes that share compounds with HMGB2           About GenesLikeMe



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for HMGB2 gene (3 alternative transcripts): 
    NM_001130688.1  NM_001130689.1  NM_002129.3  

    Unigene Cluster for HMGB2:

    High mobility group box 2
    Hs.434953  [show with all ESTs]
    Unigene Representative Sequence: BM555162
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000296503(uc011ckc.1 uc003itb.2) ENST00000438704 ENST00000446922(uc003ita.3)
    ENST00000511316 ENST00000506267
    miRNA
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    Block miRNA regulation of human, mouse, rat HMGB2 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HMGB2 (see all 32):
    hsa-miR-520d-5p hsa-miR-181c hsa-miR-300 hsa-miR-4328 hsa-miR-4272 hsa-let-7a-2* hsa-miR-421 hsa-miR-548l
    SwitchGear 3'UTR luciferase reporter plasmidHMGB2 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector (see all 3): HMGB2 (NM_002129)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HMGB2
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HMGB2
    Primer
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    OriGene qPCR primer pairs and template standards for HMGB2
    OriGene qSTAR qPCR primer pairs in human, mouse for HMGB2
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat HMGB2
      QuantiTect SYBR Green Assays in human, mouse, rat HMGB2
      QuantiFast Probe-based Assays in human, mouse, rat HMGB2

    Additional mRNA sequence: 

    AK311864.1 BC000903.2 BC001063.2 BC100019.1 BT019782.1 BT019783.1 X62534.1 Z17240.1 

    Selected DOTS entries (see all 27):

    DT.449733  DT.100672906  DT.100672915  DT.95172427  DT.100672916  DT.121238516  DT.97817430  DT.121238528 
    DT.423214  DT.95172429  DT.92324876  DT.92451695  DT.97817257  DT.100672905  DT.40133229  DT.92451701 
    DT.95172446  DT.102835225  DT.92040812  DT.92451703  DT.95358472  DT.100050472  DT.100672912  DT.92451690 

    Selected AceView cDNA sequences (see all 574):

    CR622092 CA425618 BM693600 BE252235 BM458768 CA748925 BM784609 BQ231908 
    BM743197 BU633047 BQ776126 BG035546 AI954999 BG177394 CA425522 CR603881 
    BM974131 BG942760 BM742354 AU129699 AL545657 BM823059 BQ931572 BM916513 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for HMGB2 (see all 10)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2a · 2b ^ 3a · 3b · 3c · 3d · 3e ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b · 6c
    SP1:                                      -     -     -                                                     -                     
    SP2:                                      -     -     -     -     -                       -                 -                     
    SP3:                                            -     -                                                     -                     
    SP4:                                      -     -     -                                   -                 -                     
    SP5:                                      -     -     -                                                     -                     


    ECgene alternative splicing isoforms for HMGB2

    (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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    HMGB2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCTGCAAAGG
    HMGB2 Expression
    About this image


    HMGB2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 25) fully expand
     
     Tonsil (Hematopoietic System)    fully expand to see all 3 entries
             tonsil ; non-germinal center cells   
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Epithelial Cells
             Presumptive Podocytes Podocyte Layer
             tonsil ; squamous epithelial cells   
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Metencephalon
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
    HMGB2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HMGB2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.434953
        Custom PCR Arrays for HMGB2
    Primer
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    OriGene qPCR primer pairs and template standards for HMGB2
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    QuantiFast Probe-based Assays in human, mouse, rat HMGB2
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMGB2

    (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.

    Orthologs for HMGB2 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hmgb21 , 5 high mobility group box 21, 5 90.55(n)1
    98.4(a)1
      8 (29.90 cM)5
    971651  NM_008252.31  NP_032278.11 
     575118435 
    chicken
    (Gallus gallus)
    Aves HMGB21 high mobility group box 2 83.96(n)
    92.51(a)
      396482  NM_205486.1  NP_990817.1 
    lizard
    (Anolis carolinensis)
    Reptilia HMGB26
    high mobility group box 2
    88(a)
    1 ↔ 1
    3(144519090-144523561)
    African clawed frog
    (Xenopus laevis)
    Amphibia AF549908.12   -- 77.55(n)    AF549908.1 
    zebrafish
    (Danio rerio)
    Actinopterygii hmgb2a1 high-mobility group box 2a 76.06(n)
    79.56(a)
      641484  NM_001037424.1  NP_001032501.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Dsp11 Dorsal switch protein 1 58.54(n)
    56.25(a)
      117294  NM_001144731.3  NP_001138203.1 
    worm
    (Caenorhabditis elegans)
    Secernentea hmg-1.21 hmg-1.2 51.1(n)
    43.11(a)
      175890  NM_001027429.4  NP_001022600.1 


    ENSEMBL Gene Tree for HMGB2 (if available)
    TreeFam Gene Tree for HMGB2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HMGB2 gene
    HMGB42  HMGB32  HMGB12  
    9 SIMAP similar genes for HMGB2 using alignment to 2 protein entries:     HMGB2_HUMAN (see all proteins):
    HMG1    HMGB1    HMGB1P1    DKFZp779G118    HMGB3    SP100
    HMGB4    SSRP1    WUGSC

    Find genes that share paralogs with HMGB2           About GenesLikeMe


    Selected Pseudogenes.org Pseudogenes for HMGB2 (see all 20)
    PGOHUM00000239713 PGOHUM00000249958 PGOHUM00000248187 PGOHUM00000248208 PGOHUM00000246908


    (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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    Selected SNPs for HMGB2 (see all 132)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1139629371,2
    F--174252242(+) TCCCAC/ACACTT 3 -- ds50011Minor allele frequency- A:0.00CSA 1
    rs1932609881,2
    --174252273(+) ATCATC/TTGAGG 3 -- ds50010--------
    rs68218441,2
    C,F--174252441(+) ggatcG/Ctgcca 3 -- ds50011Minor allele frequency- C:0.50WA 2
    rs2012577281,2
    --174252504(+) ATATA-/CGTATAT 3 -- ds50010--------
    rs1458134211,2
    --174252505(+) TATACA/GTATAT 3 -- ds50010--------
    rs1482171371,2
    --174252517(+) TGTGTA/GTATAT 3 -- ds50010--------
    rs2020819681,2
    --174252523(+) TATAT-/ATAC  
            
    ATATA
    3 -- ds50010--------
    rs106329831,2
    C--174252526(+) tatac-/ATatata 3 -- ds50010--------
    rs2013787891,2
    C--174252526(+) ATATAC/TATATA 3 -- ds50010--------
    rs68534271,2
    C--174252545(+) tatatA/Gtgtat 3 -- ut310--------

    HapMap Linkage Disequilibrium report for HMGB2 (174252527 - 174256276 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for HMGB2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv4610CNV Loss18451855

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HMGB2
    DNA2.0 Custom Variant and Variant Library Synthesis for HMGB2

    (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.)
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    OMIM gene information: 163906    OMIM disorders: --

    1 disease for HMGB2:    
    About MalaCards
    juvenile rheumatoid arthritis


    Find genes that share disorders with HMGB2           About GenesLikeMe

    5 Novoseek inferred disease relationships for HMGB2 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    arthritis juvenile rheumatoid 36.3 2 2403401 (2)
    hepatitis autoimmune 35.5 2 10323891 (2)
    colitis ulcerative 31.5 3 9486411 (1), 9010268 (1), 10323891 (1)
    rheumatic diseases 24.9 3 9558172 (3)
    cancer 0 1 8975778 (1)

    Genetic Association Database (GAD): HMGB2
    Human Genome Epidemiology (HuGE) Navigator: HMGB2 (2 documents)

    Export disorders for HMGB2 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 HMGB2 gene, integrated from 10 sources (see all 124):
    (articles sorted by number of sources associating them with HMGB2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Sequence of human HMG2 cDNA. (PubMed id 1754403)1, 2, 3 Majumdar A....Seidman M.M. (Nucleic Acids Res. 1991)
    2. Identification of potentially damaging amino acid substitutions leading to human male infertility. (PubMed id 19369647)1, 4 Kuzmin A....Varmuza S. (Biol. Reprod. 2009)
    3. 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)
    4. HMG2 interacts with the nucleosome assembly protein SET and is a target of the cytotoxic T-lymphocyte protease granzyme A. (PubMed id 11909973)1, 2 Fan Z.... Lieberman J. (Mol. Cell. Biol. 2002)
    5. A human HMG2 cDNA with a novel 3'-untranslated region. (PubMed id 1475204)1, 2 Alexandre S.... Lee A.S. (Nucleic Acids Res. 1992)
    6. Structure of a gene coding for human HMG2 protein. (PubMed id 1551873)1, 2 Shirakawa H. and Yoshida M. (J. Biol. Chem. 1992)
    7. The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures. (PubMed id 8339930)1, 9 Paull T.T....Johnson R.C. (amp 1993)
    8. HMGB1 and HMGB2 cell-specifically down-regulate the p53- and p73-dependent sequence-specific transactivation from the human Bax gene promoter. (PubMed id 11748232)1, 9 Stros M....Nakagawara A. (J. Biol. Chem. 2002)
    9. High-mobility group chromatin proteins 1 and 2 functionally interact with steroid hormone receptors to enhance their DNA binding in vitro and transcriptional activity in mammalian cells. (PubMed id 9671457)1, 9 Boonyaratanakornkit V....Edwards D.P. (Mol. Cell. Biol. 1998)
    10. HMGB1 and HMGB2 proteins up-regulate cellular expression of human topoisomerase IIalpha. (PubMed id 19223331)1, 9 Stros M....PospA-silovA! S. (Nucleic Acids Res. 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    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: 3148 HGNC: 5000 AceView: HMGB2 Ensembl:ENSG00000164104 euGenes: HUgn3148
    ECgene: HMGB2 H-InvDB: HMGB2

    (According to HUGE)
    About This Section

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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)
    About This Section

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    NameDescription
    PharmGKB entry for HMGB2 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for HMGB2 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HMGB2 gene:
    Search GeneIP for patents involving HMGB2

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



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