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HMGXB3 Gene

protein-coding   GIFtS: 40
GCID: GC05P149361

HMG Box Domain Containing 3


(Previous symbol: HMGX3)
  Search for HMGXB3
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
HMG Box Domain Containing 31 2     KIAA01943
HMGX31 2     HMG Box-Containing Protein 33
SMF2 3     Protein SMF3
HMG Domain-Containing Protein 32     

External Ids:    HGNC: 289821   Entrez Gene: 229932   Ensembl: ENSG000001137167   UniProtKB: Q127663   

Export aliases for HMGXB3 gene to outside databases

Previous GC identifer: GC05P144528


(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 HMGXB3 Gene:
This gene is one of the non-canonical high mobility group (HMG) genes. The encoded protein contains an HMG-box
domain found in DNA binding proteins such as transcription factors and chromosomal proteins. (provided by RefSeq,
Aug 2011)

GeneCards Summary for HMGXB3 Gene:
HMGXB3 (HMG box domain containing 3) is a protein-coding gene. GO annotations related to this gene include kinase activity.




(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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Regulatory elements:
   Regulatory transcription factor binding sites in the HMGXB3 gene promoter:
         AhR   AML1a   AP-2alpha isoform 2   AP-4   CUTL1   Evi-1   Arnt   PPAR-alpha   Sox9   AP-2alphaA   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for HMGXB3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HMGXB3


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

Entrez Gene cytogenetic band: 5q32   Ensembl cytogenetic band:  5q32   HGNC cytogenetic band: 5q33.1

HMGXB3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HMGXB3 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P149361:  view genomic region     (about GC identifiers)

Start:
149,379,884 bp from pter      End:
149,432,706 bp from pter
Size:
52,823 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, 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: HMGX3_HUMAN, Q12766 (See protein sequence)
Recommended Name: HMG domain-containing protein 3  
Size: 1538 amino acids; 168334 Da
Secondary accessions: G5E9Y4 Q86UG3 Q9UMF4
Alternative splicing: 2 isoforms:  Q12766-1   Q12766-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for HMGXB3: NX_Q12766

Explore proteomics data for HMGXB3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See HMGXB3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_055798.2  
    ENSEMBL proteins: 
     ENSP00000422231   ENSP00000421917   ENSP00000426631  

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    Search eBioscience for ELISAs for HMGXB3 


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

    1 InterPro protein domain:
     IPR009071 HMG_box_dom

    Graphical View of Domain Structure for InterPro Entry Q12766

    ProtoNet protein and cluster: Q12766

    UniProtKB/Swiss-Prot: HMGX3_HUMAN, Q12766
    Similarity: Contains 1 HMG box DNA-binding domain


    Find genes that share domains with HMGXB3           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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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0016301kinase activity NAS9027509
         
    Find genes that share ontologies with HMGXB3           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HMGXB3
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    miRNA
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    miRTarBase miRNAs that target HMGXB3:
    hsa-mir-92a-3p (MIRT049848), hsa-mir-484 (MIRT041726), hsa-mir-324-5p (MIRT043043), hsa-mir-454-3p (MIRT039237), hsa-mir-615-3p (MIRT040316)

    Block miRNA regulation of human, mouse, rat HMGXB3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HMGXB3 (see all 37):
    hsa-miR-3685 hsa-miR-302d hsa-miR-520e hsa-miR-578 hsa-miR-372 hsa-miR-9 hsa-miR-4274 hsa-miR-133a
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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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
    HMGX3_HUMAN, Q12766: Nucleus (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0005634nucleus IEA--

    Find genes that share ontologies with HMGXB3           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HMGXB3
    Interactions:

        Search GeneGlobe Interaction Network for HMGXB3

    Selected Interacting proteins for HMGXB3 (Q127662, 3) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SMN1Q166372, 3MINT-8271201 I2D: score=2 
    SMN2Q166372, 3MINT-8271201 I2D: score=2 
    ANXA7P200732, 3MINT-8248450 I2D: score=2 
    CDK4P118022, 3MINT-8251370 I2D: score=2 
    CDKN1AP389362, 3MINT-8251959 I2D: score=2 
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--
    GO:0016310phosphorylation NAS9027509

    Find genes that share ontologies with HMGXB3           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 HMGXB3 (HMGX3)



    (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 HMGXB3 gene: 
    NM_014983.2  

    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000503427(uc003lrk.4) ENST00000502717 ENST00000514469 ENST00000513318
    ENST00000510472
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate HMGXB3 (see all 37):
    hsa-miR-3685 hsa-miR-302d hsa-miR-520e hsa-miR-578 hsa-miR-372 hsa-miR-9 hsa-miR-4274 hsa-miR-133a
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat HMGXB3
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      QuantiTect SYBR Green Assays in human, mouse, rat HMGXB3
      QuantiFast Probe-based Assays in human, mouse, rat HMGXB3

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for HMGXB3    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19a · 19b ^
    SP1:                                                              -     -                                                           -                           
    SP2:                                                              -     -                 -     -     -                                                         
    SP3:                                                                                      -     -     -                                                         
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 20
    SP1:      
    SP2:      
    SP3:      
    SP4:      
    SP5:      


    ECgene alternative splicing isoforms for HMGXB3

    (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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    HMGXB3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTTAATTTA
    HMGXB3 Expression
    About this image

    HMGXB3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HMGXB3 Protein Expression
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMGXB3

    (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 chordates.

    Orthologs for HMGXB3 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hmgxb31 , 5 HMG box domain containing 31, 5 87.73(n)1
    89.36(a)1
      18 (34.41 cM)5
    1068941  NM_178277.11  NP_840061.11 
     611312795 
    chicken
    (Gallus gallus)
    Aves HMGXB31 HMG box domain containing 3 71.68(n)
    72.83(a)
      416278  XM_414598.3  XP_414598.3 
    lizard
    (Anolis carolinensis)
    Reptilia HMGXB36
    HMG box domain containing 3
    67(a)
    1 ↔ 1
    2(139621414-139651876)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia hmgxb31 HMG box domain containing 3 63.73(n)
    61.61(a)
      100147705  NM_001127168.1  NP_001120640.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1018864341 HMG domain-containing protein 3-like 54.82(n)
    47.97(a)
      101886434  XM_005169575.1  XP_005169632.1 


    ENSEMBL Gene Tree for HMGXB3 (if available)
    TreeFam Gene Tree for HMGXB3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (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 HMGXB3 (see all 1129)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs359216671,2
    C--149383197(+) TTTTTT/-CTGCC 1 -- int11Minor allele frequency- -:0.00NA 2
    rs721494041,2
    C--149387619(+) TGTTT-/CACACAC 1 -- int10--------
    rs718924271,2
    C--149400309(+) TTTTT-/T/TTTT
            
    GAAGA
    1 -- int11CSA 2
    rs608892961,2
    C--149405068(+) TTTTT-/TTAACAC 1 -- int10--------
    rs605375711,2
    C--149405701(+) TTGCTT/-TTTTT 1 -- int11Minor allele frequency- -:0.50CSA 2
    rs341412741,2
    C--149408894(+) TTTTTT/-TTTTT 1 -- int11Minor allele frequency- -:0.50NA 2
    rs602267671,2
    C--149428973(+) CCCCC-/C/CC  
            
    TTAAC
    1 -- int12NA CSA 4
    rs1499265071,2
    C--149430869(+) AGTGCC/TCCAGC 1 -- int10--------
    rs2161301,2
    C,F,O,H--149430915(+) TGCCTT/CGGAGG 1 -- int128Minor allele frequency- C:0.39MN NS EA NA WA 3092
    rs1874484161,2
    --149430979(+) GACTCC/TAGAAA 1 -- int10--------

    HapMap Linkage Disequilibrium report for HMGXB3 (149379884 - 149432706 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for HMGXB3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv830518CNV Loss17160897
    esv24664CNV Gain+Loss19812545

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HMGXB3
    DNA2.0 Custom Variant and Variant Library Synthesis for HMGXB3

    (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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    Find genes that share disorders with HMGXB3           About GenesLikeMe

    Genetic Association Database (GAD): HMGXB3

    Export disorders for HMGXB3 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 HMGXB3 gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with HMGXB3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Prediction of the coding sequences of unidentified human genes. V. The coding sequences of 40 new genes (KIAA0161-KIAA0200) deduced by analysis of cDNA clones from human cell line KG-1. (PubMed id 8724849)1, 2, 3 Nagase T.... Nomura N. (DNA Res. 1996)
    2. Common genetic variation and the control of HIV-1 in humans. (PubMed id 20041166)1, 4 Fellay J....Goldstein D.B. (PLoS Genet. 2009)
    3. Sequence analysis of two genomic regions containing the KIT and the FMS receptor tyrosine kinase genes. (PubMed id 9027509)1, 2 Andre C.... Galibert F. (Genomics 1997)
    4. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    5. A directed protein interaction network for investigating intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (Sci Signal 2011)
    6. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    7. Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project. (PubMed id 17903300)4 Fox C.S....Atwood L.D. (BMC Med. Genet. 2007)
    8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    10. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (Nature 2004)

    (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)
    About This Section

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    Entrez Gene: 22993 HGNC: 28982 Ensembl:ENSG00000113716 euGenes: HUgn22993 ECgene: HMGXB3
    H-InvDB: HMGXB3

    (According to HUGE)
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    HUGE: KIAA0194

    (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 HMGXB3 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 HMGXB3 gene:
    Search GeneIP for patents involving HMGXB3

    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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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