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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HMGXB4 Gene

protein-coding   GIFtS: 47
GCID: GC22P035653

HMG Box Domain Containing 4

(Previous name: high-mobility group protein 2-like 1)
(Previous symbol: HMG2L1)
  Search for HMGXB4
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
HMG Box Domain Containing 41 2     HMG Box-Containing Protein 42 3
HMG2L11 2 3 5     THC2116302
High-Mobility Group Protein 2-Like 11 2     HMG Domain-Containing Protein 42
High Mobility Group Protein 2-Like 12 3     Protein HMGBCG3
HMGBCG2 3     

External Ids:    HGNC: 50031   Entrez Gene: 100422   Ensembl: ENSG000001002817   OMIM: 6047025   UniProtKB: Q9UGU53   
ORGUL members:         
NONCODE14:n408020      

Export aliases for HMGXB4 gene to outside databases

Previous GC identifers: GC22P033983 GC22P018614


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for HMGXB4 Gene:
High mobility group (HMG) proteins are nonhistone chromosomal proteins. See HMG2 (MIM 163906) for additional
information on HMG proteins.(supplied by OMIM, Nov 2010)

GeneCards Summary for HMGXB4 Gene: 
HMGXB4 (HMG box domain containing 4) is a protein-coding gene, and is affiliated with the lncRNA class. GO annotations related to this gene include DNA binding.

UniProtKB/Swiss-Prot: HMGX4_HUMAN, Q9UGU5
Function: Negatively regulates Wnt/beta-catenin signaling during development (By similarity)




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000022.10  NC_018933.2  NT_011520.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HMGXB4 gene promoter:
         GR   c-Fos   AP-1   AML1a   p300   RREB-1   POU6F1 (c2)   Ik-2   COMP1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHMGXB4 promoter sequence
   Search SABiosciences Chromatin IP Primers for HMGXB4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HMGXB4


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

Entrez Gene cytogenetic band: 22q13.1   Ensembl cytogenetic band:  22q12.3   HGNC cytogenetic band: 22q13

HMGXB4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HMGXB4 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P035653:  view genomic region     (about GC identifiers)

Start:
35,653,445 bp from pter      End:
35,691,800 bp from pter
Size:
38,356 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: HMGX4_HUMAN, Q9UGU5 (See protein sequence)
Recommended Name: HMG domain-containing protein 4  
Size: 601 amino acids; 65712 Da
Subcellular location: Nucleus (Potential)
Secondary accessions: O75672 O75673 Q9UMT5

Explore the universe of human proteins at neXtProt for HMGXB4: NX_Q9UGU5

Explore proteomics data for HMGXB4 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9UGU5

  • HMGXB4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    HMGXB4 Protein Expression
    REFSEQ proteins: NP_001003681.1  
    ENSEMBL proteins: 
     ENSP00000401658   ENSP00000395532   ENSP00000415500   ENSP00000216106   ENSP00000398302  

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    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus NAS--
    GO:0016589NURF complex IDA--

    HMGXB4 for ontologies           About GeneDecksing



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

    2 InterPro protein domains:
     IPR025228 DUF4171
     IPR009071 HMG_box_dom

    Graphical View of Domain Structure for InterPro Entry Q9UGU5

    ProtoNet protein and cluster: Q9UGU5

    UniProtKB/Swiss-Prot: HMGX4_HUMAN, Q9UGU5
    Similarity: Contains 1 HMG box DNA-binding domain


    HMGXB4 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HMGX4_HUMAN, Q9UGU5
    Function: Negatively regulates Wnt/beta-catenin signaling during development (By similarity)

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding NAS--
         
    HMGXB4 for ontologies           About GeneDecksing


    Animal Models:
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HMGXB4

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    5/10 Interacting proteins for HMGXB4 (Q9UGU52, 3 ENSP000002161064) via UniProtKB, MINT, STRING, and/or I2D (see all 10)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NR1H2P550552, 3MINT-8263885 I2D: score=2 
    TNNT1P138052, 3MINT-8274907 I2D: score=2 
    TSC22D1Q157142, 3MINT-8275402 I2D: score=2 
    URODP061322, 3, ENSP000002463374MINT-8276916 I2D: score=2 STRING: ENSP00000246337
    HABP4Q5JVS03, ENSP000003643984I2D: score=2 STRING: ENSP00000364398
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008333endosome to lysosome transport NAS10329004
    GO:0016055Wnt receptor signaling pathway IEA--
    GO:0030178negative regulation of Wnt receptor signaling pathway ISS--

    HMGXB4 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for HMGXB4 (HMGX4)

    Search CenterWatch for drugs/clinical trials and news about HMGXB4 / HMGX4

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for HMGXB4 gene (3 alternative transcripts): 
    NM_005487.3  NM_014250.1  NM_001003681.2  

    Unigene Cluster for HMGXB4:

    HMG box domain containing 4
    Hs.588815  [show with all ESTs]
    Unigene Representative Sequence: NR_027780
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000420166 ENST00000418170(uc003ank.3 uc003anl.3) ENST00000466438
    ENST00000455359 ENST00000216106 ENST00000498325 ENST00000464480 ENST00000498212
    ENST00000444518(uc011amh.1)
    miRNA
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    Inhib. RNA
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    Additional mRNA sequence: 

    AJ010069.1 AJ010070.1 AK299833.1 AL079310.1 BC004194.2 BC011723.2 BC017326.2 BC025303.2 
    BC033783.2 BC040447.1 BC052624.1 BC062413.1 BC080611.1 BC104754.1 BC104756.1 BC111373.1 
    CR456504.1 NR_027780.1 

    13 DOTS entries:

    DT.414194  DT.97835740  DT.101960334  DT.100820014  DT.100655215  DT.100035944  DT.100696551  DT.97807146 
    DT.91755099  DT.91874892  DT.95260231  DT.95274258  DT.95274259 

    24/224 AceView cDNA sequences (see all 224):

    BE877254 BC040447 AI376174 AI203042 AW073484 BQ013268 CB119482 BC011723 
    AA595272 BC052624 AI453696 AI656803 AI471703 AI970068 CF529434 AW004073 
    H55266 BF056467 BC025303 AJ010070 BM677532 W42451 CA417107 CB242414 

    GeneLoc Exon Structure

    5/9 Alternative Splicing Database (ASD) splice patterns (SP) for HMGXB4 (see all 9)    About this scheme

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


    ECgene alternative splicing isoforms for HMGXB4

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    HMGXB4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GATAGTATAG
    HMGXB4 Expression
    About this image


    See HMGXB4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HMGXB4

    SOURCE GeneReport for Unigene cluster: Hs.588815
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    In Situ
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    (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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for HMGXB4 gene from 6/16 species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hmgxb41 , 5 HMG box domain containing 41, 5 85.41(n)1
    87.88(a)1
      8 (35.57 cM)5
    708231  NM_178017.11  NP_821136.11 
     749933565 
    chicken
    (Gallus gallus)
    Aves HMGXB41 HMG box domain containing 4 73.11(n)
    74.09(a)
      418059  XM_416295.3  XP_416295.3 
    lizard
    (Anolis carolinensis)
    Reptilia HMGXB46
    Uncharacterized protein
    72(a)
    1 ↔ 1
    5(21405671-21425449)
    African clawed frog
    (Xenopus laevis)
    Amphibia HMG2L12 HMG-box protein HMG2L1 77.3(n)    AY281348.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5597421 novel protein similar to human high-mobility group more 57.92(n)
    59.04(a)
      559742  NM_001127512.1  NP_001120984.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG46176
    --
    25(a)
    1 ↔ 1
    X(6996352-6998524)


    ENSEMBL Gene Tree for HMGXB4 (if available)
    TreeFam Gene Tree for HMGXB4 (if available)

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

    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/847 SNPs in HMGXB4 are shown (see all 847)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs359841181,2
    C--19595756(+) TCTAC-/AAAA  
            
    AAAAA
    2 -- int10--------
    rs1178229961,2
    F--35651452(+) GCAGTG/AAGCTG 2 -- us2k11Minor allele frequency- A:0.01NA 120
    rs1881972441,2
    --35651460(+) CTGTGA/CTCGTG 2 -- us2k10--------
    rs1499582251,2
    C--35651537(+) CCACAA/GGGACA 2 -- us2k10--------
    rs81419381,2
    C,F--35651584(+) ggagTC/TATCAC 2 -- us2k12Minor allele frequency- T:0.20WA 120
    rs57500901,2
    C,A,H--35651726(+) ctcttC/Ttgggg 2 -- us2k1 trp34Minor allele frequency- T:0.00NS EA 418
    rs1809911081,2
    --35651779(+) GACCAA/GTGGAT 2 -- us2k10--------
    rs1864913541,2
    --35651797(+) TCTGAA/GGAACA 2 -- us2k10--------
    rs1897788921,2
    --35651800(+) GAAGAA/CCAAAA 2 -- us2k10--------
    rs1464776241,2
    C--35651882(+) GCAATA/CTAACA 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for HMGXB4 (35653445 - 35691800 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for HMGXB4:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2170801CNV Deletion18987734
    nsv914994CNV Loss21882294

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    HMGXB4 for disorders           About MalaCards
    OMIM gene information: 604702    OMIM disorders: --


    HMGXB4 for disorders           About GeneDecksing

    Human Genome Epidemiology (HuGE) Navigator: HMGXB4 (0 documents)

    Export disorders for HMGXB4 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 HMGXB4 gene, integrated from 9 sources (see all 17):
    (articles sorted by number of sources associating them with HMGXB4)
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    1. TOM1 genes map to human chromosome 22q13.1 and mouse chromosome 8C1 and encode proteins similar to the endosomal proteins HGS and STAM. (PubMed id 10329004)1, 2, 3 Seroussi E....Dumanski J.P. (1999)
    2. The DNA sequence of human chromosome 22. (PubMed id 10591208)1, 2, 3 Dunham I....O'Brien K.P. (1999)
    3. Repression of smooth muscle differentiation by a nove l high mobility group box-containing protein, HMG2L1. (PubMed id 20511232)1, 3 Zhou J....Wang X. (2010)
    4. A genome annotation-driven approach to cloning the human ORFeome. (PubMed id 15461802)1, 2 Collins J.E.... Dunham I. (2004)
    5. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. (PubMed id 12529303)1, 2 Collins J.E.... Dunham I. (2003)
    6. A Y2H-seq approach defines the human protein methyltransferase interactome. (PubMed id 23455924)1 Weimann M.... Stelzl U. (2013)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    8. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)
    9. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)
    10. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 10042 HGNC: 5003 AceView: HMG2L1 Ensembl:ENSG00000100281 euGenes: HUgn10042
    ECgene: HMGXB4 H-InvDB: HMGXB4

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for HMGXB4 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 HMGXB4 gene:
    Search GeneIP for patents involving HMGXB4

    GeneCards and IP:
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