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

HMGXB4 Gene

protein-coding   GIFtS: 46
GCID: GC22P035653

HMG box domain containing 4

(Previous name: high-mobility group protein 2-like 1 )
(Previous symbol: HMG2L1)
 Explore 1 disease affiliated with
HMGXB4 via
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 Human Malady Compendium 
Biological research products
for HMGXB4    

Aliases
for HMGXB4 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
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     HMGBCG2 3
HMG2L11 2 3 5     HMG Box-Containing Protein 42 3
THC2116301 2     HMG Domain-Containing Protein 42
High-Mobility Group Protein 2-Like 11 2     Protein HMGBCG3
High Mobility Group Protein 2-Like 12 3     

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

Export aliases for HMGXB4 gene to outside databases

Previous GC identifers: GC22P033983 GC22P018614


Summaries
for HMGXB4 gene

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

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




Genomic Views
for HMGXB4 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000022.10  NC_018933.1  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 plasmid: HMGXB4 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

Proteins
for HMGXB4 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UGU5

    • HMGXB4 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

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

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for HMGXB4

    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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    Protein Domains /
    Families
    for HMGXB4 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HMGXB4 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR025228 DUF4171
     IPR009071 HMG_superfamily

    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


    Function
    for HMGXB4 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

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

    miRNA
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    Gene Editing
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    Clone
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    In Situ Assay
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    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



    Pathways & Interactions
    for HMGXB4 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 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



    Drugs & Compounds
    for HMGXB4 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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
    Search CenterWatch for drugs/clinical trials and news about HMGXB4 / HMGX4 

    Transcripts
    for HMGXB4 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, 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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    8/40 QIAGEN miScript miRNA Assays for microRNAs that regulate HMGXB4 (see all 40):
    hsa-miR-300 hsa-miR-15a hsa-miR-624* hsa-miR-570 hsa-miR-424 hsa-miR-124 hsa-miR-506 hsa-miR-497*
    SwitchGear 3'UTR luciferase reporter plasmid: HMGXB4 3' UTR sequence
    Inhib. RNA
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    Additional cDNA 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):

    AI288320 NM_001003681 BM787986 CB119482 CB242414 AI359479 AA595272 CF528563 
    BM677532 AA053680 BQ687053 AI015842 AI471703 AI453696 BE877254 BC033783 
    BQ012590 AI656803 BX394366 AI365200 CA310885 BC011723 BE855495 BF056467 

    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

    Expression
    for HMGXB4 gene

    (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
    CGAP TAG: GATAGTATAG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene 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
    for HMGXB4 gene

    (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 6/20 species (see all 20)    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
    		 --
    		 69(a)
    		 1 ↔ 1
    		 5(21409540-21421173)
    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
    		 --
    		 20(a)
    		 1 ↔ 1
    		 X(6996352-6998524)


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

    Paralogs
    for HMGXB4 gene

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

    Genomic Variants
    for HMGXB4 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/707 NCBI SNPs in HMGXB4 are shown (see all 707)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 22 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1178229961,2
    		--35651452(+) GCAGTG/AAGCTG 2 -- us2k11Minor allele frequency- A:0.01NA 120
    rs1881972441,2
    		--35651460(+) CTGTGA/CTCGTG 2 -- us2k10--------
    rs1499582251,2
    		--35651537(+) CCACAA/GGGACA 2 -- us2k10--------
    rs81419381,2
    		C,--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
    		--35651882(+) GCAATA/CTAACA 2 -- us2k10--------
    rs1816058401,2
    		--35651939(+) AGCTGC/TGGAGA 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for HMGXB4 (35653445 - 35691800 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for HMGXB4: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HMGXB4
    DNA2.0 Custom Variant and Variant Library Synthesis for HMGXB4

    Disorders / Diseases
    for HMGXB4 gene

    (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.)
    About This Section
    HMGXB4 for disorders           About GeneDecksing

    OMIM gene information: 604702    OMIM disorders: --

    1 disease for HMGXB4:    About MalaCards
    bipolar affective disorder

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

    Export disorders for HMGXB4 gene to outside databases

    Publications
    for HMGXB4 gene

    (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)
    About This Section

    PubMed articles for HMGXB4 gene, integrated from 9 sources (see all 16):
    (articles sorted by number of sources associating them with HMGXB4)    		    Utopia: connect your pdf to the dynamic
    world of online information

    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 census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    7. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)
    8. 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)
    9. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    10. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)

    External Searches for HMGXB4 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing HMGXB4 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 10042 HGNC: 5003 AceView: HMG2L1 Ensembl:ENSG00000100281 euGenes: HUgn10042
    ECgene: HMGXB4 H-InvDB: HMGXB4

    Other Databases showing HMGXB4 gene

    (According to HUGE)
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    Specialized Databases showing HMGXB4 gene

    (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

    Intellectual Property
    for HMGXB4 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for HMGXB4 gene:
    Search GeneIP for patents involving HMGXB4

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