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    HMGXB4 HMG-box containing 4 [ Homo sapiens (human) ]

    Gene ID: 10042, updated on 3-Nov-2024

    Summary

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    Official Symbol
    HMGXB4provided by HGNC
    Official Full Name
    HMG-box containing 4provided by HGNC
    Primary source
    HGNC:HGNC:5003
    See related
    Ensembl:ENSG00000100281 MIM:604702; AllianceGenome:HGNC:5003
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    P53N; HMG2L1; HMGBCG; THC211630
    Summary
    High mobility group (HMG) proteins are nonhistone chromosomal proteins. See HMG2 (MIM 163906) for additional information on HMG proteins.[supplied by OMIM, Nov 2010]
    Expression
    Ubiquitous expression in testis (RPKM 8.3), bone marrow (RPKM 7.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HMGXB4 in Genome Data Viewer
    Location:
    22q12.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (35241536..35295807)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (35700425..35753698)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (35653486..35691800)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905110 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:35472054-35473253 Neighboring gene intestine specific homeobox Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18892 Neighboring gene long intergenic non-protein coding RNA 1399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18893 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:35531129-35531665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18894 Neighboring gene Sharpr-MPRA regulatory region 1139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18895 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35554225-35555056 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:35567219-35568418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35573611-35574112 Neighboring gene COX7B pseudogene 1 Neighboring gene uncharacterized LOC105373017 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35652780-35653280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13652 Neighboring gene RNA, U7 small nuclear 167 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35695462-35695984 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35695985-35696507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35697031-35697552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35713551-35714052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35714053-35714552 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35714588-35715088 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35715089-35715589 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:35718923-35720122 Neighboring gene Sharpr-MPRA regulatory region 10159 Neighboring gene target of myb1 membrane trafficking protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35726353-35726853 Neighboring gene microRNA 3909 Neighboring gene microRNA 6069

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Analysis of the P(53N) a Novel Protein Encoded on Chromosome 22q12.1-12.3 in Glioblastomas and Ependymomas Specimens. Frankel BM, et al. J Mol Neurosci, 2021 Aug. PMID 33595778
    2. Gene-based SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3: association with HMG2L1 and TOM1. Potash JB, et al. Am J Med Genet B Neuropsychiatr Genet, 2008 Jan 5. PMID 17671966
    3. Integrative analysis of copy number and gene expression data suggests novel pathogenetic mechanisms in primary myelofibrosis. Salati S, et al. Int J Cancer, 2016 Apr 1. PMID 26547506
    4. Repression of smooth muscle differentiation by a novel high mobility group box-containing protein, HMG2L1. Zhou J, et al. J Biol Chem, 2010 Jul 23. PMID 20511232, Free PMC Article
    5. TOM1 genes map to human chromosome 22q13.1 and mouse chromosome 8C1 and encode proteins similar to the endosomal proteins HGS and STAM. Seroussi E, et al. Genomics, 1999 May 1. PMID 10329004

    See all (50) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Analysis of the P(53N) a Novel Protein Encoded on Chromosome 22q12.1-12.3 in Glioblastomas and Ependymomas Specimens.
      Title: Analysis of the P(53N) a Novel Protein Encoded on Chromosome 22q12.1-12.3 in Glioblastomas and Ependymomas Specimens.
    2. These results highlight a previously un-reported role of HMGXB4 in the hematopoietic system and transcriptional imbalances of HMGXB4 could contribute to the aberrant expansion of the megakaryocytic lineage in primary myelofibrosis patients
      Title: Integrative analysis of copy number and gene expression data suggests novel pathogenetic mechanisms in primary myelofibrosis.
    3. the first evidence of this novel HMG2L1 molecule playing an important role in attenuating smooth muscle differentiation
      Title: Repression of smooth muscle differentiation by a novel high mobility group box-containing protein, HMG2L1.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. high-mobility group protein 2-like 1 and SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3
      Title: Gene-based SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3: association with HMG2L1 and TOM1.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endosome to lysosome transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of Wnt signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of NURF complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    HMG domain-containing protein 4
    Names
    HMG box domain containing 4
    HMG box-containing protein 4
    high mobility group protein 2-like 1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001003681.3 → NP_001003681.1  HMG domain-containing protein 4 isoform 1

      See identical proteins and their annotated locations for NP_001003681.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer protein (isoform 1).
      Source sequence(s)
      AI471703, BC040447, BC052624, DW452042
      Consensus CDS
      CCDS33641.1
      UniProtKB/Swiss-Prot
      O75672, O75673, Q9UGU5, Q9UMT5
      UniProtKB/TrEMBL
      Q2M3X1
      Related
      ENSP00000216106.5, ENST00000216106.6
      Conserved Domains (2) summary
      cd00084
      Location:407 → 470
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
      pfam13775
      Location:107 → 225
      DUF4171; Domain of unknown function (DUF4171)

    2. NM_001362972.2 → NP_001349901.1  HMG domain-containing protein 4 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks a 5' exon and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AI471703, AL008635
      UniProtKB/TrEMBL
      Q2M3X1
      Conserved Domains (2) summary
      cd00084
      Location:298 → 361
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
      pfam13775
      Location:1 → 123
      DUF4171; Domain of unknown function (DUF4171)

    RNA

    1. NR_027780.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI471703, AL079310, DW452042
      Related
      ENST00000418170.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      35241536..35295807
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441067.1 → XP_047297023.1  HMG domain-containing protein 4 isoform X2

      UniProtKB/Swiss-Prot
      O75672, O75673, Q9UGU5, Q9UMT5

    2. XM_006724101.5 → XP_006724164.2  HMG domain-containing protein 4 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      35700425..35753698
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324974.1 → XP_054180949.1  HMG domain-containing protein 4 isoform X2

    2. XM_054324973.1 → XP_054180948.1  HMG domain-containing protein 4 isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_005487.3: Suppressed sequence

      Description
      NM_005487.3: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

    2. NM_014250.1: Suppressed sequence

      Description
      NM_014250.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UGU5.2 GenPept UniProtKB/Swiss-Prot:Q9UGU5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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