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    HMGB3 high mobility group box 3 [ Homo sapiens (human) ]

    Gene ID: 3149, updated on 5-May-2024

    Summary

    Official Symbol
    HMGB3provided by HGNC
    Official Full Name
    high mobility group box 3provided by HGNC
    Primary source
    HGNC:HGNC:5004
    See related
    Ensembl:ENSG00000029993 MIM:300193; AllianceGenome:HGNC:5004
    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
    HMG4; HMG-4; HMG2A; HMG-2a
    Summary
    This gene encodes a member of a family of proteins containing one or more high mobility group DNA-binding motifs. The encoded protein plays an important role in maintaining stem cell populations, and may be aberrantly expressed in tumor cells. A mutation in this gene was associated with microphthalmia, syndromic 13. There are numerous pseudogenes of this gene on multiple chromosomes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
    Expression
    Broad expression in placenta (RPKM 24.9), bone marrow (RPKM 7.8) and 21 other tissues See more
    Orthologs
    NEW
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    Genomic context

    Location:
    Xq28
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (150980507..150990771)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (149248003..149258240)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (150148980..150159244)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2927 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:150093760-150094594 Neighboring gene RNA, U6 small nuclear 383, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:150136026-150136543 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:150150822-150151517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21055 Neighboring gene ribosomal protein L19 pseudogene 21 Neighboring gene ribosomal protein L12 pseudogene 50

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC90319

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding, bending IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA binding, bending ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables RNA binding HDA PubMed 
    enables double-stranded DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables four-way junction DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA geometric change ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in DNA recombination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    high mobility group protein B3
    Names
    high mobility group protein 2a
    high-mobility group (nonhistone chromosomal) protein 4

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_034209.1 RefSeqGene

      Range
      7828..15264
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001301228.2NP_001288157.1  high mobility group protein B3 isoform a

      See identical proteins and their annotated locations for NP_001288157.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the shorter isoform (a). Variants 1, 2, and 3 encode the same isoform (a).
      Source sequence(s)
      AF003626, BC070482, Y10043
      Consensus CDS
      CCDS35428.1
      UniProtKB/Swiss-Prot
      O15347, O95556, Q6NS40
      UniProtKB/TrEMBL
      E7ES08
      Related
      ENSP00000442758.1, ENST00000448905.6
      Conserved Domains (2) summary
      pfam00505
      Location:93160
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:1378
      HMG_box_2; HMG-box domain
    2. NM_001301229.2NP_001288158.1  high mobility group protein B3 isoform a

      See identical proteins and their annotated locations for NP_001288158.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to vaiant 1. Variants 1, 2, and 3 encode the same isoform (a).
      Source sequence(s)
      AF003626, BC070482, DB191695, Y10043
      Consensus CDS
      CCDS35428.1
      UniProtKB/Swiss-Prot
      O15347, O95556, Q6NS40
      UniProtKB/TrEMBL
      E7ES08
      Conserved Domains (2) summary
      pfam00505
      Location:93160
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:1378
      HMG_box_2; HMG-box domain
    3. NM_001301231.2NP_001288160.1  high mobility group protein B3 isoform b

      See identical proteins and their annotated locations for NP_001288160.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded isoform (b) has a longer N-terminus than isoform a.
      Source sequence(s)
      AF003626, BC037210, BF979310, Y10043
      UniProtKB/TrEMBL
      E7ES08
      Conserved Domains (2) summary
      pfam00505
      Location:113180
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:3398
      HMG_box_2; HMG-box domain
    4. NM_005342.4NP_005333.2  high mobility group protein B3 isoform a

      See identical proteins and their annotated locations for NP_005333.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to vaiant 1. Variants 1, 2, and 3 encode the same isoform (a).
      Source sequence(s)
      AF003626, BC037210, Y10043
      Consensus CDS
      CCDS35428.1
      UniProtKB/Swiss-Prot
      O15347, O95556, Q6NS40
      UniProtKB/TrEMBL
      E7ES08
      Related
      ENSP00000359393.3, ENST00000325307.12
      Conserved Domains (2) summary
      pfam00505
      Location:93160
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:1378
      HMG_box_2; HMG-box domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      150980507..150990771
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442063.1XP_047298019.1  high mobility group protein B3 isoform X2

      UniProtKB/Swiss-Prot
      O15347, O95556, Q6NS40
    2. XM_047442062.1XP_047298018.1  high mobility group protein B3 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      149248003..149258240
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326956.1XP_054182931.1  high mobility group protein B3 isoform X2

      UniProtKB/Swiss-Prot
      O15347, O95556, Q6NS40
    2. XM_054326955.1XP_054182930.1  high mobility group protein B3 isoform X1