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

Gene ID: 3149, updated on 14-Nov-2024

Summary

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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
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Genomic context

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See HMGB3 in Genome Data Viewer
Location:
Xq28
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (150980507..150990771)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (149248003..149258240)
RS_2024_09 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

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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. Prognostic value of HMGB3 expression in patients with non-small cell lung cancer. Song N, et al. Tumour Biol, 2013 Oct. PMID 23609034
  2. HMGB3 promotes growth and migration in colorectal cancer by regulating WNT/β-catenin pathway. Zhang Z, et al. PLoS One, 2017. PMID 28678825, Free PMC Article
  3. Targeting the High-Mobility Group Box 3 Protein Sensitizes Chemoresistant Ovarian Cancer Cells to Cisplatin. Mukherjee A, et al. Cancer Res, 2019 Jul 1. PMID 31061066, Free PMC Article
  4. Increased expression of HMGB3: a novel independent prognostic marker of worse outcome in patients with esophageal squamous cell carcinoma. Gao J, et al. Int J Clin Exp Pathol, 2015. PMID 25755721, Free PMC Article
  5. Overexpression of HMGB3 protein promotes cell proliferation, migration and is associated with poor prognosis in urinary bladder cancer patients. Li M, et al. Tumour Biol, 2015 Jun. PMID 25647262

See all (108) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ELAVL1 regulates glycolysis in nasopharyngeal carcinoma cells through the HMGB3/beta-catenin axis.
    Title: ELAVL1 regulates glycolysis in nasopharyngeal carcinoma cells through the HMGB3/β-catenin axis.
  2. HMGB3 and SUB1 Bind to and Facilitate the Repair of N[2]-Alkylguanine Lesions in DNA.
    Title: HMGB3 and SUB1 Bind to and Facilitate the Repair of N(2)-Alkylguanine Lesions in DNA.
  3. Structure and Functions of HMGB3 Protein.
    Title: Structure and Functions of HMGB3 Protein.
  4. Exosomal HMGB3 released by glioma cells confers the activation of NLRP3 inflammasome and pyroptosis in tumor-associated macrophages.
    Title: Exosomal HMGB3 released by glioma cells confers the activation of NLRP3 inflammasome and pyroptosis in tumor-associated macrophages.
  5. HMGB3 promotes the malignant phenotypes and stemness of epithelial ovarian cancer through the MAPK/ERK signaling pathway.
    Title: HMGB3 promotes the malignant phenotypes and stemness of epithelial ovarian cancer through the MAPK/ERK signaling pathway.
  6. Circ-IGF1R Affects the Progression of Colorectal Cancer by Activating the miR-362-5p/HMGB3-Mediated Wnt/beta-Catenin Signal Pathway.
    Title: Circ-IGF1R Affects the Progression of Colorectal Cancer by Activating the miR-362-5p/HMGB3-Mediated Wnt/β-Catenin Signal Pathway.
  7. SOX9 and HMGB3 co-operatively transactivate NANOG and promote prostate cancer progression.
    Title: SOX9 and HMGB3 co-operatively transactivate NANOG and promote prostate cancer progression.
  8. Long Noncoding RNA Brain Cytoplasmic RNA 1 Induces Cisplatin-Resistance of Cervical Cancer Cells by Sponging MicroRNA-330-5p and Upregulating High-Mobility Group Box 3.
    Title: Long Noncoding RNA Brain Cytoplasmic RNA 1 Induces Cisplatin-Resistance of Cervical Cancer Cells by Sponging MicroRNA-330-5p and Upregulating High-Mobility Group Box 3.
  9. HMGB3 promotes PARP inhibitor resistance through interacting with PARP1 in ovarian cancer.
    Title: HMGB3 promotes PARP inhibitor resistance through interacting with PARP1 in ovarian cancer.
  10. LINC00319 promotes cancer stem cell-like properties in laryngeal squamous cell carcinoma via E2F1-mediated upregulation of HMGB3.
    Title: LINC00319 promotes cancer stem cell-like properties in laryngeal squamous cell carcinoma via E2F1-mediated upregulation of HMGB3.
Submit: New GeneRIF Correction See all GeneRIFs (42)

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

Associated conditions

Description Tests
X-linked colobomatous microphthalmia-microcephaly-intellectual disability-short stature syndrome
MedGen: C3806742 OMIM: 300915 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC90319

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 negative regulation of B cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of myeloid cell differentiation IEA
Inferred from Electronic Annotation
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

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

NCBI Reference Sequences (RefSeq)

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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_001301228.2 → NP_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:93 → 160
    HMG_box; HMG (high mobility group) box
    pfam09011
    Location:13 → 78
    HMG_box_2; HMG-box domain

  2. NM_001301229.2 → NP_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:93 → 160
    HMG_box; HMG (high mobility group) box
    pfam09011
    Location:13 → 78
    HMG_box_2; HMG-box domain

  3. NM_001301231.2 → NP_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:113 → 180
    HMG_box; HMG (high mobility group) box
    pfam09011
    Location:33 → 98
    HMG_box_2; HMG-box domain

  4. NM_005342.4 → NP_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:93 → 160
    HMG_box; HMG (high mobility group) box
    pfam09011
    Location:13 → 78
    HMG_box_2; HMG-box domain

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_000023.11 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    O15347, O95556, Q6NS40

  2. XM_047442062.1 → XP_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_054326956.1 → XP_054182931.1  high mobility group protein B3 isoform X2

    UniProtKB/Swiss-Prot
    O15347, O95556, Q6NS40

  2. XM_054326955.1 → XP_054182930.1  high mobility group protein B3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15347.4 GenPept UniProtKB/Swiss-Prot:O15347

Gene LinkOut

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