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

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: mouse all
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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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
miR-142-3p simultaneously targets HMGA1, HMGA2, HMGB1, and HMGB3 and inhibits tumorigenic properties and in-vivo metastatic potential of human cervical cancer cells.
Title: miR-142-3p simultaneously targets HMGA1, HMGA2, HMGB1, and HMGB3 and inhibits tumorigenic properties and in-vivo metastatic potential of human cervical cancer cells.
LINC00857 promotes colorectal cancer progression by sponging miR-150-5p and upregulating HMGB3 (high mobility group box 3) expression.
Title: LINC00857 promotes colorectal cancer progression by sponging miR-150-5p and upregulating HMGB3 (high mobility group box 3) expression.
HDAC3 increases HMGB3 expression to facilitate the immune escape of breast cancer cells via down-regulating microRNA-130a-3p.
Title: HDAC3 increases HMGB3 expression to facilitate the immune escape of breast cancer cells via down-regulating microRNA-130a-3p.
High mobility group box 3 promotes cervical cancer proliferation by regulating Wnt/beta-catenin pathway.
Title: High mobility group box 3 promotes cervical cancer proliferation by regulating Wnt/β-catenin pathway.

Submit: New GeneRIF Correction See all GeneRIFs (39)

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	Compare labs

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

RH98216 (e-PCR)
- UniSTS:85515

D11S2560 (e-PCR)
- UniSTS:37928

D8S2279 (e-PCR)
- UniSTS:473907

ECD09851 (e-PCR)
- UniSTS:290892

STS-Z40721 (e-PCR)
- UniSTS:65629

HMGB3__6575 (e-PCR)
- UniSTS:463983

SHGC-58788 (e-PCR)
- UniSTS:94334

SHGC-53292 (e-PCR)
- UniSTS:73608

SHGC-132841 (e-PCR)
- UniSTS:170921

REN99877 (e-PCR)
- UniSTS:424674

RH45008 (e-PCR)
- UniSTS:5357

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 more info	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

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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

NG_034209.1 RefSeqGene

Range

7828..15264

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

150980507..150990771

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

O15347, O95556, Q6NS40
XM_047442062.1 → XP_047298018.1 high mobility group protein B3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

149248003..149258240

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

O15347, O95556, Q6NS40
XM_054326955.1 → XP_054182930.1 high mobility group protein B3 isoform X1