Format

Send to:

Choose Destination

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

Gene ID: 3149, updated on 7-Jun-2020

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
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

Genomic context

See HMGB3 in Genome Data Viewer
Location:
Xq28
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (150980507..150990775)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (150149056..150159248)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene CD99 molecule like 2 Neighboring gene peptidylprolyl isomerase A pseudogene 91 Neighboring gene RNA, U6 small nuclear 383, pseudogene 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

Homology

Clone Names

  • MGC90319

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding, bending IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA binding, bending ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA binding HDA PubMed 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
double-stranded DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
four-way junction DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
DNA geometric change ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA recombination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA recombination ISS
Inferred from Sequence or Structural Similarity
more info
 
chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
multicellular organism development TAS
Traceable Author Statement
more info
PubMed 
negative regulation of B cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of myeloid cell differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of innate immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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)

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
    5000..15264
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001301228.1NP_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
    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
    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/Swiss-Prot
    O15347
    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
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    150980507..150990775
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452369.1XP_024308137.1  high mobility group protein B3 isoform X1

    Conserved Domains (2) summary
    pfam00505
    Location:93160
    HMG_box; HMG (high mobility group) box
    pfam09011
    Location:1378
    HMG_box_2; HMG-box domain
Support Center