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HMGXB3 HMG-box containing 3 [ Homo sapiens (human) ]

Gene ID: 22993, updated on 5-Mar-2024

Summary

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Official Symbol
HMGXB3provided by HGNC
Official Full Name
HMG-box containing 3provided by HGNC
Primary source
HGNC:HGNC:28982
See related
Ensembl:ENSG00000113716 MIM:619800; AllianceGenome:HGNC:28982
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SMF; HMGX3
Summary
This gene is one of the non-canonical high mobility group (HMG) genes. The encoded protein contains an HMG-box domain found in DNA binding proteins such as transcription factors and chromosomal proteins. [provided by RefSeq, Aug 2011]
Expression
Ubiquitous expression in prostate (RPKM 10.5), testis (RPKM 9.2) and 25 other tissues See more
Orthologs
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Genomic context

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See HMGXB3 in Genome Data Viewer
Location:
5q32
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (150000739..150053128)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (150537285..150589675)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149380302..149432691)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16504 Neighboring gene solute carrier family 26 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23393 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:149379441-149380229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23394 Neighboring gene tigger transposable element derived 6 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23395 Neighboring gene ribosomal protein S20 pseudogene 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:149439174-149439376 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:149444398-149444573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149447500-149448210 Neighboring gene colony stimulating factor 1 receptor Neighboring gene RORalpha allelically-responsive CSF1R enhancer Neighboring gene CSF1R promoter/intronic regulatory region Neighboring gene LTR-CSF1R promoter Neighboring gene Sharpr-MPRA regulatory region 12786 Neighboring gene ribosomal protein L7 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149490949-149491461 Neighboring gene CSF1R promoter E1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149497723-149498310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149499971-149500878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149507353-149507854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149509491-149510101 Neighboring gene platelet derived growth factor receptor beta Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149515109-149515620 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149515621-149516130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149516131-149516642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149517153-149517664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149526270-149526796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149532128-149532648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149532649-149533168

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
  • 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. Circular RNA EGLN3 silencing represses renal cell carcinoma progression through the miR-1224-3p/HMGXB3 axis. Zhang G, et al. Acta Histochem, 2021 Sep. PMID 34274607
  2. Nucleotide sequence and structural organization of the human FMS proto-oncogene. Hampe A, et al. Oncogene Res, 1989. PMID 2524025
  3. Regulation of closely juxtaposed proto-oncogene c-fms and HMGXB3 gene expression by mRNA 3' end polymorphism in breast cancer cells. Woo HH, et al. RNA, 2021 Sep. PMID 34155128, Free PMC Article
  4. Sequence analysis of two genomic regions containing the KIT and the FMS receptor tyrosine kinase genes. Andre C, et al. Genomics, 1997 Jan 15. PMID 9027509
  5. Development of a screening set for new (CAG/CTG)n dynamic mutations. Gastier JM, et al. Genomics, 1996 Feb 15. PMID 8786123

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Circular RNA EGLN3 silencing represses renal cell carcinoma progression through the miR-1224-3p/HMGXB3 axis.
    Title: Circular RNA EGLN3 silencing represses renal cell carcinoma progression through the miR-1224-3p/HMGXB3 axis.
  2. Regulation of closely juxtaposed proto-oncogene c-fms and HMGXB3 gene expression by mRNA 3' end polymorphism in breast cancer cells.
    Title: Regulation of closely juxtaposed proto-oncogene c-fms and HMGXB3 gene expression by mRNA 3' end polymorphism in breast cancer cells.
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

EBI GWAS Catalog

Description
Common genetic variation and the control of HIV-1 in humans.
EBI GWAS Catalog

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

Clone Names

  • KIAA0194

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
HMG domain-containing protein 3
Names
HMG box domain containing 3

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_021389.2 RefSeqGene

    Range
    5002..57391
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001366501.2 → NP_001353430.1  HMG domain-containing protein 3 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC011382, AC011406
    UniProtKB/TrEMBL
    E9PEK0
    Conserved Domains (2) summary
    smart00398
    Location:41 → 100
    HMG; high mobility group
    cl26464
    Location:276 → 424
    Atrophin-1; Atrophin-1 family

  2. NM_014983.3 → NP_055798.3  HMG domain-containing protein 3 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC011382, AC011406
    Consensus CDS
    CCDS54935.1
    UniProtKB/Swiss-Prot
    G5E9Y4, Q12766, Q86UG3, Q9UMF4
    UniProtKB/TrEMBL
    E9PEK0
    Related
    ENSP00000421917.1, ENST00000502717.6
    Conserved Domains (3) summary
    smart00398
    Location:41 → 100
    HMG; high mobility group
    PHA03247
    Location:442 → 590
    PHA03247; large tegument protein UL36; Provisional
    pfam18717
    Location:743 → 863
    CxC4; CxC4 like cysteine cluster associated with KDZ transposases

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    150000739..150053128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047416963.1 → XP_047272919.1  HMG domain-containing protein 3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    150537285..150589675
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352106.1 → XP_054208081.1  HMG domain-containing protein 3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q12766.3 GenPept UniProtKB/Swiss-Prot:Q12766

Gene LinkOut

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