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HMGXB4 HMG-box containing 4 [ Homo sapiens (human) ]

Gene ID: 10042, updated on 3-Apr-2024

Summary

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Official Symbol
HMGXB4provided by HGNC
Official Full Name
HMG-box containing 4provided by HGNC
Primary source
HGNC:HGNC:5003
See related
Ensembl:ENSG00000100281 MIM:604702; AllianceGenome:HGNC:5003
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
P53N; HMG2L1; HMGBCG; THC211630
Summary
High mobility group (HMG) proteins are nonhistone chromosomal proteins. See HMG2 (MIM 163906) for additional information on HMG proteins.[supplied by OMIM, Nov 2010]
Expression
Ubiquitous expression in testis (RPKM 8.3), bone marrow (RPKM 7.9) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
22q12.3
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (35241536..35295807)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (35700425..35753698)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (35653486..35691800)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905110 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:35472054-35473253 Neighboring gene intestine specific homeobox Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18892 Neighboring gene long intergenic non-protein coding RNA 1399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18893 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:35531129-35531665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18894 Neighboring gene Sharpr-MPRA regulatory region 1139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18895 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35554225-35555056 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:35567219-35568418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35573611-35574112 Neighboring gene COX7B pseudogene 1 Neighboring gene uncharacterized LOC105373017 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35652780-35653280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13652 Neighboring gene RNA, U7 small nuclear 167 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35695462-35695984 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35695985-35696507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35697031-35697552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35713551-35714052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35714053-35714552 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35714588-35715088 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35715089-35715589 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:35718923-35720122 Neighboring gene Sharpr-MPRA regulatory region 10159 Neighboring gene target of myb1 membrane trafficking protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35726353-35726853 Neighboring gene microRNA 3909 Neighboring gene microRNA 6069

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. Analysis of the P(53N) a Novel Protein Encoded on Chromosome 22q12.1-12.3 in Glioblastomas and Ependymomas Specimens. Frankel BM, et al. J Mol Neurosci, 2021 Aug. PMID 33595778
  2. Integrative analysis of copy number and gene expression data suggests novel pathogenetic mechanisms in primary myelofibrosis. Salati S, et al. Int J Cancer, 2016 Apr 1. PMID 26547506
  3. Gene-based SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3: association with HMG2L1 and TOM1. Potash JB, et al. Am J Med Genet B Neuropsychiatr Genet, 2008 Jan 5. PMID 17671966
  4. Repression of smooth muscle differentiation by a novel high mobility group box-containing protein, HMG2L1. Zhou J, et al. J Biol Chem, 2010 Jul 23. PMID 20511232, Free PMC Article
  5. TOM1 genes map to human chromosome 22q13.1 and mouse chromosome 8C1 and encode proteins similar to the endosomal proteins HGS and STAM. Seroussi E, et al. Genomics, 1999 May 1. PMID 10329004

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Analysis of the P(53N) a Novel Protein Encoded on Chromosome 22q12.1-12.3 in Glioblastomas and Ependymomas Specimens.
    Title: Analysis of the P(53N) a Novel Protein Encoded on Chromosome 22q12.1-12.3 in Glioblastomas and Ependymomas Specimens.
  2. These results highlight a previously un-reported role of HMGXB4 in the hematopoietic system and transcriptional imbalances of HMGXB4 could contribute to the aberrant expansion of the megakaryocytic lineage in primary myelofibrosis patients
    Title: Integrative analysis of copy number and gene expression data suggests novel pathogenetic mechanisms in primary myelofibrosis.
  3. the first evidence of this novel HMG2L1 molecule playing an important role in attenuating smooth muscle differentiation
    Title: Repression of smooth muscle differentiation by a novel high mobility group box-containing protein, HMG2L1.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. high-mobility group protein 2-like 1 and SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3
    Title: Gene-based SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3: association with HMG2L1 and TOM1.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
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

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in endosome to lysosome transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of Wnt signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of NURF complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
HMG domain-containing protein 4
Names
HMG box domain containing 4
HMG box-containing protein 4
high mobility group protein 2-like 1

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.

mRNA and Protein(s)

  1. NM_001003681.3 → NP_001003681.1  HMG domain-containing protein 4 isoform 1

    See identical proteins and their annotated locations for NP_001003681.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer protein (isoform 1).
    Source sequence(s)
    AI471703, BC040447, BC052624, DW452042
    Consensus CDS
    CCDS33641.1
    UniProtKB/Swiss-Prot
    O75672, O75673, Q9UGU5, Q9UMT5
    UniProtKB/TrEMBL
    Q2M3X1
    Related
    ENSP00000216106.5, ENST00000216106.6
    Conserved Domains (2) summary
    cd00084
    Location:407 → 470
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
    pfam13775
    Location:107 → 225
    DUF4171; Domain of unknown function (DUF4171)

  2. NM_001362972.2 → NP_001349901.1  HMG domain-containing protein 4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks a 5' exon and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AI471703, AL008635
    UniProtKB/TrEMBL
    Q2M3X1
    Conserved Domains (2) summary
    cd00084
    Location:298 → 361
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
    pfam13775
    Location:1 → 123
    DUF4171; Domain of unknown function (DUF4171)

RNA

  1. NR_027780.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI471703, AL079310, DW452042
    Related
    ENST00000418170.5

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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    35241536..35295807
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047441067.1 → XP_047297023.1  HMG domain-containing protein 4 isoform X2

    UniProtKB/Swiss-Prot
    O75672, O75673, Q9UGU5, Q9UMT5

  2. XM_006724101.5 → XP_006724164.2  HMG domain-containing protein 4 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    35700425..35753698
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324974.1 → XP_054180949.1  HMG domain-containing protein 4 isoform X2

  2. XM_054324973.1 → XP_054180948.1  HMG domain-containing protein 4 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_005487.3: Suppressed sequence

    Description
    NM_005487.3: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  2. NM_014250.1: Suppressed sequence

    Description
    NM_014250.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UGU5.2 GenPept UniProtKB/Swiss-Prot:Q9UGU5

Gene LinkOut

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