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HMGB4 high mobility group box 4 [ Homo sapiens (human) ]

Gene ID: 127540, updated on 5-Mar-2024

Summary

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Official Symbol
HMGB4provided by HGNC
Official Full Name
high mobility group box 4provided by HGNC
Primary source
HGNC:HGNC:24954
See related
Ensembl:ENSG00000176256 MIM:617285; AllianceGenome:HGNC:24954
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
dJ1007G16.5
Summary
Predicted to enable DNA binding activity, bending. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward testis (RPKM 70.9) See more
Orthologs
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Genomic context

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Location:
1p35.1
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (33860475..33864791)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (33722055..33726370)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (34326076..34330392)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene CUB and Sushi multiple domains 2 Neighboring gene uncharacterized LOC124903976 Neighboring gene heat shock protein family D (Hsp60) member 1 pseudogene 14 Neighboring gene CSMD2 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:34484896-34485714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:34503797-34504791 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:34516720-34516822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:34526371-34526872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:34526873-34527372 Neighboring gene NANOG hESC enhancer GRCh37_chr1:34553505-34554025 Neighboring gene RNA, 5S ribosomal pseudogene 42

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. A transcript finishing initiative for closing gaps in the human transcriptome. Sogayar MC, et al. Genome Res, 2004 Jul. PMID 15197164, Free PMC Article
  2. Convergent animal and human evidence suggests a role of PPM1A gene in response to antidepressants. Malki K, et al. Biol Psychiatry, 2011 Feb 15. PMID 20970119
  3. Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. Virok DP, et al. J Proteome Res, 2011 Apr 1. PMID 21244100
  4. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Dias Neto E, et al. Proc Natl Acad Sci U S A, 2000 Mar 28. PMID 10737800, Free PMC Article
  5. Proteomic characterization of the human sperm nucleus. de Mateo S, et al. Proteomics, 2011 Jul. PMID 21630459

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Convergent animal and human evidence suggests a role of PPM1A gene in response to antidepressants.
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

Clone Names

  • FLJ40388, MGC88128

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding, bending IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
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 nucleus HDA PubMed 

General protein information

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Preferred Names
high mobility group protein B4
Names
HMG2 like

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_001352984.2 → NP_001339913.1  high mobility group protein B4 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks a portion of the 5' coding region compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AK130859, BC070148, BI827031
    UniProtKB/TrEMBL
    Q6NSH1
    Related
    ENST00000425537.1
    Conserved Domains (1) summary
    cd00084
    Location:19 → 84
    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 ...

  2. NM_001379301.1 → NP_001366230.1  high mobility group protein B4 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 encode the same isoform (1).
    Source sequence(s)
    AL121980
    Consensus CDS
    CCDS30668.1
    UniProtKB/Swiss-Prot
    B2R4X7, Q0QWA4, Q8WW32
    Related
    ENSP00000505691.1, ENST00000681531.1
    Conserved Domains (2) summary
    cd00084
    Location:93 → 158
    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 ...
    cl00082
    Location:8 → 78
    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 ...

  3. NM_145205.6 → NP_660206.2  high mobility group protein B4 isoform 1

    See identical proteins and their annotated locations for NP_660206.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 3 encode the same isoform.
    Source sequence(s)
    AK097707, AK130859, AL121980, BI827031, CF272581, KF495903
    Consensus CDS
    CCDS30668.1
    UniProtKB/Swiss-Prot
    B2R4X7, Q0QWA4, Q8WW32
    Related
    ENSP00000429214.1, ENST00000519684.5
    Conserved Domains (2) summary
    cd00084
    Location:93 → 158
    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 ...
    cl00082
    Location:8 → 78
    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 ...

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    33860475..33864791
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    33722055..33726370
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WW32.2 GenPept UniProtKB/Swiss-Prot:Q8WW32

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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