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

    Gene ID: 127540, updated on 2-Nov-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, Nov 2024]
    Expression
    Restricted expression toward testis (RPKM 70.9) See more
    Orthologs
    mouse all
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    Genomic context

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    See HMGB4 in Genome Data Viewer
    Location:
    1p35.1
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (33860475..33864791)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (33722055..33726370)
    RS_2024_09 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 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 (15) 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_2024_08

    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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