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

    Gene ID: 22993, updated on 10-Dec-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (150000739..150053128)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (150537285..150589675)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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 (14) 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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    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)

    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_2024_08

    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

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

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