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    KDM3B lysine demethylase 3B [ Homo sapiens (human) ]

    Gene ID: 51780, updated on 3-Dec-2024

    Summary

    Official Symbol
    KDM3Bprovided by HGNC
    Official Full Name
    lysine demethylase 3Bprovided by HGNC
    Primary source
    HGNC:HGNC:1337
    See related
    Ensembl:ENSG00000120733 MIM:609373; AllianceGenome:HGNC:1337
    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
    5qNCA; DIJOS; NET22; C5orf7; JMJD1B
    Summary
    Predicted to enable chromatin DNA binding activity; histone H3K9 demethylase activity; and transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. Biomarker of acute lymphoblastic leukemia; breast cancer; colorectal cancer; and lung non-small cell carcinoma. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 15.2), thyroid (RPKM 13.7) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See KDM3B in Genome Data Viewer
    Location:
    5q31.2
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (138352685..138437027)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (138878903..138963243)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (137688374..137772716)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene cell division cycle 25C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16389 Neighboring gene uncharacterized LOC100128966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16390 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16392 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16393 Neighboring gene family with sequence similarity 53 member C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:137706464-137706964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:137706965-137707465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:137775379-137775912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23204 Neighboring gene receptor accessory protein 2 Neighboring gene CRISPRi-validated cis-regulatory element chr5.3152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23205 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:137799954-137801153 Neighboring gene early growth response 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Diets-Jongmans syndrome
    MedGen: C5394263 OMIM: 618846 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog
    Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1082

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables FAD-dependent histone H3K9me/H3K9me2 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables antioxidant activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables chromatin DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K9 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K9me/H3K9me2 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in cellular oxidant detoxification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of histone deacetylase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    lysine-specific demethylase 3B
    Names
    [histone H3]-dimethyl-L-lysine(9) demethylase 3B
    jmjC domain-containing histone demethylation protein 2B
    jumonji domain containing 1B
    jumonji domain-containing protein 1B
    lysine (K)-specific demethylase 3B
    nuclear protein 5qNCA
    NP_057688.3
    XP_005272075.1
    XP_011541790.1
    XP_011541791.1
    XP_016865073.1
    XP_047273269.1
    XP_054208792.1
    XP_054208793.1
    XP_054208794.1
    XP_054208795.1
    XP_054208796.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_016604.4NP_057688.3  lysine-specific demethylase 3B

      Status: VALIDATED

      Source sequence(s)
      AC104116, AC113403
      Consensus CDS
      CCDS34242.1
      UniProtKB/Swiss-Prot
      A6H8X7, Q7LBC6, Q9BVH6, Q9BW93, Q9BZ52, Q9NYF4, Q9UPS0
      UniProtKB/TrEMBL
      A4FUT8
      Related
      ENSP00000326563.5, ENST00000314358.10
      Conserved Domains (3) summary
      smart00558
      Location:15021574
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:15991704
      cupin_like; Conserved domain found in cupin and related proteins
      cl25496
      Location:424756
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

    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
      138352685..138437027
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417313.1XP_047273269.1  lysine-specific demethylase 3B isoform X2

      UniProtKB/TrEMBL
      A4FUT8
    2. XM_005272018.5XP_005272075.1  lysine-specific demethylase 3B isoform X3

      UniProtKB/TrEMBL
      A4FUT8
      Conserved Domains (2) summary
      smart00558
      Location:13021374
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:13991504
      cupin_like; Conserved domain found in cupin and related proteins
    3. XM_011543489.3XP_011541791.1  lysine-specific demethylase 3B isoform X2

      UniProtKB/TrEMBL
      A4FUT8
      Conserved Domains (2) summary
      smart00558
      Location:14541526
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:15511656
      cupin_like; Conserved domain found in cupin and related proteins
    4. XM_011543488.3XP_011541790.1  lysine-specific demethylase 3B isoform X1

      UniProtKB/TrEMBL
      A4FUT8
      Conserved Domains (2) summary
      smart00558
      Location:14581530
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:15551660
      cupin_like; Conserved domain found in cupin and related proteins
    5. XM_017009584.2XP_016865073.1  lysine-specific demethylase 3B isoform X4

      UniProtKB/TrEMBL
      A4FUT8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      138878903..138963243
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352819.1XP_054208794.1  lysine-specific demethylase 3B isoform X2

      UniProtKB/TrEMBL
      A4FUT8
    2. XM_054352820.1XP_054208795.1  lysine-specific demethylase 3B isoform X3

      UniProtKB/TrEMBL
      A4FUT8
    3. XM_054352818.1XP_054208793.1  lysine-specific demethylase 3B isoform X2

      UniProtKB/TrEMBL
      A4FUT8
    4. XM_054352817.1XP_054208792.1  lysine-specific demethylase 3B isoform X1

      UniProtKB/TrEMBL
      A4FUT8
    5. XM_054352821.1XP_054208796.1  lysine-specific demethylase 3B isoform X4

      UniProtKB/TrEMBL
      A4FUT8