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

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

    Summary

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    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 H3-methyl-lysine-9 demethylase activity; and transcription coregulator activity. Predicted to be involved in histone H3-K9 demethylation and 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, Apr 2022]
    Expression
    Ubiquitous expression in ovary (RPKM 15.2), thyroid (RPKM 13.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    5q31.2
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (138352685..138437027)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (138878903..138963243)
    105.20220307 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

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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. Histone lysine demethylase 3B (KDM3B) regulates the propagation of autophagy via transcriptional activation of autophagy-related genes. Jung H, et al. PLoS One, 2020. PMID 32716961, Free PMC Article
    2. Histone demethylase KDM3B protects against ferroptosis by upregulating SLC7A11. Wang Y, et al. FEBS Open Bio, 2020 Apr. PMID 32107878, Free PMC Article
    3. JMJD1B, a novel player in histone H3 and H4 processing to ensure genome stability. Saavedra F, et al. Epigenetics Chromatin, 2020 Feb 18. PMID 32070414, Free PMC Article
    4. Systematic characterization of chromatin modifying enzymes identifies KDM3B as a critical regulator in castration resistant prostate cancer. Saraç H, et al. Oncogene, 2020 Mar. PMID 31822799, Free PMC Article
    5. De Novo and Inherited Pathogenic Variants in KDM3B Cause Intellectual Disability, Short Stature, and Facial Dysmorphism. Diets IJ, et al. Am J Hum Genet, 2019 Apr 4. PMID 30929739, Free PMC Article

    See all (83) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Histone demethylase KDM3B protects against ferroptosis by upregulating SLC7A11.
      Title: Histone demethylase KDM3B protects against ferroptosis by upregulating SLC7A11.
    2. JMJD1B, a novel player in histone H3 and H4 processing to ensure genome stability.
      Title: JMJD1B, a novel player in histone H3 and H4 processing to ensure genome stability.
    3. Systematic characterization of chromatin modifying enzymes identifies KDM3B as a critical regulator in castration resistant prostate cancer.
      Title: Systematic characterization of chromatin modifying enzymes identifies KDM3B as a critical regulator in castration resistant prostate cancer.
    4. Histone lysine demethylase 3B (KDM3B) regulates the propagation of autophagy via transcriptional activation of autophagy-related genes.
      Title: Histone lysine demethylase 3B (KDM3B) regulates the propagation of autophagy via transcriptional activation of autophagy-related genes.
    5. pathogenic variants in KDM3B cause a syndrome characterized by intellectual disability, short stature, and facial dysmorphism
      Title: De Novo and Inherited Pathogenic Variants in KDM3B Cause Intellectual Disability, Short Stature, and Facial Dysmorphism.
    6. The results implicate KDM3B as a crucial epigenetic factor in cell cycle regulation that manipulates chromatin dynamics and transcription in hepatocarcinoma.
      Title: Histone demethylase KDM3B regulates the transcriptional network of cell-cycle genes in hepatocarcinoma HepG2 cells.
    7. we found that KDM3B exhibits potential tumor-suppressive activity and transcriptionally modulates HOXA1 expression via RARE in AML.
      Title: KDM3B shows tumor-suppressive activity and transcriptionally regulates HOXA1 through retinoic acid response elements in acute myeloid leukemia.
    8. H3K9 demethylase KDM3B represses transcription of the angiogenesis regulatory gene, ANGPT1.
      Title: Transcriptional repression of ANGPT1 by histone H3K9 demethylase KDM3B.
    9. High expression of KDM3B and KDM5A is associated with a better prognosis (no recurrence after mastectomy p=0.005 and response to docetaxel p=0.005)in breast cancer patients.
      Title: Histone lysine demethylases in breast cancer.
    10. evidence that the H3K9-me1/2 demethylase KDM3B might play a role in leukemogenesis via activation of lmo2 through interdependent actions with the histone acetyltransferase complex containing CBP
      Title: KDM3B is the H3K9 demethylase involved in transcriptional activation of lmo2 in leukemia.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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

    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

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1082

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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
    part_of 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

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    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)

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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_016604.4 → NP_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:1502 → 1574
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:1599 → 1704
      cupin_like; Conserved domain found in cupin and related proteins
      cl25496
      Location:424 → 756
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

    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_000005.10 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

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

    2. XM_005272018.5 → XP_005272075.1  lysine-specific demethylase 3B isoform X3

      UniProtKB/TrEMBL
      A4FUT8
      Conserved Domains (2) summary
      smart00558
      Location:1302 → 1374
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:1399 → 1504
      cupin_like; Conserved domain found in cupin and related proteins

    3. XM_011543489.3 → XP_011541791.1  lysine-specific demethylase 3B isoform X2

      UniProtKB/TrEMBL
      A4FUT8
      Conserved Domains (2) summary
      smart00558
      Location:1454 → 1526
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:1551 → 1656
      cupin_like; Conserved domain found in cupin and related proteins

    4. XM_011543488.3 → XP_011541790.1  lysine-specific demethylase 3B isoform X1

      UniProtKB/TrEMBL
      A4FUT8
      Conserved Domains (2) summary
      smart00558
      Location:1458 → 1530
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:1555 → 1660
      cupin_like; Conserved domain found in cupin and related proteins

    5. XM_017009584.2 → XP_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_054352819.1 → XP_054208794.1  lysine-specific demethylase 3B isoform X2

    2. XM_054352820.1 → XP_054208795.1  lysine-specific demethylase 3B isoform X3

    3. XM_054352818.1 → XP_054208793.1  lysine-specific demethylase 3B isoform X2

    4. XM_054352817.1 → XP_054208792.1  lysine-specific demethylase 3B isoform X1

    5. XM_054352821.1 → XP_054208796.1  lysine-specific demethylase 3B isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7LBC6.2 GenPept UniProtKB/Swiss-Prot:Q7LBC6

    Gene LinkOut

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

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