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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
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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
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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

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