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

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 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

Location:: 5q31.2

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (138352685..138437027)
110	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_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Histone demethylase KDM3B protects against ferroptosis by upregulating SLC7A11.
Title: Histone demethylase KDM3B protects against ferroptosis by upregulating SLC7A11.
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.
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.
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.
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.
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.
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.
H3K9 demethylase KDM3B represses transcription of the angiogenesis regulatory gene, ANGPT1.
Title: Transcriptional repression of ANGPT1 by histone H3K9 demethylase KDM3B.
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.
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 EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH36167 (e-PCR)
- UniSTS:12326

JMJD1B (e-PCR)
- UniSTS:504899

RH78329 (e-PCR)
- UniSTS:81003

D5S1701 (e-PCR)
- UniSTS:28287

RH68817 (e-PCR)
- UniSTS:16565

RH93228 (e-PCR)
- UniSTS:83902

Homology

Homologs of the KDM3B gene: The KDM3B gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 453 organisms have orthologs with human gene KDM3B
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chromatin DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	PubMed

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in histone H3-K9 demethylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
is_active_in chromatin	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of histone deacetylase complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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

EC 1.14.11.65

XP_005272075.1

EC 1.14.11.65

XP_011541790.1

EC 1.14.11.65

XP_011541791.1

EC 1.14.11.65

XP_016865073.1

EC 1.14.11.65

XP_047273269.1

EC 1.14.11.65

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)

NM_016604.4 → NP_057688.3 lysine-specific demethylase 3B

Status: VALIDATED

Source sequence(s)

AC104116, AC113403

Consensus CDS

CCDS34242.1

UniProtKB/Swiss-Prot

Q9UPS0

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: Homo sapiens Annotation Release 110 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

138352685..138437027

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047417313.1 → XP_047273269.1 lysine-specific demethylase 3B isoform X2
XM_005272018.5 → XP_005272075.1 lysine-specific demethylase 3B isoform X3

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

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

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
XM_017009584.2 → XP_016865073.1 lysine-specific demethylase 3B isoform X4