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

Gene ID: 51780, updated on 5-Jan-2022

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
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, Nov 2021]
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

See KDM3B in Genome Data Viewer
Location:
5q31.2
Exon count:
28
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (138352685..138437027)
105.20201022 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 uncharacterized LOC100128966 Neighboring gene family with sequence similarity 53 member C Neighboring gene CRISPRi-validated cis-regulatory element chr5.3152 Neighboring gene receptor accessory protein 2

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
Biological insights from 108 schizophrenia-associated genetic loci.
GeneReviews: Not available
Diets-Jongmans syndrome
MedGen: C5394263 OMIM: 618846 GeneReviews: Not available
Compare labs
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
GeneReviews: Not available
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1082

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 H3-di/monomethyl-lysine-9 demethylase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3-methyl-lysine-9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 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

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_024301883.1

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

    Status: VALIDATED

    Source sequence(s)
    AC104116, AC113403
    Consensus CDS
    CCDS34242.1
    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: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_005272018.4XP_005272075.1  lysine-specific demethylase 3B isoform X4

    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
  2. XM_024446115.1XP_024301883.1  lysine-specific demethylase 3B isoform X3

    Conserved Domains (2) summary
    smart00558
    Location:13441416
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:14411546
    cupin_like; Conserved domain found in cupin and related proteins
  3. XM_011543489.2XP_011541791.1  lysine-specific demethylase 3B isoform X2

    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_011543488.2XP_011541790.1  lysine-specific demethylase 3B isoform X1

    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_017009584.1XP_016865073.1  lysine-specific demethylase 3B isoform X5

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