U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Kdm6b KDM1 lysine (K)-specific demethylase 6B [ Mus musculus (house mouse) ]

Gene ID: 216850, updated on 23-Apr-2024

Summary

Official Symbol
Kdm6bprovided by MGI
Official Full Name
KDM1 lysine (K)-specific demethylase 6Bprovided by MGI
Primary source
MGI:MGI:2448492
See related
Ensembl:ENSMUSG00000018476 AllianceGenome:MGI:2448492
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Jmjd3; 1700064E03Rik
Summary
Enables beta-catenin binding activity; histone H3-tri/di-methyl-lysine-27 demethylase activity; and sequence-specific DNA binding activity. Involved in several processes, including histone H3-K27 demethylation; mesodermal cell differentiation; and positive regulation of cold-induced thermogenesis. Acts upstream of or within several processes, including cellular response to hydrogen peroxide; histone demethylation; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including brain; gut; liver; metanephros; and olfactory epithelium. Orthologous to human KDM6B (lysine demethylase 6B). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 16.9), duodenum adult (RPKM 10.2) and 25 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Location:
11 B3; 11 42.6 cM
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (69289334..69311188, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (69398508..69420367, complement)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E7004 Neighboring gene STARR-positive B cell enhancer ABC_E5241 Neighboring gene cytochrome b5 domain containing 1 Neighboring gene STARR-positive B cell enhancer ABC_E2996 Neighboring gene STARR-positive B cell enhancer ABC_E5242 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:69223376-69223485 Neighboring gene transmembrane protein 88 Neighboring gene N(alpha)-acetyltransferase 38, NatC auxiliary subunit Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:69231989-69232098 Neighboring gene predicted gene, 51903 Neighboring gene dynein, axonemal, heavy chain 2 Neighboring gene STARR-seq mESC enhancer starr_29847 Neighboring gene STARR-seq mESC enhancer starr_29849 Neighboring gene ephrin B3

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Clone Names

  • KIAA0346, mKIAA0346

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables beta-catenin binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
 
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K27me2/H3K27me3 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables histone H3K27me2/H3K27me3 demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3K27me2/H3K27me3 demethylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H3K27me2/H3K27me3 demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in cardiac muscle cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell fate commitment IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cellular response to hydrogen peroxide IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in endothelial cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in heart development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in hippocampus development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within inflammatory response IEA
Inferred from Electronic Annotation
more info
 
involved_in mesodermal cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of cold-induced thermogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of MLL3/4 complex IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
lysine-specific demethylase 6B
Names
[histone H3]-trimethyl-L-lysine(27) demethylase 6B
jmjC domain-containing protein 3
jumonji domain containing 3
jumonji domain-containing protein 3
NP_001017426.1
XP_030101676.1
XP_030101677.1
XP_030101678.1
XP_030101679.1
XP_030101680.1
XP_030101681.1
XP_030101682.1
XP_030101683.1
XP_030101684.1
XP_030101685.1
XP_030101686.1
XP_036012463.1
XP_036012464.1

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_001017426.2NP_001017426.1  lysine-specific demethylase 6B

    See identical proteins and their annotated locations for NP_001017426.1

    Status: VALIDATED

    Source sequence(s)
    AL596125
    Consensus CDS
    CCDS24895.1
    UniProtKB/Swiss-Prot
    Q3UWY9, Q4VC26, Q5NCY0, Q6ZQD3
    Related
    ENSMUSP00000091620.5, ENSMUST00000094077.5
    Conserved Domains (3) summary
    pfam02373
    Location:13751483
    JmjC; JmjC domain, hydroxylase
    smart00558
    Location:13411405
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    69289334..69311188 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030245817.2XP_030101677.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  2. XM_030245818.2XP_030101678.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  3. XM_030245816.2XP_030101676.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  4. XM_036156570.1XP_036012463.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  5. XM_030245819.2XP_030101679.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  6. XM_030245826.2XP_030101686.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  7. XM_030245823.2XP_030101683.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  8. XM_036156571.1XP_036012464.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  9. XM_030245824.2XP_030101684.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  10. XM_030245820.2XP_030101680.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  11. XM_030245825.2XP_030101685.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  12. XM_030245822.2XP_030101682.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase
  13. XM_030245821.2XP_030101681.1  lysine-specific demethylase 6B isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:13421406
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00006
    Location:106136
    TPR; TPR repeat [structural motif]
    pfam02373
    Location:13761484
    JmjC; JmjC domain, hydroxylase