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

Gene ID: 216850, updated on 3-Oct-2021

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
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; BC038313; 1700064E03Rik
Expression
Ubiquitous expression in thymus adult (RPKM 16.9), duodenum adult (RPKM 10.2) and 25 other tissues See more
Orthologs
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Genomic context

See Kdm6b in Genome Data Viewer
Location:
11; 11 B3
Exon count:
32
Annotation release Status Assembly Chr Location
109 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)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (69212010..69227177, complement)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene cytochrome b5 domain containing 1 Neighboring gene transmembrane protein 88 Neighboring gene N(alpha)-acetyltransferase 38, NatC auxiliary subunit Neighboring gene predicted gene, 51903 Neighboring gene dynein, axonemal, heavy chain 2 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

Homology

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
PubMed 
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
PubMed 
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3-tri/di-methyl-lysine-27 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone H3-tri/di-methyl-lysine-27 demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3-tri/di-methyl-lysine-27 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
PubMed 
involved_in histone H3-K27 demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in histone H3-K27 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within histone H3-K27 demethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in histone H3-K27 demethylation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within histone demethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
PubMed 
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
PubMed 
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)

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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_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
    Q5NCY0
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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
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