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Kdm4b lysine (K)-specific demethylase 4B [ Mus musculus (house mouse) ]

Gene ID: 193796, updated on 5-Mar-2024

Summary

Official Symbol
Kdm4bprovided by MGI
Official Full Name
lysine (K)-specific demethylase 4Bprovided by MGI
Primary source
MGI:MGI:2442355
See related
Ensembl:ENSMUSG00000024201 AllianceGenome:MGI:2442355
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
Jmjd2b; 4732474L06Rik
Summary
Enables histone H3-methyl-lysine-9 demethylase activity. Acts upstream of or within histone H3-K36 demethylation; histone H3-K9 demethylation; and negative regulation of histone H3-K9 trimethylation. Located in pericentric heterochromatin. Is expressed in several structures, including early conceptus; genitourinary system; heart; nervous system; and sensory organ. Human ortholog(s) of this gene implicated in autosomal dominant non-syndromic intellectual disability; breast cancer; colorectal cancer; malignant peripheral nerve sheath tumor; and stomach cancer. Orthologous to human KDM4B (lysine demethylase 4B). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 19.4), ovary adult (RPKM 19.2) and 28 other tissues See more
Orthologs
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Genomic context

See Kdm4b in Genome Data Viewer
Location:
17 D; 17 29.27 cM
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (56632975..56710774)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (56325970..56403774)

Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E3208 Neighboring gene STARR-positive B cell enhancer ABC_E3209 Neighboring gene arrestin domain containing 5 Neighboring gene ubiquitin-like, containing PHD and RING finger domains, 1 Neighboring gene STARR-positive B cell enhancer ABC_E141 Neighboring gene STARR-positive B cell enhancer ABC_E8923 Neighboring gene predicted gene, 32715 Neighboring gene protein tyrosine phosphatase receptor type S Neighboring gene microRNA 6977 Neighboring gene STARR-positive B cell enhancer ABC_E5622 Neighboring gene STARR-positive B cell enhancer mm9_chr17:56601992-56602293 Neighboring gene predicted gene, 32822 Neighboring gene predicted gene 9258

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)
  • Targeted (5)  1 citation
  • Endonuclease-mediated (3) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Clone Names

  • MGC6349

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K36 demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3K36 demethylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H3K36 demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone H3K9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables histone H3K9 demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3K9 demethylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H3K9 demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone H3K9me2/H3K9me3 demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in brain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of gene expression 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
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
part_of pericentric heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
lysine-specific demethylase 4B
Names
[histone H3]-trimethyl-L-lysine(9) demethylase 4B
jmjC domain-containing histone demethylation protein 3B
jumonji domain-containing protein 2B
NP_001344838.1
NP_742144.1
XP_006523957.1
XP_006523958.1
XP_006523959.1
XP_006523960.1
XP_006523961.1
XP_017172842.1
XP_017172843.1
XP_017172844.1
XP_017172845.1
XP_030105461.1
XP_030105462.1
XP_030105463.1
XP_030105464.1
XP_030105465.1
XP_030105466.1

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_001357909.1NP_001344838.1  lysine-specific demethylase 4B isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC026385, BP762845, CT009637
    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:881931
    TUDOR; Tudor domain
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    cl22851
    Location:757866
    PHD_SF; PHD finger superfamily
  2. NM_172132.3NP_742144.1  lysine-specific demethylase 4B isoform 1

    See identical proteins and their annotated locations for NP_742144.1

    Status: VALIDATED

    Source sequence(s)
    AK141879, BP762845, CA324771, CJ093438, CT009637
    Consensus CDS
    CCDS28904.1
    UniProtKB/Swiss-Prot
    Q3UR22, Q6ZQ30, Q91VY5, Q99K42
    UniProtKB/TrEMBL
    B0V2M9
    Related
    ENSMUSP00000025036.5, ENSMUST00000025036.11
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:910944
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:785894
    PHD_SF; PHD finger superfamily

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_000083.7 Reference GRCm39 C57BL/6J

    Range
    56632975..56710774
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006523896.3XP_006523959.1  lysine-specific demethylase 4B isoform X6

    UniProtKB/TrEMBL
    B0V2M9
    Related
    ENSMUSP00000084045.6, ENSMUST00000086835.12
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:903937
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:778887
    PHD_SF; PHD finger superfamily
  2. XM_030249601.1XP_030105461.1  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:948982
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:823932
    PHD_SF; PHD finger superfamily
  3. XM_006523894.3XP_006523957.1  lysine-specific demethylase 4B isoform X4

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:910944
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:785894
    PHD_SF; PHD finger superfamily
  4. XM_006523895.3XP_006523958.1  lysine-specific demethylase 4B isoform X5

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:904938
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:779888
    PHD_SF; PHD finger superfamily
  5. XM_006523898.3XP_006523961.1  lysine-specific demethylase 4B isoform X8

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:897931
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:772881
    PHD_SF; PHD finger superfamily
  6. XM_006523897.3XP_006523960.1  lysine-specific demethylase 4B isoform X7

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:901935
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:776885
    PHD_SF; PHD finger superfamily
  7. XM_030249602.1XP_030105462.1  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:948982
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:823932
    PHD_SF; PHD finger superfamily
  8. XM_030249603.2XP_030105463.1  lysine-specific demethylase 4B isoform X3

    UniProtKB/Swiss-Prot
    Q3UR22, Q6ZQ30, Q91VY5, Q99K42
    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:910944
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:785894
    PHD_SF; PHD finger superfamily
  9. XM_030249604.1XP_030105464.1  lysine-specific demethylase 4B isoform X6

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:903937
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:778887
    PHD_SF; PHD finger superfamily
  10. XM_030249605.1XP_030105465.1  lysine-specific demethylase 4B isoform X7

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:901935
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:776885
    PHD_SF; PHD finger superfamily
  11. XM_017317354.2XP_017172843.1  lysine-specific demethylase 4B isoform X2

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:920954
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:795904
    PHD_SF; PHD finger superfamily
  12. XM_017317353.2XP_017172842.1  lysine-specific demethylase 4B isoform X2

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:920954
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:795904
    PHD_SF; PHD finger superfamily
  13. XM_017317355.2XP_017172844.1  lysine-specific demethylase 4B isoform X9

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:882916
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:757866
    PHD_SF; PHD finger superfamily
  14. XM_017317356.2XP_017172845.1  lysine-specific demethylase 4B isoform X10

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:876910
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:751860
    PHD_SF; PHD finger superfamily
  15. XM_030249606.2XP_030105466.1  lysine-specific demethylase 4B isoform X11

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:875909
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:750859
    PHD_SF; PHD finger superfamily