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Kdm4c lysine (K)-specific demethylase 4C [ Mus musculus (house mouse) ]

Gene ID: 76804, updated on 9-May-2024

Summary

Official Symbol
Kdm4cprovided by MGI
Official Full Name
lysine (K)-specific demethylase 4Cprovided by MGI
Primary source
MGI:MGI:1924054
See related
Ensembl:ENSMUSG00000028397 AllianceGenome:MGI:1924054
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
Gasc1; Jmjd2c; 2410141F18Rik
Summary
Enables androgen receptor binding activity; enzyme binding activity; and histone demethylase activity. Acts upstream of or within several processes, including blastocyst formation; histone H3-K9 demethylation; and negative regulation of histone H3-K9 trimethylation. Located in pericentric heterochromatin. Is expressed in early conceptus; eye; genitourinary system; hippocampus; and rib. Human ortholog(s) of this gene implicated in autistic disorder; breast cancer; carcinoma (multiple); head and neck cancer; and withdrawal disorder. Orthologous to human KDM4C (lysine demethylase 4C). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bladder adult (RPKM 3.8), CNS E18 (RPKM 3.7) and 26 other tissues See more
Orthologs
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Genomic context

See Kdm4c in Genome Data Viewer
Location:
4 C3; 4 36.06 cM
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (74160734..74324101)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (74242497..74405864)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene FERM domain containing 3 Neighboring gene ribosomal protein L7A pseudogene Neighboring gene STARR-seq mESC enhancer starr_10543 Neighboring gene STARR-seq mESC enhancer starr_10544 Neighboring gene zinc finger protein 384 pseudogene Neighboring gene STARR-positive B cell enhancer mm9_chr4:73965324-73965624 Neighboring gene STARR-seq mESC enhancer starr_10545 Neighboring gene predicted gene, 26379 Neighboring gene predicted gene 11254

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

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables H3K9me3 modified histone binding ISO
Inferred from Sequence Orthology
more info
 
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables enzyme binding ISO
Inferred from Sequence Orthology
more info
 
enables histone H3K36 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
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
 
contributes_to histone H3K9me2/H3K9me3 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 histone demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables nuclear androgen receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables nuclear androgen receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables nuclear receptor coactivator activity ISO
Inferred from Sequence Orthology
more info
 
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
 
enables zinc ion binding ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of chromatin ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of pericentric heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
lysine-specific demethylase 4C
Names
[histone H3]-trimethyl-L-lysine(9) demethylase 4C
gene amplified in squamous cell carcinoma 1
jmjC domain-containing histone demethylation protein 3C
jumonji domain containing 2C
jumonji domain-containing protein 2C
NP_001165566.1
NP_001343490.1
NP_659036.1
XP_006538414.1
XP_006538415.1
XP_030109752.1
XP_030109753.1
XP_036020428.1

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_001172095.1NP_001165566.1  lysine-specific demethylase 4C isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR and uses an upstream start codon, compared to variant 1. The resulting isoform (2) has a longer N-terminus, compared to isoform 1.
    Source sequence(s)
    BC042424, BF019842
    UniProtKB/Swiss-Prot
    Q8VCD7
    Conserved Domains (4) summary
    smart00333
    Location:892948
    TUDOR; Tudor domain
    pfam02373
    Location:194310
    JmjC; JmjC domain, hydroxylase
    cl15840
    Location:3374
    JmjN; jmjN domain
    cl22851
    Location:770879
    PHD_SF; PHD finger superfamily
  2. NM_001356561.1NP_001343490.1  lysine-specific demethylase 4C isoform 3

    Status: VALIDATED

    Source sequence(s)
    AK042792, AK173023, BF019842
    Conserved Domains (3) summary
    pfam02373
    Location:102218
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:805839
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:678787
    PHD_SF; PHD finger superfamily
  3. NM_144787.2NP_659036.1  lysine-specific demethylase 4C isoform 1

    See identical proteins and their annotated locations for NP_659036.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript but encodes the shorter isoform (1).
    Source sequence(s)
    AK173023, BF019842
    Consensus CDS
    CCDS18287.1
    UniProtKB/Swiss-Prot
    Q3UNP7, Q69ZZ5, Q8BUY6, Q8BWA1, Q8VCD7
    UniProtKB/TrEMBL
    A2BEG5
    Related
    ENSMUSP00000030102.6, ENSMUST00000030102.12
    Conserved Domains (5) summary
    cd15715
    Location:753862
    ePHD_JMJD2C; Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:880914
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl15840
    Location:1657
    JmjN; jmjN domain
    cl22851
    Location:643744
    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_000070.7 Reference GRCm39 C57BL/6J

    Range
    74160734..74324101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036164535.1XP_036020428.1  lysine-specific demethylase 4C isoform X3

    Conserved Domains (4) summary
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    cl02573
    Location:877925
    Tudor_SF; Tudor domain superfamily
    cl15840
    Location:1657
    JmjN; jmjN domain
    cl22851
    Location:753862
    PHD_SF; PHD finger superfamily
  2. XM_030253892.1XP_030109752.1  lysine-specific demethylase 4C isoform X4

    Conserved Domains (3) summary
    pfam02373
    Location:1112
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:699733
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:572681
    PHD_SF; PHD finger superfamily
  3. XM_030253893.1XP_030109753.1  lysine-specific demethylase 4C isoform X4

    Conserved Domains (3) summary
    pfam02373
    Location:1112
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:699733
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:572681
    PHD_SF; PHD finger superfamily
  4. XM_006538352.5XP_006538415.1  lysine-specific demethylase 4C isoform X2

    See identical proteins and their annotated locations for XP_006538415.1

    UniProtKB/Swiss-Prot
    Q3UNP7, Q69ZZ5, Q8BUY6, Q8BWA1, Q8VCD7
    UniProtKB/TrEMBL
    A2BEG5
    Conserved Domains (5) summary
    cd15715
    Location:753862
    ePHD_JMJD2C; Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:880914
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl15840
    Location:1657
    JmjN; jmjN domain
    cl22851
    Location:643744
    PHD_SF; PHD finger superfamily
  5. XM_006538351.2XP_006538414.1  lysine-specific demethylase 4C isoform X1

    See identical proteins and their annotated locations for XP_006538414.1

    Conserved Domains (3) summary
    pfam02373
    Location:102218
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:805839
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:678787
    PHD_SF; PHD finger superfamily

RNA

  1. XR_004942008.1 RNA Sequence