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

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: human all
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Genomic context

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_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

KDM4C promotes mouse hippocampal neural stem cell proliferation through modulating ApoE expression.
Title: KDM4C promotes mouse hippocampal neural stem cell proliferation through modulating ApoE expression.
The histone demethylase JMJD2C constitutes a novel NFE2 target gene that is required for the survival of JAK2[V617F] mutated cells.
Title: The histone demethylase JMJD2C constitutes a novel NFE2 target gene that is required for the survival of JAK2(V617F) mutated cells.
Essential Roles of the Histone Demethylase KDM4C in Renal Development and Acute Kidney Injury.
Title: Essential Roles of the Histone Demethylase KDM4C in Renal Development and Acute Kidney Injury.
Targeting KDM4C enhances CD8(+) T cell mediated antitumor immunity by activating chemokine CXCL10 transcription in lung cancer.
Title: Targeting KDM4C enhances CD8(+) T cell mediated antitumor immunity by activating chemokine CXCL10 transcription in lung cancer.
Interplay among H3K9-editing enzymes SUV39H1, JMJD2C and SRC-1 drives p66Shc transcription and vascular oxidative stress in obesity.
Title: Interplay among H3K9-editing enzymes SUV39H1, JMJD2C and SRC-1 drives p66Shc transcription and vascular oxidative stress in obesity.
KDM4 knockdown resulted in the down-regulation of miR-29 expression.
Title: The histone demethylase Kdm4 suppresses activation of hepatic stellate cell by inducing MiR-29 transcription.
LSD1 and JMJD2C disable oncogenic Ras- or Braf-induced senescence by enabling the expression of E2F target genes
Title: Targeting the Senescence-Overriding Cooperative Activity of Structurally Unrelated H3K9 Demethylases in Melanoma.
Jmjd2c and G9a are novel enhancer-associated factors; Jmjd2c is a molecular scaffold for the assembly of essential enhancer-protein complexes with an impact on timely gene activation
Title: Jmjd2c facilitates the assembly of essential enhancer-protein complexes at the onset of embryonic stem cell differentiation.
The authors show that Jmjd2a and Jmjd2c both localize to H3K4me3-positive promoters, where they have widespread and redundant roles in preventing accumulation of H3K9me3 and H3K36me3.
Title: Continual removal of H3K9 promoter methylation by Jmjd2 demethylases is vital for ESC self-renewal and early development.
Number of GFAP-positive astrocytes in the brain of Gasc1 hypomorphic mutant mice is increased at 2-3 months of age.
Title: Increase in GFAP-positive astrocytes in histone demethylase GASC1/KDM4C/JMJD2C hypomorphic mutant mice.

Submit: New GeneRIF Correction See all GeneRIFs (19)

Variation

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Alleles

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

Gene trapped (1) 1 citation
Targeted (5) 1 citation
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Kdm4c (e-PCR), detects polymorphism
- UniSTS:530699

D10Mit157.2 (e-PCR), detects polymorphism
- UniSTS:126061

Rara (e-PCR), detects polymorphism
- UniSTS:144323

RH124430 (e-PCR)
- UniSTS:161252

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

Process	Evidence Code	Pubs
involved_in androgen receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within blastocyst formation	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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
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
acts_upstream_of_or_within regulation of stem cell differentiation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within stem cell population maintenance	IGI Inferred from Genetic Interaction more info	PubMed

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

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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

EC 1.14.11.66

NP_001343490.1

EC 1.14.11.66

NP_659036.1

EC 1.14.11.66

XP_006538414.1

EC 1.14.11.66

XP_006538415.1

EC 1.14.11.66

XP_030109752.1

EC 1.14.11.66

XP_030109753.1

EC 1.14.11.66

XP_036020428.1

EC 1.14.11.66

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)

NM_001172095.1 → NP_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:892 → 948

TUDOR; Tudor domain

pfam02373
Location:194 → 310

JmjC; JmjC domain, hydroxylase

cl15840
Location:33 → 74

JmjN; jmjN domain

cl22851
Location:770 → 879

PHD_SF; PHD finger superfamily
NM_001356561.1 → NP_001343490.1 lysine-specific demethylase 4C isoform 3

Status: VALIDATED

Source sequence(s)

AK042792, AK173023, BF019842

Conserved Domains (3) summary

pfam02373
Location:102 → 218

JmjC; JmjC domain, hydroxylase

pfam18104
Location:805 → 839

Tudor_2; Jumonji domain-containing protein 2A Tudor domain

cl22851
Location:678 → 787

PHD_SF; PHD finger superfamily
NM_144787.2 → NP_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:753 → 862

ePHD_JMJD2C; Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)

pfam02373
Location:177 → 293

JmjC; JmjC domain, hydroxylase

pfam18104
Location:880 → 914

Tudor_2; Jumonji domain-containing protein 2A Tudor domain

cl15840
Location:16 → 57

JmjN; jmjN domain

cl22851
Location:643 → 744

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

NC_000070.7 Reference GRCm39 C57BL/6J

Range

74160734..74324101

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (4) summary

pfam02373
Location:177 → 293

JmjC; JmjC domain, hydroxylase

cl02573
Location:877 → 925

Tudor_SF; Tudor domain superfamily

cl15840
Location:16 → 57

JmjN; jmjN domain

cl22851
Location:753 → 862

PHD_SF; PHD finger superfamily
XM_030253892.1 → XP_030109752.1 lysine-specific demethylase 4C isoform X4

Conserved Domains (3) summary

pfam02373
Location:1 → 112

JmjC; JmjC domain, hydroxylase

pfam18104
Location:699 → 733

Tudor_2; Jumonji domain-containing protein 2A Tudor domain

cl22851
Location:572 → 681

PHD_SF; PHD finger superfamily
XM_030253893.1 → XP_030109753.1 lysine-specific demethylase 4C isoform X4

Conserved Domains (3) summary

pfam02373
Location:1 → 112

JmjC; JmjC domain, hydroxylase

pfam18104
Location:699 → 733

Tudor_2; Jumonji domain-containing protein 2A Tudor domain

cl22851
Location:572 → 681

PHD_SF; PHD finger superfamily
XM_006538352.5 → XP_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:753 → 862

ePHD_JMJD2C; Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)

pfam02373
Location:177 → 293

JmjC; JmjC domain, hydroxylase

pfam18104
Location:880 → 914

Tudor_2; Jumonji domain-containing protein 2A Tudor domain

cl15840
Location:16 → 57

JmjN; jmjN domain

cl22851
Location:643 → 744

PHD_SF; PHD finger superfamily
XM_006538351.2 → XP_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:102 → 218

JmjC; JmjC domain, hydroxylase

pfam18104
Location:805 → 839

Tudor_2; Jumonji domain-containing protein 2A Tudor domain

cl22851
Location:678 → 787

PHD_SF; PHD finger superfamily