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KDM4C lysine demethylase 4C [ Homo sapiens (human) ]

Gene ID: 23081, updated on 11-Sep-2019

Summary

Official Symbol
KDM4Cprovided by HGNC
Official Full Name
lysine demethylase 4Cprovided by HGNC
Primary source
HGNC:HGNC:17071
See related
Ensembl:ENSG00000107077 MIM:605469
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GASC1; JHDM3C; JMJD2C; TDRD14C
Summary
This gene is a member of the Jumonji domain 2 (JMJD2) family. The encoded protein is a trimethylation-specific demethylase, and converts specific trimethylated histone residues to the dimethylated form. This enzymatic action regulates gene expression and chromosome segregation. Chromosomal aberrations and changes in expression of this gene may be found in tumor cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
Expression
Ubiquitous expression in lymph node (RPKM 3.4), bone marrow (RPKM 3.3) and 25 other tissues See more
Orthologs

Genomic context

See KDM4C in Genome Data Viewer
Location:
9p24.1
Exon count:
30
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (6720863..7175648)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (6720863..7175648)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L35a pseudogene 20 Neighboring gene long intergenic non-protein coding RNA 2851 Neighboring gene PRELI domain containing 3B pseudogene 11 Neighboring gene small nuclear ribonucleoprotein polypeptide E pseudogene 2 Neighboring gene actin gamma 1 pseudogene 14 Neighboring gene uncharacterized LOC105375969 Neighboring gene uncharacterized LOC105375970 Neighboring gene uncharacterized LOC102723994

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
NHGRI GWA Catalog
Preliminary evidence of genetic determinants of adiponectin response to fenofibrate in the Genetics of Lipid Lowering Drugs and Diet Network.
NHGRI GWA Catalog
Radiation pharmacogenomics: a genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines.
NHGRI GWA Catalog

Pathways from BioSystems

  • Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3, organism-specific biosystem (from REACTOME)
    Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3, organism-specific biosystemPKN1, activated by phosphorylation at threonine T774, binds activated AR (androgen receptor) and promotes transcription from AR-regulated promoters. On one hand, phosphorylated PKN1 promotes the form...
  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Coregulation of Androgen receptor activity, organism-specific biosystem (from Pathway Interaction Database)
    Coregulation of Androgen receptor activity, organism-specific biosystem
    Coregulation of Androgen receptor activity
  • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
    HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
  • RHO GTPase Effectors, organism-specific biosystem (from REACTOME)
    RHO GTPase Effectors, organism-specific biosystemRHO GTPases regulate cell behaviour by activating a number of downstream effectors that regulate cytoskeletal organization, intracellular trafficking and transcription (reviewed by Sahai and Marshall...
  • RHO GTPases activate PKNs, organism-specific biosystem (from REACTOME)
    RHO GTPases activate PKNs, organism-specific biosystemProtein kinases N (PKN), also known as protein kinase C-related kinases (PKR) feature a C-terminal serine/threonine kinase domain and three RHO-binding motifs at the N-terminus. RHO GTPases RHOA, RHO...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Rho GTPases, organism-specific biosystem (from REACTOME)
    Signaling by Rho GTPases, organism-specific biosystemThe Rho family of small guanine nucleotide binding proteins is one of five generally recognized branches of the Ras superfamily. Like most Ras superfamily members, typical Rho proteins function as bi...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ25668, FLJ25949, KIAA0780

Gene Ontology Provided by GOA

Function Evidence Code Pubs
androgen receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone demethylase activity EXP
Inferred from Experiment
more info
PubMed 
histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-K36 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-K36 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-K9 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-K9 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-K9 specific) IMP
Inferred from Mutant Phenotype
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
blastocyst formation IEA
Inferred from Electronic Annotation
more info
 
chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H3-K36 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 demethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of histone H3-K9 trimethylation IEA
Inferred from Electronic Annotation
more info
 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of stem cell differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
histone methyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pericentric heterochromatin IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
lysine-specific demethylase 4C
Names
JmjC domain-containing histone demethylation protein 3C
gene amplified in squamous cell carcinoma 1 protein
jumonji domain-containing protein 2C
lysine (K)-specific demethylase 4C
tudor domain containing 14C
NP_001140167.1
NP_001140168.1
NP_001291268.1
NP_001291269.1
NP_001291270.1
NP_001340926.1
NP_001340927.1
NP_001340928.1
NP_001340929.1
NP_001340930.1
NP_055876.2
XP_011516113.1
XP_016869987.1
XP_016869988.1
XP_016869990.1
XP_016869991.1
XP_016869993.1
XP_024303226.1
XP_024303227.1

NCBI Reference Sequences (RefSeq)

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_001146695.3NP_001140167.1  lysine-specific demethylase 4C isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL354707, AL445592, AL513412
    Consensus CDS
    CCDS55286.1
    UniProtKB/Swiss-Prot
    Q9H3R0
    Related
    ENSP00000445427.1, ENST00000543771.5
    Conserved Domains (4) summary
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:644746
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl15840
    Location:1657
    JmjN; jmjN domain
    cl22851
    Location:755808
    PHD_SF; PHD finger superfamily
  2. NM_001146696.2NP_001140168.1  lysine-specific demethylase 4C isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL354707, AL445592, AL513412
    Consensus CDS
    CCDS55285.1
    UniProtKB/Swiss-Prot
    Q9H3R0
    Related
    ENSP00000440656.3, ENST00000536108.5
    Conserved Domains (4) summary
    pfam02373
    Location:199315
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:666768
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl15840
    Location:3879
    JmjN; jmjN domain
    cl22851
    Location:777830
    PHD_SF; PHD finger superfamily
  3. NM_001304339.3NP_001291268.1  lysine-specific demethylase 4C isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL161443, AL354707, AL445592, AL513412
    Related
    ENSP00000370707.3, ENST00000381306.7
    Conserved Domains (5) summary
    smart00333
    Location:879933
    TUDOR; Tudor domain
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:644746
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cd15715
    Location:755864
    ePHD_JMJD2C; Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl15840
    Location:1657
    JmjN; jmjN domain
  4. NM_001304340.3NP_001291269.1  lysine-specific demethylase 4C isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL161443, AL354707, AL445592, AL513412
    Conserved Domains (4) summary
    smart00333
    Location:624678
    TUDOR; Tudor domain
    pfam02373
    Location:1112
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:389491
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl22851
    Location:500609
    PHD_SF; PHD finger superfamily
  5. NM_001304341.3NP_001291270.1  lysine-specific demethylase 4C isoform 7

    Status: REVIEWED

    Source sequence(s)
    AL354707
    Consensus CDS
    CCDS78379.1
    UniProtKB/TrEMBL
    B0QZ60
    Related
    ENSP00000383990.3, ENST00000401787.7
    Conserved Domains (1) summary
    cl15840
    Location:1657
    JmjN; jmjN domain
  6. NM_001353997.2NP_001340926.1  lysine-specific demethylase 4C isoform 8

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL161443, AL354707, AL445592, AL513412
    Conserved Domains (5) summary
    smart00333
    Location:912966
    TUDOR; Tudor domain
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:644746
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cd15715
    Location:755864
    ePHD_JMJD2C; Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl15840
    Location:1657
    JmjN; jmjN domain
  7. NM_001353998.2NP_001340927.1  lysine-specific demethylase 4C isoform 9

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL354707, AL445592, AL513412
    Conserved Domains (4) summary
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:644746
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl15840
    Location:1657
    JmjN; jmjN domain
    cl22851
    Location:755772
    PHD_SF; PHD finger superfamily
  8. NM_001353999.2NP_001340928.1  lysine-specific demethylase 4C isoform 10

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL161443, AL354707, AL445592, AL513412
    Conserved Domains (3) summary
    smart00333
    Location:475529
    TUDOR; Tudor domain
    cd15577
    Location:207309
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl22851
    Location:318427
    PHD_SF; PHD finger superfamily
  9. NM_001354000.2NP_001340929.1  lysine-specific demethylase 4C isoform 11

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL161443, AL354707, AL445592, AL513412
    Related
    ENSP00000405739.2, ENST00000428870.6
    Conserved Domains (3) summary
    smart00333
    Location:442496
    TUDOR; Tudor domain
    cd15577
    Location:207309
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl22851
    Location:318427
    PHD_SF; PHD finger superfamily
  10. NM_001354001.2NP_001340930.1  lysine-specific demethylase 4C isoform 11

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL161443, AL354707, AL445592, AL513412
    Conserved Domains (3) summary
    smart00333
    Location:442496
    TUDOR; Tudor domain
    cd15577
    Location:207309
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl22851
    Location:318427
    PHD_SF; PHD finger superfamily
  11. NM_015061.5NP_055876.2  lysine-specific demethylase 4C isoform 1

    See identical proteins and their annotated locations for NP_055876.2

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL161443, AL354707, AL445592, AL513412
    Consensus CDS
    CCDS6471.1
    UniProtKB/Swiss-Prot
    Q9H3R0
    Related
    ENSP00000370710.3, ENST00000381309.7
    Conserved Domains (5) summary
    smart00333
    Location:879933
    TUDOR; Tudor domain
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:644746
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cd15715
    Location:755864
    ePHD_JMJD2C; Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl15840
    Location:1657
    JmjN; jmjN domain

RNA

  1. NR_130707.3 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL354707, AL445592, AL513412
    Related
    ENST00000438023.5
  2. NR_148677.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL161443, AL354707, AL445592, AL513412
  3. NR_148678.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL161443, AL354707, AL445592, AL513412
  4. NR_148679.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL161443, AL354707, AL445592, AL513412
  5. NR_148680.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL137020, AL161443, AL354707, AL445592, AL513412

RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    6720863..7175648
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447459.1XP_024303227.1  lysine-specific demethylase 4C isoform X7

    Conserved Domains (3) summary
    smart00333
    Location:442496
    TUDOR; Tudor domain
    cd15577
    Location:207309
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl22851
    Location:318427
    PHD_SF; PHD finger superfamily
  2. XM_017014499.2XP_016869988.1  lysine-specific demethylase 4C isoform X2

    Conserved Domains (4) summary
    smart00333
    Location:772826
    TUDOR; Tudor domain
    pfam02373
    Location:37153
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:504606
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cd15715
    Location:615724
    ePHD_JMJD2C; Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
  3. XM_011517811.3XP_011516113.1  lysine-specific demethylase 4C isoform X3

    See identical proteins and their annotated locations for XP_011516113.1

    Conserved Domains (4) summary
    smart00333
    Location:731785
    TUDOR; Tudor domain
    pfam02373
    Location:1112
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:463565
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl22851
    Location:574683
    PHD_SF; PHD finger superfamily
  4. XM_024447458.1XP_024303226.1  lysine-specific demethylase 4C isoform X2

    Conserved Domains (4) summary
    smart00333
    Location:772826
    TUDOR; Tudor domain
    pfam02373
    Location:37153
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:504606
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cd15715
    Location:615724
    ePHD_JMJD2C; Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
  5. XM_017014501.2XP_016869990.1  lysine-specific demethylase 4C isoform X4

  6. XM_017014498.2XP_016869987.1  lysine-specific demethylase 4C isoform X1

    Conserved Domains (5) summary
    smart00333
    Location:878933
    TUDOR; Tudor domain
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:644746
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cd15715
    Location:755864
    ePHD_JMJD2C; Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl15840
    Location:1657
    JmjN; jmjN domain
  7. XM_017014502.2XP_016869991.1  lysine-specific demethylase 4C isoform X5

  8. XM_017014504.2XP_016869993.1  lysine-specific demethylase 4C isoform X6

    Conserved Domains (3) summary
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:644746
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl15840
    Location:1657
    JmjN; jmjN domain

RNA

  1. XR_001746252.2 RNA Sequence

  2. XR_001746255.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001146694.1: Suppressed sequence

    Description
    NM_001146694.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Support Center