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

Gene ID: 23081, updated on 8-May-2016
Official Symbol
KDM4Cprovided by HGNC
Official Full Name
lysine demethylase 4Cprovided by HGNC
Primary source
HGNC:HGNC:17071
See related
Ensembl:ENSG00000107077 Ensembl:ENSG00000274527 Ensembl:ENSG00000282960 HPRD:12016; MIM:605469; Vega:OTTHUMG00000019536; Vega:OTTHUMG00000187508
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]
Orthologs
Location:
9p24.1
Exon count:
32
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 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 uncharacterized LOC105375968 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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
  • 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...
Products Interactant Other Gene Complex Source Pubs Description

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 
dioxygenase activity 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 TAS
Traceable Author Statement
more info
 
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 IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
histone H3-K9 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 demethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
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_055876.2

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

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks multiple 3' coding exons and contains an alternate 3' terminal exon, resulting in a different 3' coding region and 3' UTR, compared to variant 1. The resulting protein (isoform 3) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK304032, AK310439, AL137020, BC060771, BC104859, BX111090
    Consensus CDS
    CCDS55286.1
    UniProtKB/Swiss-Prot
    Q9H3R0
    Related
    ENSP00000445427, OTTHUMP00000275274, ENST00000543771, OTTHUMT00000475168
    Conserved Domains (4) summary
    pfam02375
    Location:1751
    JmjN; jmjN domain
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:644746
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl22851
    Location:755808
    PHD_SF; PHD finger superfamily
  2. NM_001146696.1NP_001140168.1  lysine-specific demethylase 4C isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains multiple differences in the 5' and 3' regions compared to variant 1, including initiation of translation at an alternate start codon. The resulting protein (isoform 4) has a longer N-terminus, a distinct C-terminus, and is shorter than isoform 1.
    Source sequence(s)
    AK310439, AL137020, BC104859, BX111090
    Consensus CDS
    CCDS55285.1
    UniProtKB/Swiss-Prot
    Q9H3R0
    Related
    ENSP00000442382, ENST00000535193
    Conserved Domains (4) summary
    pfam02375
    Location:3973
    JmjN; jmjN domain
    pfam02373
    Location:199315
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:666768
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl22851
    Location:777830
    PHD_SF; PHD finger superfamily
  3. NM_001304339.1NP_001291268.1  lysine-specific demethylase 4C isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The resulting protein (isoform 5) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AI017056, AK296401, AK314355, AL137020, AL513412, BC060771
    UniProtKB/TrEMBL
    B7Z3V6
    Related
    ENSP00000370707, OTTHUMP00000021053, ENST00000381306, OTTHUMT00000051693
    Conserved Domains (5) summary
    pfam02375
    Location:1751
    JmjN; jmjN domain
    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)
  4. NM_001304340.1NP_001291269.1  lysine-specific demethylase 4C isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains multiple differences in the coding region, compared to variant 1, including initiation of translation at a downstream start codon. The resulting protein (isoform 6) is shorter than isoform 1.
    Source sequence(s)
    AI017056, AK296401, AK304095, AL513412, BC060771
    UniProtKB/TrEMBL
    B4E239, B7Z3V6
    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_001304341.1NP_001291270.1  lysine-specific demethylase 4C isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks multiple 3' coding exons and its transcription extends past a splice site used in variant 1, resulting in a different 3' coding region and 3' UTR. The resulting protein (isoform 7) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    BC053678, BC060771
    Consensus CDS
    CCDS78379.1
    UniProtKB/TrEMBL
    B0QZ60
    Related
    ENSP00000383990, OTTHUMP00000197650, ENST00000401787, OTTHUMT00000318592
    Conserved Domains (1) summary
    cl15840
    Location:1657
    JmjN; jmjN domain
  6. NM_015061.3NP_055876.2  lysine-specific demethylase 4C isoform 1

    See identical proteins and their annotated locations for NP_055876.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AI017056, AK296401, AK303651, BC060771, BC104861
    Consensus CDS
    CCDS6471.1
    UniProtKB/Swiss-Prot
    Q9H3R0
    UniProtKB/TrEMBL
    B4E142, B7Z3V6
    Related
    ENSP00000370710, OTTHUMP00000021052, ENST00000381309, OTTHUMT00000051692
    Conserved Domains (5) summary
    pfam02375
    Location:1751
    JmjN; jmjN domain
    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)

RNA

  1. NR_130707.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) contains multiple differences in the internal exons and differs at the 3' end, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI969877, AL513412, BC060771, BC104859, BX645680
    Related
    ENST00000438023, OTTHUMT00000318593

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p2 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011517810.1XP_011516112.1  

    See identical proteins and their annotated locations for XP_011516112.1

    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
  2. XM_011517811.1XP_011516113.1  

    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
  3. XM_006716741.1XP_006716804.1  

    See identical proteins and their annotated locations for XP_006716804.1

    Conserved Domains (5) summary
    pfam02375
    Location:1751
    JmjN; jmjN domain
    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)
  4. XM_011517808.1XP_011516110.1  

    See identical proteins and their annotated locations for XP_011516110.1

    Conserved Domains (5) summary
    pfam02375
    Location:1751
    JmjN; jmjN domain
    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)
  5. XM_011517809.1XP_011516111.1  

    Conserved Domains (5) summary
    pfam02375
    Location:1751
    JmjN; jmjN domain
    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)
  6. XM_011517815.1XP_011516117.1  

    Conserved Domains (3) summary
    pfam02375
    Location:1751
    JmjN; jmjN domain
    pfam02373
    Location:177293
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:644746
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
  7. XM_011517812.1XP_011516114.1  

    Conserved Domains (4) summary
    smart00333
    Location:714768
    TUDOR; Tudor domain
    pfam02373
    Location:1395
    JmjC; JmjC domain, hydroxylase
    cd15577
    Location:446548
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl22851
    Location:557666
    PHD_SF; PHD finger superfamily
  8. XM_011517814.1XP_011516116.1  

    Conserved Domains (4) summary
    smart00333
    Location:669723
    TUDOR; Tudor domain
    cd15577
    Location:401503
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl22851
    Location:512621
    PHD_SF; PHD finger superfamily
    cl22893
    Location:150
    JmjC; JmjC domain, hydroxylase
  9. XM_011517816.1XP_011516118.1  

    Related
    ENSP00000405739, OTTHUMP00000275228, ENST00000428870, OTTHUMT00000475042
    Conserved Domains (3) summary
    smart00333
    Location:599653
    TUDOR; Tudor domain
    cd15577
    Location:331433
    PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
    cl22851
    Location:442551
    PHD_SF; PHD finger superfamily

RNA

  1. XR_929221.1 RNA Sequence

  2. XR_929223.1 RNA Sequence

  3. XR_929222.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018920.2 Alternate CHM1_1.1

    Range
    6721531..7175696
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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.