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

    Gene ID: 23081, updated on 27-Nov-2024

    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; AllianceGenome:HGNC:17071
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See KDM4C in Genome Data Viewer
    Location:
    9p24.1
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (6720863..7175648)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (6715554..7172114)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (6720863..7175648)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28200 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:6707295-6707509 Neighboring gene uncharacterized LOC124902117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28203 Neighboring gene long intergenic non-protein coding RNA 2851 Neighboring gene PRELI domain containing 3B pseudogene 11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28205 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:6756064-6756775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28206 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:6761325-6762007 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6766791-6767436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6767437-6768080 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6771154-6772127 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:6775214-6775806 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6776399-6776990 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:6776991-6777582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6789083-6789798 Neighboring gene SNRPE pseudogene 2 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:6808287-6808846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6834601-6835322 Neighboring gene actin gamma 1 pseudogene 14 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28209 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19772 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:6940065-6940565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:7147699-7148200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:7148201-7148700 Neighboring gene NANOG hESC enhancer GRCh37_chr9:7185598-7186113 Neighboring gene uncharacterized LOC105375969 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:7240589-7241138 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:7284400-7285015 Neighboring gene uncharacterized LOC105375970 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:7319761-7320960 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

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ25668, FLJ25949, KIAA0780

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in 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
    [histone H3]-trimethyl-L-lysine(9) demethylase 4C
    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_016869987.1
    XP_047278982.1
    XP_047278983.1
    XP_047278984.1
    XP_047278985.1
    XP_047278986.1
    XP_054218414.1
    XP_054218415.1
    XP_054218416.1
    XP_054218417.1
    XP_054218418.1
    XP_054218419.1
    XP_054218420.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001146695.4NP_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
      cd15577
      Location:644746
      PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
      pfam02373
      Location:177293
      JmjC; JmjC domain, hydroxylase
      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
      Conserved Domains (4) summary
      cd15577
      Location:666768
      PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
      pfam02373
      Location:199315
      JmjC; JmjC domain, hydroxylase
      cl15840
      Location:3879
      JmjN; jmjN domain
      cl22851
      Location:777830
      PHD_SF; PHD finger superfamily
    3. NM_001304339.4NP_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 (6) summary
      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)
      pfam02373
      Location:177293
      JmjC; JmjC domain, hydroxylase
      cd20465
      Location:879932
      Tudor_JMJD2C_rpt1; first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
      cd20468
      Location:936995
      Tudor_JMJD2C_rpt2; second Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
      cl15840
      Location:1657
      JmjN; jmjN domain
    4. NM_001304340.4NP_001291269.1  lysine-specific demethylase 4C isoform 6

      Status: REVIEWED

      Source sequence(s)
      AL137020, AL161443, AL354707, AL445592, AL513412
      UniProtKB/TrEMBL
      B4E239
      Conserved Domains (5) summary
      cd15577
      Location:389491
      PHD_JMJD2C; PHD finger found in Jumonji domain-containing protein 2C (JMJD2C)
      pfam02373
      Location:1112
      JmjC; JmjC domain, hydroxylase
      cd20465
      Location:624677
      Tudor_JMJD2C_rpt1; first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
      cd20468
      Location:681740
      Tudor_JMJD2C_rpt2; second Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
      cl22851
      Location:500609
      PHD_SF; PHD finger superfamily
    5. NM_001304341.4NP_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_001353997.3NP_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_001353998.3NP_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_001353999.3NP_001340928.1  lysine-specific demethylase 4C isoform 10

      Status: REVIEWED

      Source sequence(s)
      AL137020, AL161443, AL354707, AL445592, AL513412
      UniProtKB/TrEMBL
      C9J879
      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_001354000.3NP_001340929.1  lysine-specific demethylase 4C isoform 11

      Status: REVIEWED

      Source sequence(s)
      AL137020, AL161443, AL354707, AL445592, AL513412
      UniProtKB/TrEMBL
      C9J879
      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_001354001.3NP_001340930.1  lysine-specific demethylase 4C isoform 11

      Status: REVIEWED

      Source sequence(s)
      AL137020, AL161443, AL354707, AL445592, AL513412
      UniProtKB/TrEMBL
      C9J879
      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_015061.6NP_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
      B4E1Y4, B7ZL46, F5H347, F5H7P0, O94877, Q2M3M0, Q5JUC9, Q5VYJ2, Q5VYJ3, Q9H3R0
      Related
      ENSP00000370710.3, ENST00000381309.8
      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_130707.4 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL354707, AL445592, AL513412
      Related
      ENST00000438023.5
    2. NR_148677.3 RNA Sequence

      Status: REVIEWED

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

      Status: REVIEWED

      Source sequence(s)
      AL137020, AL161443, AL354707, AL445592, AL513412
    4. NR_148679.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL137020, AL161443, AL354707, AL445592, AL513412
    5. NR_148680.3 RNA Sequence

      Status: REVIEWED

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

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_017014498.3XP_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
    2. XM_047423029.1XP_047278985.1  lysine-specific demethylase 4C isoform X2

    3. XM_047423028.1XP_047278984.1  lysine-specific demethylase 4C isoform X3

    4. XM_047423027.1XP_047278983.1  lysine-specific demethylase 4C isoform X2

    5. XM_047423026.1XP_047278982.1  lysine-specific demethylase 4C isoform X2

    6. XM_047423030.1XP_047278986.1  lysine-specific demethylase 4C isoform X4

      Related
      ENSP00000405739.2, ENST00000428870.6

    RNA

    1. XR_001746255.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      6715554..7172114
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362439.1XP_054218414.1  lysine-specific demethylase 4C isoform X1

    2. XM_054362445.1XP_054218420.1  lysine-specific demethylase 4C isoform X5

    3. XM_054362443.1XP_054218418.1  lysine-specific demethylase 4C isoform X2

    4. XM_054362442.1XP_054218417.1  lysine-specific demethylase 4C isoform X3

    5. XM_054362441.1XP_054218416.1  lysine-specific demethylase 4C isoform X2

    6. XM_054362440.1XP_054218415.1  lysine-specific demethylase 4C isoform X2

    7. XM_054362444.1XP_054218419.1  lysine-specific demethylase 4C isoform X4

    RNA

    1. XR_008487968.1 RNA Sequence

    2. XR_008487969.1 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.