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    Kdm5c lysine (K)-specific demethylase 5C [ Mus musculus (house mouse) ]

    Gene ID: 20591, updated on 2-Oct-2018

    Summary

    Official Symbol
    Kdm5cprovided by MGI
    Official Full Name
    lysine (K)-specific demethylase 5Cprovided by MGI
    Primary source
    MGI:MGI:99781
    See related
    Ensembl:ENSMUSG00000025332 Vega:OTTMUSG00000017219
    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
    Smcx; Jarid1c; mKIAA0234; D930009K15Rik
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 13.0), ovary adult (RPKM 12.8) and 28 other tissues See more
    Orthologs

    Genomic context

    See Kdm5c in Genome Data Viewer
    Location:
    X F3; X 68.46 cM
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) X NC_000086.7 (152233197..152279102)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) X NC_000086.6 (148667773..148708897)

    Chromosome X - NC_000086.7Genomic Context describing neighboring genes Neighboring gene predicted gene 15266 Neighboring gene IQ motif and Sec7 domain 2 Neighboring gene Kdm5c adjacent non-coding transcript Neighboring gene TSPY-like 2

    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 FunctionsWhat's a GeneRIF?

    Variation

    Alleles

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

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    RNA polymerase II transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    histone demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    histone demethylase activity (H3-K4 specific) ISO
    Inferred from Sequence Orthology
    more info
     
    histone demethylase activity (H3-trimethyl-K4 specific) IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    methylated histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
     
    zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    histone H3-K4 demethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone H3-K4 demethylation ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    oxidation-reduction process IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of circadian rhythm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    rhythmic process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    histone methyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    lysine-specific demethylase 5C
    Names
    histone demethylase JARID1C
    jumonji, AT rich interactive domain 1C (Rbp2 like)
    jumonji/ARID domain-containing protein 1C
    selected mouse cDNA on the X

    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_013668.4NP_038696.2  lysine-specific demethylase 5C

      Status: VALIDATED

      Source sequence(s)
      AC083816, AI553515, AK150152, AK155651, BC043096
      Consensus CDS
      CCDS41178.1
      UniProtKB/Swiss-Prot
      P41230
      Related
      ENSMUSP00000108207.2, OTTMUSP00000018727, ENSMUST00000112588.8, OTTMUST00000041691
      Conserved Domains (7) summary
      smart00501
      Location:80170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:501617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7721098
      PLU-1; PLU-1-like protein
      cl22851
      Location:11871247
      PHD_SF; PHD finger superfamily

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000086.7 Reference GRCm38.p4 C57BL/6J

      Range
      152233197..152279102
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006528769.3XP_006528832.1  lysine-specific demethylase 5C isoform X1

      See identical proteins and their annotated locations for XP_006528832.1

      UniProtKB/Swiss-Prot
      P41230
      Related
      ENSMUSP00000108203.1, OTTMUSP00000018728, ENSMUST00000112584.7, OTTMUST00000041692
      Conserved Domains (7) summary
      smart00501
      Location:80170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:501617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7721098
      PLU-1; PLU-1-like protein
      cl22851
      Location:11871247
      PHD_SF; PHD finger superfamily
    2. XM_006528773.3XP_006528836.1  lysine-specific demethylase 5C isoform X6

      Conserved Domains (7) summary
      smart00501
      Location:80170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:501617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7721098
      PLU-1; PLU-1-like protein
      cl22851
      Location:11411201
      PHD_SF; PHD finger superfamily
    3. XM_017318443.1XP_017173932.1  lysine-specific demethylase 5C isoform X7

    4. XM_006528770.3XP_006528833.1  lysine-specific demethylase 5C isoform X2

      Conserved Domains (7) summary
      smart00501
      Location:80170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:500616
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:325370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:706758
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7711097
      PLU-1; PLU-1-like protein
      cl22851
      Location:11861246
      PHD_SF; PHD finger superfamily
    5. XM_017318442.1XP_017173931.1  lysine-specific demethylase 5C isoform X3

    6. XM_006528771.3XP_006528834.1  lysine-specific demethylase 5C isoform X4

      Conserved Domains (7) summary
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      smart01014
      Location:25124
      ARID; ARID/BRIGHT DNA binding domain
      pfam02373
      Location:460576
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:285330
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:666718
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7311057
      PLU-1; PLU-1-like protein
      cl22851
      Location:11461206
      PHD_SF; PHD finger superfamily
    7. XM_006528774.3XP_006528837.1  lysine-specific demethylase 5C isoform X8

      Conserved Domains (7) summary
      smart00501
      Location:80170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:501617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7721098
      PLU-1; PLU-1-like protein
      cl22851
      Location:11871247
      PHD_SF; PHD finger superfamily
    8. XM_006528772.3XP_006528835.1  lysine-specific demethylase 5C isoform X5

      See identical proteins and their annotated locations for XP_006528835.1

      UniProtKB/Swiss-Prot
      P41230
      Related
      ENSMUSP00000080814.6, OTTMUSP00000018729, ENSMUST00000082177.12, OTTMUST00000041694
      Conserved Domains (7) summary
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      smart01014
      Location:25124
      ARID; ARID/BRIGHT DNA binding domain
      pfam02373
      Location:460576
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:285330
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:666718
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7311057
      PLU-1; PLU-1-like protein
      cl22851
      Location:11461206
      PHD_SF; PHD finger superfamily
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