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    KDM5C lysine demethylase 5C [ Bos taurus (cattle) ]

    Gene ID: 281490, updated on 6-Jun-2024

    Summary

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    Official Symbol
    KDM5Cprovided by VGNC
    Official Full Name
    lysine demethylase 5Cprovided by VGNC
    Primary source
    VGNC:VGNC:49972
    See related
    BGD:BT14589; Ensembl:ENSBTAG00000014943
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Bos taurus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae; Bovinae; Bos
    Also known as
    SMCX; JARID1C
    Orthologs
    human mouse all
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    Genomic context

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    See KDM5C in Genome Data Viewer
    Location:
    chromosome: X
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2023_09 current ARS-UCD2.0 (GCF_002263795.3) X NC_037357.1 (90644122..90675135, complement)

    Chromosome X - NC_037357.1Genomic Context describing neighboring genes Neighboring gene palmitoyltransferase ZDHHC3-like Neighboring gene TSPY like 2 Neighboring gene KANTR integral membrane protein Neighboring gene IQ motif and Sec7 domain ArfGEF 2 Neighboring gene small ribosomal subunit protein uS2-like

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_037357.1 Chromosome X Reference ARS-UCD2.0 Primary Assembly

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. A whole-genome assembly of the domestic cow, Bos taurus. Zimin AV, et al. Genome Biol, 2009. PMID 19393038, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables histone demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lysine-specific demethylase 5C
    Names
    Smcx homolog, X chromosome
    jumonji, AT rich interactive domain 1C
    NP_776610.2
    XP_005228256.1
    XP_005228258.1
    XP_010820283.1
    XP_024843522.1
    XP_024843523.1
    XP_024843524.1
    XP_024843525.1
    XP_024843526.1
    XP_024843527.1
    XP_024843528.1
    XP_024843529.1
    XP_024843530.1
    XP_059739257.1

    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)

    1. NM_174185.3 → NP_776610.2  lysine-specific demethylase 5C

      Status: VALIDATED

      Source sequence(s)
      NKLS02000030
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:501 → 617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326 → 371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707 → 759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:772 → 1098
      PLU-1; PLU-1-like protein
      cl22851
      Location:1187 → 1247
      PHD_SF; PHD finger superfamily

    RefSeqs of Annotated Genomes: GCF_002263795.3-RS_2023_09

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

    Reference ARS-UCD2.0 Primary Assembly

    Genomic

    1. NC_037357.1 Reference ARS-UCD2.0 Primary Assembly

      Range
      90644122..90675135 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005228201.5 → XP_005228258.1  lysine-specific demethylase 5C isoform X10

      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      smart01014
      Location:25 → 124
      ARID; ARID/BRIGHT DNA binding domain
      pfam02373
      Location:460 → 576
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:285 → 330
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:666 → 718
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:731 → 1057
      PLU-1; PLU-1-like protein
      cl22851
      Location:1146 → 1206
      PHD_SF; PHD finger superfamily

    2. XM_010821981.4 → XP_010820283.1  lysine-specific demethylase 5C isoform X9

      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      smart01014
      Location:25 → 124
      ARID; ARID/BRIGHT DNA binding domain
      pfam02373
      Location:460 → 576
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:285 → 330
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:666 → 718
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:731 → 1057
      PLU-1; PLU-1-like protein
      cl22851
      Location:1146 → 1206
      PHD_SF; PHD finger superfamily

    3. XM_024987760.2 → XP_024843528.1  lysine-specific demethylase 5C isoform X8

      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:500 → 616
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:325 → 370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:706 → 758
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:771 → 1097
      PLU-1; PLU-1-like protein
      cl22851
      Location:1186 → 1246
      PHD_SF; PHD finger superfamily

    4. XM_024987759.2 → XP_024843527.1  lysine-specific demethylase 5C isoform X7

      Conserved Domains (8) summary
      smart00501
      Location:80 → 170
      BRIGHT; ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:500 → 616
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:325 → 370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:706 → 758
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:771 → 1097
      PLU-1; PLU-1-like protein
      cl22851
      Location:1186 → 1246
      PHD_SF; PHD finger superfamily
      cl25642
      Location:1290 → 1426
      DUF390; Protein of unknown function (DUF390)

    5. XM_005228199.4 → XP_005228256.1  lysine-specific demethylase 5C isoform X6

      See identical proteins and their annotated locations for XP_005228256.1

      UniProtKB/TrEMBL
      F1MYV2
      Related
      ENSBTAP00000019893.6, ENSBTAT00000019893.7
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:501 → 617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326 → 371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707 → 759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:772 → 1098
      PLU-1; PLU-1-like protein
      cl22851
      Location:1187 → 1247
      PHD_SF; PHD finger superfamily

    6. XM_024987755.2 → XP_024843523.1  lysine-specific demethylase 5C isoform X2

      Conserved Domains (8) summary
      smart00501
      Location:132 → 222
      BRIGHT; ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:552 → 668
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:377 → 422
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:758 → 810
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:823 → 1149
      PLU-1; PLU-1-like protein
      cl22851
      Location:1238 → 1298
      PHD_SF; PHD finger superfamily
      cl25642
      Location:1342 → 1478
      DUF390; Protein of unknown function (DUF390)

    7. XM_059883274.1 → XP_059739257.1  lysine-specific demethylase 5C isoform X13

    8. XM_024987762.2 → XP_024843530.1  lysine-specific demethylase 5C isoform X12

      Conserved Domains (8) summary
      smart00501
      Location:132 → 222
      BRIGHT; ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:378 → 423
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:551 → 603
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:616 → 942
      PLU-1; PLU-1-like protein
      cl21464
      Location:427 → 461
      cupin_like; Conserved domain found in cupin and related proteins
      cl22851
      Location:1031 → 1091
      PHD_SF; PHD finger superfamily
      cl25642
      Location:1135 → 1271
      DUF390; Protein of unknown function (DUF390)

    9. XM_024987758.2 → XP_024843526.1  lysine-specific demethylase 5C isoform X5

      Conserved Domains (7) summary
      smart00501
      Location:132 → 222
      BRIGHT; ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:553 → 669
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:378 → 423
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:759 → 811
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:824 → 1150
      PLU-1; PLU-1-like protein
      cl22851
      Location:1239 → 1299
      PHD_SF; PHD finger superfamily

    10. XM_024987756.2 → XP_024843524.1  lysine-specific demethylase 5C isoform X3

      Conserved Domains (7) summary
      smart00501
      Location:132 → 222
      BRIGHT; ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:553 → 669
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:378 → 423
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:759 → 811
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:824 → 1150
      PLU-1; PLU-1-like protein
      cl22851
      Location:1239 → 1299
      PHD_SF; PHD finger superfamily

    11. XM_024987757.2 → XP_024843525.1  lysine-specific demethylase 5C isoform X4

      Conserved Domains (7) summary
      smart00501
      Location:132 → 222
      BRIGHT; ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:553 → 669
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:378 → 423
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:759 → 811
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:824 → 1150
      PLU-1; PLU-1-like protein
      cl22851
      Location:1239 → 1299
      PHD_SF; PHD finger superfamily

    12. XM_024987754.2 → XP_024843522.1  lysine-specific demethylase 5C isoform X1

      Conserved Domains (8) summary
      smart00501
      Location:132 → 222
      BRIGHT; ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:553 → 669
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:378 → 423
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:759 → 811
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:824 → 1150
      PLU-1; PLU-1-like protein
      cl22851
      Location:1239 → 1299
      PHD_SF; PHD finger superfamily
      cl25642
      Location:1343 → 1479
      DUF390; Protein of unknown function (DUF390)

    13. XM_024987761.2 → XP_024843529.1  lysine-specific demethylase 5C isoform X11

      Conserved Domains (7) summary
      smart00501
      Location:26 → 116
      BRIGHT; ARID (A/T-rich interaction domain) domain
      pfam02373
      Location:447 → 563
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:272 → 317
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:653 → 705
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:718 → 1044
      PLU-1; PLU-1-like protein
      cl22851
      Location:1133 → 1193
      PHD_SF; PHD finger superfamily
      cl25642
      Location:1237 → 1373
      DUF390; Protein of unknown function (DUF390)
    Nucleotide Protein Strain
    Heading Accession and Version

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