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    KDM5B lysine demethylase 5B [ Bos taurus (domestic cattle) ]

    Gene ID: 540633, updated on 10-Oct-2024

    Summary

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    Official Symbol
    KDM5Bprovided by VGNC
    Official Full Name
    lysine demethylase 5Bprovided by VGNC
    Primary source
    VGNC:VGNC:30531
    See related
    BGD:BT22811; Ensembl:ENSBTAG00000006175
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Bos taurus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae; Bovinae; Bos
    Also known as
    JARID1B
    Orthologs
    human mouse all
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    Genomic context

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    See KDM5B in Genome Data Viewer
    Location:
    chromosome: 16
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2023_09 current ARS-UCD2.0 (GCF_002263795.3) 16 NC_037343.1 (79949956..80023619)

    Chromosome 16 - NC_037343.1Genomic Context describing neighboring genes Neighboring gene RAB interacting factor Neighboring gene alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase-like protein MGAT4E Neighboring gene uncharacterized LOC132342411 Neighboring gene microRNA mir-10180

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_037343.1 Chromosome 16 Reference ARS-UCD2.0 Primary Assembly

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Spatiotemporal expression of DNA demethylation enzymes and histone demethylases in bovine embryos. Pagé-Larivière F, et al. Cell Reprogram, 2014 Feb. PMID 24459992
    2. A whole-genome assembly of the domestic cow, Bos taurus. Zimin AV, et al. Genome Biol, 2009. PMID 19393038, Free PMC Article
    3. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
    4. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, 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 5B
    Names
    jumonji, AT rich interactive domain 1B

    NCBI Reference Sequences (RefSeq)

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    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_037343.1 Reference ARS-UCD2.0 Primary Assembly

      Range
      79949956..80023619
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024976577.2 → XP_024832345.1  lysine-specific demethylase 5B isoform X1

      UniProtKB/TrEMBL
      A0AAA9SAM5, F1MUR2
      Related
      ENSBTAP00000028871.6, ENSBTAT00000028871.7
      Conserved Domains (9) summary
      smart00501
      Location:93 → 183
      BRIGHT; ARID (A/T-rich interaction domain) domain
      smart00545
      Location:26 → 67
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:481 → 597
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:306 → 351
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:1173 → 1216
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:1481 → 1530
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:687 → 739
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:752 → 1081
      PLU-1; PLU-1-like protein
      cl26267
      Location:1095 → 1217
      ING; Inhibitor of growth proteins N-terminal histone-binding

    2. XM_024976576.2 → XP_024832344.1  lysine-specific demethylase 5B isoform X3

      UniProtKB/TrEMBL
      A0AAA9SAM5, A0AAA9SJ17
      Related
      ENSBTAP00000086240.1, ENSBTAT00000096847.1
      Conserved Domains (9) summary
      smart00501
      Location:93 → 183
      BRIGHT; ARID (A/T-rich interaction domain) domain
      smart00545
      Location:26 → 67
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:436 → 552
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:261 → 306
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:1128 → 1171
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:1436 → 1485
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:642 → 694
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:707 → 1036
      PLU-1; PLU-1-like protein
      cl26267
      Location:1050 → 1172
      ING; Inhibitor of growth proteins N-terminal histone-binding

    3. XM_024976578.2 → XP_024832346.1  lysine-specific demethylase 5B isoform X4

      UniProtKB/TrEMBL
      A0AAA9S298, A0AAA9SAM5
      Related
      ENSBTAP00000080031.1, ENSBTAT00000123090.1
      Conserved Domains (9) summary
      smart00501
      Location:93 → 183
      BRIGHT; ARID (A/T-rich interaction domain) domain
      smart00545
      Location:26 → 67
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:367 → 483
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:192 → 237
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:1059 → 1102
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:1367 → 1416
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:573 → 625
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:638 → 967
      PLU-1; PLU-1-like protein
      cl26267
      Location:981 → 1103
      ING; Inhibitor of growth proteins N-terminal histone-binding

    4. XM_059875608.1 → XP_059731591.1  lysine-specific demethylase 5B isoform X5

    5. XM_059875609.1 → XP_059731592.1  lysine-specific demethylase 5B isoform X5

    6. XM_059875610.1 → XP_059731593.1  lysine-specific demethylase 5B isoform X5

    7. XM_059875607.1 → XP_059731590.1  lysine-specific demethylase 5B isoform X2

    Nucleotide Protein Strain
    Heading Accession and Version

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