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    kdm4b lysine (K)-specific demethylase 4B [ Xenopus tropicalis (tropical clawed frog) ]

    Gene ID: 394661, updated on 4-Nov-2024

    Summary

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    Official Symbol
    kdm4bprovided by Xenbase
    Official Full Name
    lysine (K)-specific demethylase 4Bprovided by Xenbase
    Primary source
    Xenbase:XB-GENE-1012886
    See related
    Ensembl:ENSXETG00000005352 AllianceGenome:Xenbase:XB-GENE-1012886
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Xenopus tropicalis
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana
    Also known as
    jmjd2b
    Summary
    Predicted to enable lipid transporter activity. Predicted to be involved in cellular response to estrogen stimulus and response to estradiol. Predicted to act upstream of or within chromatin organization. Predicted to be located in nucleus. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder; breast cancer; colorectal cancer; malignant peripheral nerve sheath tumor; and stomach cancer. Orthologous to human KDM4B (lysine demethylase 4B). [provided by Alliance of Genome Resources, Nov 2024]
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    Genomic context

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    See kdm4b in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    104 current UCB_Xtro_10.0 (GCF_000004195.4) 1 NC_030677.2 (91027843..91339710)
    103 previous assembly Xenopus_tropicalis_v9.1 (GCF_000004195.3) 1 NC_030677.1 (72175072..72475577)

    Chromosome 1 - NC_030677.2Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC116408312 Neighboring gene adhesion G protein-coupled receptor L3 Neighboring gene U2 spliceosomal RNA Neighboring gene uncharacterized LOC105946089 Neighboring gene uncharacterized LOC101732465 Neighboring gene protein tyrosine phosphatase receptor type S

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative. Klein SL, et al. Dev Dyn, 2002 Dec. PMID 12454917
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Clone Names

    • MGC75779

    Gene Ontology Provided by Xenbase

    Function Evidence Code Pubs
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9me2/H3K9me3 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables lipid transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cellular response to estrogen stimulus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to estradiol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 4B
    Names
    jumonji domain containing 2B
    NP_989064.2
    XP_012813654.1
    XP_012813665.1
    XP_012813676.1
    XP_012813681.1
    XP_017947205.1
    XP_031752955.1
    XP_031752981.1
    XP_031752983.1
    XP_031752997.1

    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_203733.2 → NP_989064.2  lysine-specific demethylase 4B

      See identical proteins and their annotated locations for NP_989064.2

      Status: VALIDATED

      Source sequence(s)
      AAMC04000001, BX689173, CX320023, CX384686, CX397664, CX482833, CX881818, CX914131, DN035577
      UniProtKB/TrEMBL
      A0A6I8Q521, A0A6I8QA80
      Related
      ENSXETP00000066285.1, ENSXETT00000094681.2
      Conserved Domains (6) summary
      smart00545
      Location:14 → 55
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15576
      Location:624 → 719
      PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      cd15714
      Location:728 → 837
      ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      pfam02373
      Location:175 → 291
      JmjC; JmjC domain, hydroxylase
      cd20464
      Location:850 → 903
      Tudor_JMJD2B_rpt1; first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins
      cd20467
      Location:907 → 962
      Tudor_JMJD2B_rpt2; second Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins

    RefSeqs of Annotated Genomes: Xenopus tropicalis Annotation Release 104 details...Open this link in a new tab

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

    Reference UCB_Xtro_10.0 Primary Assembly

    Genomic

    1. NC_030677.2 Reference UCB_Xtro_10.0 Primary Assembly

      Range
      91027843..91339710
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_012958227.3 → XP_012813681.1  lysine-specific demethylase 4B isoform X5

      See identical proteins and their annotated locations for XP_012813681.1

      UniProtKB/TrEMBL
      A0A6I8Q943, Q6P8C2
      Conserved Domains (1) summary
      smart00545
      Location:14 → 55
      JmjN; Small domain found in the jumonji family of transcription factors

    2. XM_012958222.3 → XP_012813676.1  lysine-specific demethylase 4B isoform X5

      See identical proteins and their annotated locations for XP_012813676.1

      UniProtKB/TrEMBL
      A0A6I8Q943, Q6P8C2
      Related
      ENSXETP00000065014.2, ENSXETT00000085316.2
      Conserved Domains (1) summary
      smart00545
      Location:14 → 55
      JmjN; Small domain found in the jumonji family of transcription factors

    3. XM_031897121.1 → XP_031752981.1  lysine-specific demethylase 4B isoform X4

      UniProtKB/TrEMBL
      F6Z9Z5
      Related
      ENSXETP00000007540.5, ENSXETT00000007540.5
      Conserved Domains (1) summary
      smart00545
      Location:14 → 55
      JmjN; Small domain found in the jumonji family of transcription factors

    4. XM_031897137.1 → XP_031752997.1  lysine-specific demethylase 4B isoform X6

      UniProtKB/TrEMBL
      A0A6I8QRC4
      Related
      ENSXETP00000070985.2, ENSXETT00000074475.2
      Conserved Domains (1) summary
      smart00545
      Location:14 → 55
      JmjN; Small domain found in the jumonji family of transcription factors

    5. XM_031897123.1 → XP_031752983.1  lysine-specific demethylase 4B isoform X5

      UniProtKB/TrEMBL
      A0A6I8Q943, Q6P8C2
      Conserved Domains (1) summary
      smart00545
      Location:14 → 55
      JmjN; Small domain found in the jumonji family of transcription factors

    6. XM_018091716.2 → XP_017947205.1  lysine-specific demethylase 4B isoform X2

      UniProtKB/TrEMBL
      A0A6I8Q521, A0A8J0SYR0

    7. XM_031897095.1 → XP_031752955.1  lysine-specific demethylase 4B isoform X1

      UniProtKB/TrEMBL
      A0A6I8Q521, A0A6I8QA80
      Conserved Domains (6) summary
      smart00545
      Location:14 → 55
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15576
      Location:624 → 719
      PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      cd15714
      Location:728 → 837
      ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      pfam02373
      Location:175 → 291
      JmjC; JmjC domain, hydroxylase
      cd20464
      Location:850 → 903
      Tudor_JMJD2B_rpt1; first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins
      cd20467
      Location:907 → 962
      Tudor_JMJD2B_rpt2; second Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins

    8. XM_012958200.3 → XP_012813654.1  lysine-specific demethylase 4B isoform X1

      See identical proteins and their annotated locations for XP_012813654.1

      UniProtKB/TrEMBL
      A0A6I8Q521, A0A6I8QA80
      Conserved Domains (6) summary
      smart00545
      Location:14 → 55
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15576
      Location:624 → 719
      PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      cd15714
      Location:728 → 837
      ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      pfam02373
      Location:175 → 291
      JmjC; JmjC domain, hydroxylase
      cd20464
      Location:850 → 903
      Tudor_JMJD2B_rpt1; first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins
      cd20467
      Location:907 → 962
      Tudor_JMJD2B_rpt2; second Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins

    9. XM_012958211.3 → XP_012813665.1  lysine-specific demethylase 4B isoform X3

      UniProtKB/TrEMBL
      A0A6I8Q521, A0A8J0SG29
      Conserved Domains (4) summary
      smart00333
      Location:748 → 799
      TUDOR; Tudor domain
      pfam02373
      Location:70 → 186
      JmjC; JmjC domain, hydroxylase
      cd15714
      Location:623 → 732
      ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      cl22851
      Location:519 → 614
      PHD_SF; PHD finger superfamily

    RNA

    1. XR_004221360.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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