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    PKDM7D Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 837384, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PKDM7D
    Official Full Name
    Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein
    Primary source
    TAIR:AT1G08620
    Locus tag
    AT1G08620
    See related
    Araport:AT1G08620
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    F22O13.10; F22O13_10
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    Genomic context

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    See PKDM7D in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    14
    Sequence:
    Chromosome: 1; NC_003070.9 (2736656..2743881)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene Leucine-rich receptor-like protein kinase family protein Neighboring gene ncRNA Neighboring gene P-loop containing nucleoside triphosphate hydrolases superfamily protein Neighboring gene Pentatricopeptide repeat (PPR) superfamily protein Neighboring gene ncRNA Neighboring gene threonine aldolase 1 Neighboring gene Chloroplast J-like domain 1 Neighboring gene pseudo Neighboring gene uncharacterized protein Neighboring gene phosphoenolpyruvate carboxylase kinase 1

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The Histone H3K4 Demethylase JMJ16 Represses Leaf Senescence in Arabidopsis. Liu P, et al. Plant Cell, 2019 Feb. PMID 30712008, Free PMC Article
    2. Cell-type-dependent histone demethylase specificity promotes meiotic chromosome condensation in Arabidopsis. Wang J, et al. Nat Plants, 2020 Jul. PMID 32572214
    3. Arabidopsis histone H3K4 demethylase JMJ17 functions in dehydration stress response. Huang S, et al. New Phytol, 2019 Aug. PMID 31038749
    4. Identification of Arabidopsis SUMO-interacting proteins that regulate chromatin activity and developmental transitions. Elrouby N, et al. Proc Natl Acad Sci U S A, 2013 Dec 3. PMID 24255109, Free PMC Article
    5. Proteome-wide screens for small ubiquitin-like modifier (SUMO) substrates identify Arabidopsis proteins implicated in diverse biological processes. Elrouby N, et al. Proc Natl Acad Sci U S A, 2010 Oct 5. PMID 20855607, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001198011.2
    NM_001331778.1
    NM_001331779.1
    NM_100735.7

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables SUMO binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K9 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within developmental growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within_positive_effect meiotic chromosome condensation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of gene expression, epigenetic IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of gene expression, epigenetic IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within_negative_effect negative regulation of leaf senescence IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within plant organ development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within_positive_effect positive regulation of chromosome condensation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within_negative_effect reactive oxygen species biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein
    NP_001184940.1
    • PKDM7D; FUNCTIONS IN: sequence-specific DNA binding transcription factor activity; INVOLVED IN: regulation of transcription; LOCATED IN: nucleus; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Transcription factor jumonji/aspartyl beta-hydroxylase (InterPro:IPR003347), FY-rich, C-terminal (InterPro:IPR003889), FY-rich, N-terminal (InterPro:IPR003888), Transcription factor jumonji, JmjN (InterPro:IPR003349), Zinc finger, C5HC2-type (InterPro:IPR004198), FY-rich, C-terminal subgroup (InterPro:IPR018516), Transcription factor jumonji (InterPro:IPR013129), FY-rich, N-terminal subgroup (InterPro:IPR018518); BEST Arabidopsis thaliana protein match is: Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein (TAIR:AT1G30810.2).
    NP_001318955.1
    • PKDM7D; FUNCTIONS IN: sequence-specific DNA binding transcription factor activity; INVOLVED IN: regulation of transcription; LOCATED IN: nucleus; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Transcription factor jumonji/aspartyl beta-hydroxylase (InterPro:IPR003347), FY-rich, C-terminal (InterPro:IPR003889), FY-rich, N-terminal (InterPro:IPR003888), Transcription factor jumonji, JmjN (InterPro:IPR003349), Zinc finger, C5HC2-type (InterPro:IPR004198), FY-rich, C-terminal subgroup (InterPro:IPR018516), Transcription factor jumonji (InterPro:IPR013129), FY-rich, N-terminal subgroup (InterPro:IPR018518); BEST Arabidopsis thaliana protein match is: Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein (TAIR:AT1G30810.2); Has 2173 Blast hits to 1649 proteins in 190 species: Archae - 0; Bacteria - 2; Metazoa - 1159; Fungi - 446; Plants - 392; Viruses - 0; Other Eukaryotes - 174 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003070.9 Reference assembly

      Range
      2736656..2743881
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001198011.2 → NP_001184940.1  Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001184940.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      C0SUT9, Q9FRS3
      UniProtKB/TrEMBL
      A0A178WIZ8, A0A7G2DRN2
      Conserved Domains (5) summary
      smart00541
      Location:988 → 1032
      FYRN; FY-rich domain, N-terminal region
      smart00542
      Location:1038 → 1132
      FYRC; FY-rich domain, C-terminal region
      pfam02373
      Location:394 → 510
      JmjC; JmjC domain, hydroxylase
      pfam02375
      Location:147 → 179
      JmjN; jmjN domain
      pfam02928
      Location:617 → 669
      zf-C5HC2; C5HC2 zinc finger

    2. NM_100735.7 → NP_172338.5  Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8AMS3, A0A5S9TCT0, A0A654E8Z6
      Conserved Domains (6) summary
      smart00541
      Location:1002 → 1046
      FYRN; FY-rich domain, N-terminal region
      smart00542
      Location:1052 → 1146
      FYRC; FY-rich domain, C-terminal region
      TIGR00233
      Location:807 → 860
      trpS; tryptophanyl-tRNA synthetase
      pfam02373
      Location:408 → 524
      JmjC; JmjC domain, hydroxylase
      pfam02375
      Location:161 → 193
      JmjN; jmjN domain
      pfam02928
      Location:631 → 683
      zf-C5HC2; C5HC2 zinc finger

    3. NM_001331778.1 → NP_001318955.1  Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      C0SUT9, Q9FRS3
      UniProtKB/TrEMBL
      A0A178WIZ8, A0A7G2DRN2
      Conserved Domains (5) summary
      smart00541
      Location:988 → 1032
      FYRN; FY-rich domain, N-terminal region
      smart00542
      Location:1038 → 1132
      FYRC; FY-rich domain, C-terminal region
      pfam02373
      Location:394 → 510
      JmjC; JmjC domain, hydroxylase
      pfam02375
      Location:147 → 179
      JmjN; jmjN domain
      pfam02928
      Location:617 → 669
      zf-C5HC2; C5HC2 zinc finger

    4. NM_001331779.1 → NP_001320435.1  Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      C0SUT9, Q9FRS3
      UniProtKB/TrEMBL
      A0A178WIZ8, A0A7G2DRN2
      Conserved Domains (5) summary
      smart00541
      Location:988 → 1032
      FYRN; FY-rich domain, N-terminal region
      smart00542
      Location:1038 → 1132
      FYRC; FY-rich domain, C-terminal region
      pfam02373
      Location:394 → 510
      JmjC; JmjC domain, hydroxylase
      pfam02375
      Location:147 → 179
      JmjN; jmjN domain
      pfam02928
      Location:617 → 669
      zf-C5HC2; C5HC2 zinc finger
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    C0SUT9.1

    Gene LinkOut

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