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    JMJD5 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 821629, updated on 18-Sep-2024

    Summary

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    Official Symbol
    JMJD5
    Official Full Name
    2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
    Primary source
    TAIR:AT3G20810
    Locus tag
    AT3G20810
    See related
    Araport:AT3G20810
    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
    JMJ30; Jumonji C domain-containing protein 30; jumonji domain containing 5
    Summary
    JMJD5 encodes a protein which contains a jumonji-C (jmjC) domain. The jumonji-C is frequently found in proteins with histone demethylase activity. jmjd5 mutant plants have a short-period circadian phenotype.
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    Genomic context

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    See JMJD5 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    6
    Sequence:
    Chromosome: 3; NC_003074.8 (7275645..7278420)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene NAD(P)-binding Rossmann-fold superfamily protein Neighboring gene ncRNA Neighboring gene Cell differentiation, Rcd1-like protein Neighboring gene Leucine-rich repeat (LRR) family protein Neighboring gene miscRNA Neighboring gene AGC (cAMP-dependent, cGMP-dependent and protein kinase C) kinase family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Arabidopsis JMJD5/JMJ30 Acts Independently of LUX ARRHYTHMO Within the Plant Circadian Clock to Enable Temperature Compensation. Jones MA, et al. Front Plant Sci, 2019. PMID 30774641, Free PMC Article
    2. Soybean (Glycine max) prevents the progression of breast cancer cells by downregulating the level of histone demethylase JMJD5. Wang Y, et al. J Cancer Res Ther, 2018 Sep. PMID 30249876
    3. Overexpression of histone demethylase JMJD5 promotes metastasis and indicates a poor prognosis in breast cancer. Zhao Z, et al. Int J Clin Exp Pathol, 2015. PMID 26617740, Free PMC Article
    4. The Jumonji C domain-containing protein JMJ30 regulates period length in the Arabidopsis circadian clock. Lu SX, et al. Plant Physiol, 2011 Feb. PMID 21139085, Free PMC Article
    5. Histone Demethylases Coordinate the Antagonistic Interaction Between Abscisic Acid and Brassinosteroid Signaling in Arabidopsis. Wu J, et al. Front Plant Sci, 2020. PMID 33324437, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Analysis of JMJ30/JMJ32 and SnRK2.8 expression suggested that they act in the same pathway to mediate abscissic acid responses during root elongation at the seedling stage.
      Title: Histone demethylases control root elongation in response to stress-signaling hormone abscisic acid.
    2. mediates demethylation of H3K9me3 that drives tissue identity changes to promote callus formation
      Title: JMJ30-mediated demethylation of H3K9me3 drives tissue identity changes to promote callus formation in Arabidopsis.
    3. The complicated compositions of soybean will be beneficial to the therapy of breast cancer since its causes may be involved in multiple aspects. Soybean represses breast cancer development by downregulating the level of JMJD5.
      Title: Soybean (Glycine max) prevents the progression of breast cancer cells by downregulating the level of histone demethylase JMJD5.
    4. In breast neoplasms, higher expression of JMJD5 was significantly corresponded with clinical stage, histological grade, lymph node metastasis and worse overall survival.
      Title: Overexpression of histone demethylase JMJD5 promotes metastasis and indicates a poor prognosis in breast cancer.
    5. JMJ30/AT3G20810 and JMJ32/AT3G45880, two members of the JmjC domain-only group of JMJ proteins, function as H3K27 demethylases and regulate FLC expression.
      Title: Jumonji demethylases moderate precocious flowering at elevated temperature via regulation of FLC in Arabidopsis.
    6. The human homolog of JMJD5, KDM8, has been shown to have histone demethylation activity and is able to partially rescue the plant jmjd5 circadian phenotype.
      Title: JMJD5 Functions in concert with TOC1 in the arabidopsis circadian system.
    7. JMJD5 plays an interchangeable role in the timing mechanisms of plants and animals despite their highly divergent evolutionary paths. [JMJD5]
      Title: Jumonji domain protein JMJD5 functions in both the plant and human circadian systems.
    8. Expression of JMJ30 ocillates with a circadian rhythm. Loss of function affects the free-running circadian period.
      Title: The Jumonji C domain-containing protein JMJ30 regulates period length in the Arabidopsis circadian clock.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001035656.1
    NM_001338491.1
    NM_001338492.1
    NM_112972.4
    NM_180286.1

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables H3K27me3 modified histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K27me2/H3K27me3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K27me2/H3K27me3 demethylase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K36 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K9me2/H3K9me3 demethylase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_positive_effect callus formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within_positive_effect epigenetic regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_positive_effect epigenetic regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of gene expression, epigenetic IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within primary root development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of abscisic acid-activated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of brassinosteroid mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of photoperiodism, flowering IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of seedling development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to abscisic acid IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within response to abscisic acid IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to abscisic acid IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to brassinosteroid IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to temperature stimulus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to temperature stimulus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in temperature compensation of the circadian clock IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in euchromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
    NP_001030733.1
    • 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein; CONTAINS InterPro DOMAIN/s: Transcription factor jumonji/aspartyl beta-hydroxylase (InterPro:IPR003347); BEST Arabidopsis thaliana protein match is: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein (TAIR:AT5G19840.2); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).
    NP_566667.1
    • 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein; CONTAINS InterPro DOMAIN/s: Transcription factor jumonji/aspartyl beta-hydroxylase (InterPro:IPR003347); BEST Arabidopsis thaliana protein match is: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein (TAIR:AT5G19840.2); Has 1946 Blast hits to 1923 proteins in 341 species: Archae - 0; Bacteria - 483; Metazoa - 767; Fungi - 226; Plants - 240; Viruses - 3; Other Eukaryotes - 227 (source: NCBI BLink).
    NP_850617.1
    • 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein; CONTAINS InterPro DOMAIN/s: Transcription factor jumonji/aspartyl beta-hydroxylase (InterPro:IPR003347); BEST Arabidopsis thaliana protein match is: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein (TAIR:AT5G19840.2); Has 1945 Blast hits to 1922 proteins in 341 species: Archae - 0; Bacteria - 483; Metazoa - 766; Fungi - 226; Plants - 240; Viruses - 3; Other Eukaryotes - 227 (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_003074.8 Reference assembly

      Range
      7275645..7278420
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_112972.4 → NP_566667.1  2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_566667.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9XEL9, A0A654F959
      Conserved Domains (1) summary
      pfam13621
      Location:188 → 412
      Cupin_8; Cupin-like domain

    2. NM_001338491.1 → NP_001327066.1  2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1I9LR61, A0A5S9XEL9, A0A654F959
      Conserved Domains (1) summary
      cl40423
      Location:188 → 325
      cupin_RmlC-like; RmlC-like cupin superfamily

    3. NM_180286.1 → NP_850617.1  2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_850617.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8RWR1, Q9LT40
      UniProtKB/TrEMBL
      A0A5S9XEL9, A0A654F959
      Conserved Domains (1) summary
      pfam13621
      Location:199 → 423
      Cupin_8; Cupin-like domain

    4. NM_001338492.1 → NP_001327067.1  2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VNS0, A0A1I9LR62, A0A384LKB7
      Conserved Domains (1) summary
      cl40423
      Location:188 → 334
      cupin_RmlC-like; RmlC-like cupin superfamily

    5. NM_001035656.1 → NP_001030733.1  2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001030733.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9XEL9, A0A654F959, F4JET6
      Conserved Domains (1) summary
      pfam13621
      Location:188 → 397
      Cupin_8; Cupin-like domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8RWR1.1

    Gene LinkOut

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