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    CCR1 cold, circadian rhythm, and RNA binding 1 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 830082, updated on 18-Sep-2024

    Summary

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    Official Symbol
    CCR1
    Official Full Name
    cold, circadian rhythm, and RNA binding 1
    Primary source
    TAIR:AT4G39260
    Locus tag
    AT4G39260
    See related
    Araport:AT4G39260
    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
    and RNA binding 1; ATGRP8; circadian rhythm; cold; GLYCINE-RICH PROTEIN 8; glycine-rich RNA-binding protein 8; GR-RBP8; GRP8; T22F8.160; T22F8_160
    Summary
    Encodes a glycine-rich protein with RNA binding domain at the N-terminus. Protein is structurally similar to proteins induced by stress in other plants. Gene expression is induced by cold. Transcript undergoes circadian oscillations that is depressed by overexpression of AtGRP7. A substrate of the type III effector HopU1 (mono-ADP-ribosyltransferase).
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    Genomic context

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    See CCR1 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    3
    Sequence:
    Chromosome: 4; NC_003075.7 (18273829..18275216, complement)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene uncharacterized protein Neighboring gene Galactose oxidase/kelch repeat superfamily protein Neighboring gene RAD-like 1 Neighboring gene Leucine-rich repeat protein kinase family protein Neighboring gene phenylalanyl-tRNA synthetase, putative / phenylalanine-tRNA ligase

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003075.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Vessel-Specific Reintroduction of CINNAMOYL-COA REDUCTASE1 (CCR1) in Dwarfed ccr1 Mutants Restores Vessel and Xylary Fiber Integrity and Increases Biomass. De Meester B, et al. Plant Physiol, 2018 Jan. PMID 29158331, Free PMC Article
    2. Regulation of Flowering Time by the RNA-Binding Proteins AtGRP7 and AtGRP8. Steffen A, et al. Plant Cell Physiol, 2019 Sep 1. PMID 31241165
    3. Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis. Schöning JC, et al. Nucleic Acids Res, 2008 Dec. PMID 18987006, Free PMC Article
    4. An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana. Streitner C, et al. Nucleic Acids Res, 2012 Dec. PMID 23042250, Free PMC Article
    5. A circadian clock-regulated toggle switch explains AtGRP7 and AtGRP8 oscillations in Arabidopsis thaliana. Schmal C, et al. PLoS Comput Biol, 2013. PMID 23555221, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Our results suggest that the RNA-binding proteins (RBPs) AtGRP7 and AtGRP8 influence MADS-Box transcription factors in at least two different pathways of flowering time control.
      Title: Regulation of Flowering Time by the RNA-Binding Proteins AtGRP7 and AtGRP8.
    2. the yield penalty of ccr1 mutants was not caused by ferulic acid accumulation but was (largely) the consequence of collapsed vessels.
      Title: Vessel-Specific Reintroduction of CINNAMOYL-COA REDUCTASE1 (CCR1) in Dwarfed ccr1 Mutants Restores Vessel and Xylary Fiber Integrity and Increases Biomass.
    3. Proposes the first circadian slave oscillator model by studying AtGRP7 and AtGRP8 oscillations in Arabidopsis thaliana.
      Title: A circadian clock-regulated toggle switch explains AtGRP7 and AtGRP8 oscillations in Arabidopsis thaliana.
    4. AtGRP8 binds to its own and the AtGRP7 pre-mRNA, suggesting that this interaction is relevant for the splicing regulation.
      Title: Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis.
    5. Data show that AtGRP8 binds to AtGRP7 and levels of the alternatively spliced AtGRP8 transcripts that contain premature termination codons are strongly elevated in mutants impaired in the nonsense-mediated decay (NMD) components UPF1 or UPF3.
      Title: Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_120087.4
    NM_179192.2
    NM_179193.2
    NM_179194.1

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables mRNA binding HDA PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables miRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables siRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables single-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within alternative mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in extracellular transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within innate immune response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in miRNA transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of defense response to virus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within response to cold IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to cold IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within response to zinc ion IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus HDA PubMed 
    located_in cytosol HDA PubMed 
    NOT located_in cytosol RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion ISM
    Inferred from Sequence Model
    more info
    		  
    located_in nucleolus HDA PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    located_in peroxisome HDA PubMed 
    located_in plant-type cell wall HDA PubMed 
    located_in plasma membrane HDA PubMed 
    located_in plasmodesma HDA PubMed 

    General protein information

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    Preferred Names
    cold, circadian rhythm, and RNA binding 1
    NP_195637.1
    • cold, circadian rhythm, and RNA binding 1 (CCR1); FUNCTIONS IN: RNA binding, nucleotide binding, nucleic acid binding; INVOLVED IN: response to zinc ion, response to salt stress, response to cold, circadian rhythm, innate immune response; LOCATED IN: nucleolus, cell wall, peroxisome, plasma membrane, chloroplast; EXPRESSED IN: 28 plant structures; EXPRESSED DURING: 16 growth stages; CONTAINS InterPro DOMAIN/s: RNA recognition motif, glycine rich protein (InterPro:IPR015465), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: cold, circadian rhythm, and rna binding 2 (TAIR:AT2G21660.2); Has 126 Blast hits to 126 proteins in 35 species: Archae - 0; Bacteria - 12; Metazoa - 0; Fungi - 21; Plants - 62; Viruses - 0; Other Eukaryotes - 31 (source: NCBI BLink).
    NP_849523.1
    • cold, circadian rhythm, and RNA binding 1 (CCR1); FUNCTIONS IN: RNA binding, nucleotide binding, nucleic acid binding; INVOLVED IN: response to zinc ion, response to salt stress, response to cold, circadian rhythm, innate immune response; LOCATED IN: nucleolus, cell wall, peroxisome, plasma membrane, chloroplast; EXPRESSED IN: 27 plant structures; EXPRESSED DURING: 16 growth stages; CONTAINS InterPro DOMAIN/s: RNA recognition motif, glycine rich protein (InterPro:IPR015465), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: cold, circadian rhythm, and rna binding 2 (TAIR:AT2G21660.2); Has 82664 Blast hits to 34440 proteins in 1574 species: Archae - 59; Bacteria - 22063; Metazoa - 30672; Fungi - 6267; Plants - 13203; Viruses - 1104; Other Eukaryotes - 9296 (source: NCBI BLink).
    NP_849524.1
    • cold, circadian rhythm, and RNA binding 1 (CCR1); FUNCTIONS IN: RNA binding, nucleotide binding, nucleic acid binding; INVOLVED IN: response to zinc ion, response to salt stress, response to cold, circadian rhythm, innate immune response; LOCATED IN: nucleolus, cell wall, peroxisome, plasma membrane, chloroplast; EXPRESSED IN: 27 plant structures; EXPRESSED DURING: 16 growth stages; CONTAINS InterPro DOMAIN/s: RNA recognition motif, glycine rich protein (InterPro:IPR015465), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: cold, circadian rhythm, and rna binding 2 (TAIR:AT2G21660.2); Has 82664 Blast hits to 34440 proteins in 1574 species: Archae - 59; Bacteria - 22063; Metazoa - 30672; Fungi - 6267; Plants - 13203; Viruses - 1104; Other Eukaryotes - 9296 (source: NCBI BLink).
    NP_849525.1
    • cold, circadian rhythm, and RNA binding 1 (CCR1); FUNCTIONS IN: RNA binding, nucleotide binding, nucleic acid binding; INVOLVED IN: response to zinc ion, response to salt stress, response to cold, circadian rhythm, innate immune response; LOCATED IN: nucleolus, cell wall, peroxisome, plasma membrane, chloroplast; EXPRESSED IN: 27 plant structures; EXPRESSED DURING: 16 growth stages; CONTAINS InterPro DOMAIN/s: RNA recognition motif, glycine rich protein (InterPro:IPR015465), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: cold, circadian rhythm, and rna binding 2 (TAIR:AT2G21660.2); Has 82664 Blast hits to 34440 proteins in 1574 species: Archae - 59; Bacteria - 22063; Metazoa - 30672; Fungi - 6267; Plants - 13203; Viruses - 1104; Other Eukaryotes - 9296 (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_003075.7 Reference assembly

      Range
      18273829..18275216 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_120087.4 → NP_195637.1  cold, circadian rhythm, and RNA binding 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_195637.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A0A178UVJ6, B9DFJ8, Q03251, Q94CB0
      UniProtKB/TrEMBL
      A0A384L218
      Conserved Domains (1) summary
      cd21608
      Location:7 → 82
      RRM2_NsCP33_like; RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins

    2. NM_179192.2 → NP_849523.1  cold, circadian rhythm, and RNA binding 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_849523.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      F4JVC1
      Conserved Domains (1) summary
      cl17169
      Location:9 → 83
      RRM_SF; RNA recognition motif (RRM) superfamily

    3. NM_179193.2 → NP_849524.1  cold, circadian rhythm, and RNA binding 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_849524.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A7G2FB27, F4JVC0
      Conserved Domains (1) summary
      cl17169
      Location:9 → 83
      RRM_SF; RNA recognition motif (RRM) superfamily

    4. NM_179194.1 → NP_849525.1  cold, circadian rhythm, and RNA binding 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_849525.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      F4JVB9
      Conserved Domains (1) summary
      smart00360
      Location:7 → 68
      RRM; RNA recognition motif
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q03251.1

    Gene LinkOut

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