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    HCF107 high chlorophyll fluorescent 107 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 820961, updated on 18-Sep-2024

    Summary

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    Official Symbol
    HCF107
    Official Full Name
    high chlorophyll fluorescent 107
    Primary source
    TAIR:AT3G17040
    Locus tag
    AT3G17040
    See related
    Araport:AT3G17040
    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
    high chlorophyll fluorescent 107
    Summary
    It is a RNA tetratricopeptide repeat-containing protein required for normal processing of transcripts from the polycistronic chloroplast psbB-psbT-psbH-petB-petD operon coding for proteins of the photosystem II and cytochrome b6/f complexes. Localizes to the chloroplast membrane. Involved in regulating plastidial gene expression and biogenesis. It binds in the psbT?psbH intercistronic region and blocks the progression of 5' -> 3' exoribonucleases, which defines the 5' end of processed psbH transcripts and also stabilizes the downstream RNA segment. In addition, HCF107 binding remodels the structure of the psbH 5' UTR in a way that can account for its ability to enhance psbH translation.
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    Genomic context

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    See HCF107 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    7
    Sequence:
    Chromosome: 3; NC_003074.8 (5808666..5812780, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene Adenine nucleotide alpha hydrolases-like superfamily protein Neighboring gene Nucleic acid-binding proteins superfamily Neighboring gene pseudo Neighboring gene Pectin lyase-like superfamily 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. Expression of a nuclear-encoded psbH gene complements the plastidic RNA processing defect in the PSII mutant hcf107 in Arabidopsis thaliana. Levey T, et al. Plant J, 2014 Oct. PMID 25081859
    2. The nucleus-encoded HCF107 gene of Arabidopsis provides a link between intercistronic RNA processing and the accumulation of translation-competent psbH transcripts in chloroplasts. Felder S, et al. Plant Cell, 2001 Sep. PMID 11549768, Free PMC Article
    3. RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression. Hammani K, et al. Proc Natl Acad Sci U S A, 2012 Apr 10. PMID 22451905, Free PMC Article
    4. The nuclear gene HCF107 encodes a membrane-associated R-TPR (RNA tetratricopeptide repeat)-containing protein involved in expression of the plastidial psbH gene in Arabidopsis. Sane AP, et al. Plant J, 2005 Jun. PMID 15918885
    5. The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. Monte E, et al. Proc Natl Acad Sci U S A, 2004 Nov 16. PMID 15505214, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A chloroplast-localized HAT protein, HCF107, is a sequence-specific RNA binding protein.
      Title: RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression.
    2. The identification of the HCF107 gene that is involved in the 5'-end processing/stability and/or translation of the psbH gene and in the translation of the psbB gene. [HCF107]
      Title: The nuclear gene HCF107 encodes a membrane-associated R-TPR (RNA tetratricopeptide repeat)-containing protein involved in expression of the plastidial psbH gene in Arabidopsis.
    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_001202985.2
    NM_001338272.1
    NM_112580.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables mRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ribonuclease inhibitor activity 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
    acts_upstream_of_or_within RNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in RNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within mRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within plastid organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of translation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of translation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to red light IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast HDA PubMed 
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in chloroplast envelope IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chloroplast membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chloroplast stroma IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    located_in plant-type vacuole HDA PubMed 

    General protein information

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    Preferred Names
    high chlorophyll fluorescent 107
    NP_001189914.1
    • high chlorophyll fluorescent 107 (HCF107); FUNCTIONS IN: binding; INVOLVED IN: plastid organization, RNA processing, regulation of translation; LOCATED IN: chloroplast envelope; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA-processing protein, HAT helix (InterPro:IPR003107), Tetratricopeptide-like helical (InterPro:IPR011990), Tetratricopeptide repeat-containing (InterPro:IPR013026), Tetratricopeptide repeat (InterPro:IPR019734); BEST Arabidopsis thaliana protein match is: pre-mRNA splicing factor-related (TAIR:AT4G03430.1).
    NP_188329.1
    • high chlorophyll fluorescent 107 (HCF107); FUNCTIONS IN: binding; INVOLVED IN: plastid organization, RNA processing, regulation of translation; LOCATED IN: chloroplast, plasma membrane, chloroplast envelope; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA-processing protein, HAT helix (InterPro:IPR003107), Tetratricopeptide-like helical (InterPro:IPR011990), Tetratricopeptide repeat-containing (InterPro:IPR013026), Tetratricopeptide repeat (InterPro:IPR019734); BEST Arabidopsis thaliana protein match is: pre-mRNA splicing factor-related (TAIR:AT4G03430.1); Has 8355 Blast hits to 4834 proteins in 935 species: Archae - 387; Bacteria - 2714; Metazoa - 1907; Fungi - 1281; Plants - 751; Viruses - 0; Other Eukaryotes - 1315 (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
      5808666..5812780 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001338271.1 → NP_001327904.1  high chlorophyll fluorescent 107 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1I9LTR5

    2. NM_112580.5 → NP_188329.1  high chlorophyll fluorescent 107 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_188329.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8RWG2, Q9LSP3
      UniProtKB/TrEMBL
      A0A178VC71
      Conserved Domains (4) summary
      COG0457
      Location:183 → 440
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:273 → 299
      TPR; TPR repeat [structural motif]
      pfam13428
      Location:342 → 380
      TPR_14; Tetratricopeptide repeat
      pfam13432
      Location:412 → 475
      TPR_16; Tetratricopeptide repeat

    3. NM_001202985.2 → NP_001189914.1  high chlorophyll fluorescent 107 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001189914.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VC71, F4J3Z3
      Conserved Domains (4) summary
      COG0457
      Location:149 → 406
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:239 → 265
      TPR; TPR repeat [structural motif]
      pfam13428
      Location:308 → 346
      TPR_14; Tetratricopeptide repeat
      pfam13432
      Location:378 → 441
      TPR_16; Tetratricopeptide repeat

    4. NM_001338272.1 → NP_001327903.1  high chlorophyll fluorescent 107 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1I9LTR4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8RWG2.1

    Gene LinkOut

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