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    PRP39 Tetratricopeptide repeat (TPR)-like superfamily protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 839314, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PRP39
    Official Full Name
    Tetratricopeptide repeat (TPR)-like superfamily protein
    Primary source
    TAIR:AT1G04080
    Locus tag
    AT1G04080
    See related
    Araport:AT1G04080
    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
    F20D22.14
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    Genomic context

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    See PRP39 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    15
    Sequence:
    Chromosome: 1; NC_003070.9 (1051312..1056827)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene histone-lysine N-methyltransferase SUVR2-like protein Neighboring gene translocase of outer membrane 22-I Neighboring gene vacuolar sorting-associated protein (DUF946) Neighboring gene uncharacterized protein Neighboring gene indoleacetic acid-induced protein 10

    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 Arabidopsis thaliana AT PRP39-1 gene, encoding a tetratricopeptide repeat protein with similarity to the yeast pre-mRNA processing protein PRP39, affects flowering time. Wang C, et al. Plant Cell Rep, 2007 Aug. PMID 17380304
    2. Synergistic action of the Arabidopsis spliceosome components PRP39a and SmD1b in promoting posttranscriptional transgene silencing. Bazin J, et al. Plant Cell, 2023 May 29. PMID 36970782, Free PMC Article
    3. The U1 snRNP component RBP45d regulates temperature-responsive flowering in Arabidopsis. Chang P, et al. Plant Cell, 2022 Feb 3. PMID 34791475, Free PMC Article
    4. A Genetic Screen for Pre-mRNA Splicing Mutants of Arabidopsis thaliana Identifies Putative U1 snRNP Components RBM25 and PRP39a. Kanno T, et al. Genetics, 2017 Dec. PMID 28971960, Free PMC Article
    5. Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis proteins involved in RNA metabolism. de la Fuente van Bentem S, et al. Nucleic Acids Res, 2006. PMID 16807317, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Synergistic action of the Arabidopsis spliceosome components PRP39a and SmD1b in promoting posttranscriptional transgene silencing.
      Title: Synergistic action of the Arabidopsis spliceosome components PRP39a and SmD1b in promoting posttranscriptional transgene silencing.
    2. The U1 snRNP component RBP45d regulates temperature-responsive flowering in Arabidopsis.
      Title: The U1 snRNP component RBP45d regulates temperature-responsive flowering in Arabidopsis.
    3. RNA-seq experiments performed using two independent prp39a alleles revealed hundreds of common genes undergoing changes in alternative splicing, including PRP39a itself, a second putative U1 snRNP component PRP40b, and genes encoding a number of general transcription-related proteins.
      Title: A Genetic Screen for Pre-mRNA Splicing Mutants of Arabidopsis thaliana Identifies Putative U1 snRNP Components RBM25 and PRP39a.
    4. A novel Arabidopsis gene, designated AT PRP39-1, affects flowering time in A. thaliana. [AT PRP39-1]
      Title: The Arabidopsis thaliana AT PRP39-1 gene, encoding a tetratricopeptide repeat protein with similarity to the yeast pre-mRNA processing protein PRP39, affects flowering time.
    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_001160830.2
    NM_001331460.1
    NM_001331461.1
    NM_100289.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within photoperiodism, flowering IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of timing of transition from vegetative to reproductive phase IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    Tetratricopeptide repeat (TPR)-like superfamily protein
    NP_001154302.1
    • PRP39; FUNCTIONS IN: binding; INVOLVED IN: regulation of timing of transition from vegetative to reproductive phase; LOCATED IN: intracellular; EXPRESSED IN: 28 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA-processing protein, HAT helix (InterPro:IPR003107), Tetratricopeptide-like helical (InterPro:IPR011990); BEST Arabidopsis thaliana protein match is: Tetratricopeptide repeat (TPR)-like superfamily protein (TAIR:AT5G46400.1); Has 1033 Blast hits to 958 proteins in 272 species: Archae - 0; Bacteria - 147; Metazoa - 339; Fungi - 222; Plants - 216; Viruses - 4; Other Eukaryotes - 105 (source: NCBI BLink).
    NP_001184905.1
    • PRP39; INVOLVED IN: regulation of timing of transition from vegetative to reproductive phase; LOCATED IN: intracellular; EXPRESSED IN: 28 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA-processing protein, HAT helix (InterPro:IPR003107); BEST Arabidopsis thaliana protein match is: Tetratricopeptide repeat (TPR)-like superfamily protein (TAIR:AT5G46400.1).
    NP_563700.1
    • PRP39; FUNCTIONS IN: binding; INVOLVED IN: regulation of timing of transition from vegetative to reproductive phase; LOCATED IN: intracellular, nucleus; EXPRESSED IN: 28 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA-processing protein, HAT helix (InterPro:IPR003107), Tetratricopeptide-like helical (InterPro:IPR011990), Suppressor of forked (InterPro:IPR008847); BEST Arabidopsis thaliana protein match is: Tetratricopeptide repeat (TPR)-like superfamily protein (TAIR:AT5G46400.1); Has 3917 Blast hits to 3180 proteins in 483 species: Archae - 0; Bacteria - 599; Metazoa - 1588; Fungi - 801; Plants - 439; Viruses - 72; Other Eukaryotes - 418 (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
      1051312..1056827
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001197976.1 → NP_001184905.1  Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001184905.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A654EH89, F4I448
      Conserved Domains (2) summary
      smart00386
      Location:185 → 218
      HAT; HAT (Half-A-TPR) repeats
      pfam05843
      Location:186 → 257
      Suf; Suppressor of forked protein (Suf)

    2. NM_100289.4 → NP_563700.1  Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_563700.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A0A178W5N7, O64496, Q93ZR3
      UniProtKB/TrEMBL
      A0A384LP66, A0A654EH89
      Conserved Domains (3) summary
      smart00386
      Location:375 → 407
      HAT; HAT (Half-A-TPR) repeats
      COG5107
      Location:60 → 249
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      TIGR02917
      Location:409 → 541
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

    3. NM_001331460.1 → NP_001322270.1  Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A0A178W5N7, O64496, Q93ZR3
      UniProtKB/TrEMBL
      A0A384LP66, A0A654EH89
      Conserved Domains (3) summary
      smart00386
      Location:375 → 407
      HAT; HAT (Half-A-TPR) repeats
      COG5107
      Location:60 → 249
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      TIGR02917
      Location:409 → 541
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

    4. NM_001331461.1 → NP_001322271.1  Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8ATH2

    5. NM_001160830.2 → NP_001154302.1  Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001154302.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      F4I450
      Conserved Domains (1) summary
      smart00386
      Location:189 → 221
      HAT; HAT (Half-A-TPR) repeats
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q93ZR3.1

    Gene LinkOut

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