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    EMB2770 pre-mRNA splicing factor-like protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 827925, updated on 18-Sep-2024

    Summary

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    Official Symbol
    EMB2770
    Official Full Name
    pre-mRNA splicing factor-like protein
    Primary source
    TAIR:AT4G03430
    Locus tag
    AT4G03430
    See related
    Araport:AT4G03430
    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
    EMBRYO DEFECTIVE 2770; F9H3.5; F9H3_5; STA1; STABILIZED 1
    Summary
    Encodes a nuclear protein similar to the human U5 small ribonucleoprotein-associated 102-kD protein and to the yeast pre-mRNA splicing factors Prp1p and Prp6p. STA1 expression is upregulated by cold stress, and the sta1-1 mutant is defective in the splicing of the cold-induced COR15A gene. Luciferase imaging was used to isolate a recessive mutant, sta1-1, with enhanced stability of the normally unstable luciferase transcript. This mutation also causes the stabilization of some endogenous gene transcripts and has a range of developmental and stress response phenotypes.
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    Genomic context

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    See EMB2770 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    2
    Sequence:
    Chromosome: 4; NC_003075.7 (1516030..1520563, complement)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene Peroxisomal membrane 22 kDa (Mpv17/PMP22) family protein Neighboring gene Protein phosphatase 2C family protein Neighboring gene hypothetical protein (DUF789) Neighboring gene tRNA-Phe Neighboring gene miscRNA

    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. STABILIZED1 Modulates Pre-mRNA Splicing for Thermotolerance. Kim GD, et al. Plant Physiol, 2017 Apr. PMID 28223317, Free PMC Article
    2. The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs. Dou K, et al. Nucleic Acids Res, 2013 Oct. PMID 23877244, Free PMC Article
    3. STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis. Ben Chaabane S, et al. Nucleic Acids Res, 2013 Feb 1. PMID 23268445, Free PMC Article
    4. RDM16 and STA1 regulate differential usage of exon/intron in RNA directed DNA methylation pathway. Sharma RD, et al. Gene, 2017 Apr 20. PMID 28153750
    5. The splicing machinery promotes RNA-directed DNA methylation and transcriptional silencing in Arabidopsis. Zhang CJ, et al. EMBO J, 2013 Apr 17. PMID 23524848, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Findings indicate that heat-inducible STABILIZED1 (STA1) activity for pre-mRNA splicing serves as a molecular regulatory mechanism underlying the plant stress tolerance to high-temperature stress.
      Title: STABILIZED1 Modulates Pre-mRNA Splicing for Thermotolerance.
    2. The results suggest, splicing factor RDM16 and STA1 play an important role in RNA directed DNA Methylation pathway by affecting expression of key component genes including MORC6 by accumulation of exon 4, which facilitates key ATPase binding sites and MG2 + binding sites for DNA methylation.
      Title: RDM16 and STA1 regulate differential usage of exon/intron in RNA directed DNA methylation pathway.
    3. The authors propose that STA1 acts downstream of siRNA biogenesis and facilitates the production of Pol V-dependent RNA transcripts in the RNA-directed DNA methylation pathway.
      Title: The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs.
    4. The results suggest that STA1 is involved in miRNA biogenesis directly by functioning in pri-miRNA splicing and indirectly by modulating the DCL1 transcript level.
      Title: STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001340448.1
    NM_116581.2

    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 gene silencing by siRNA-directed DNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in positive regulation of primary miRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to cold IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within seed germination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Cajal body 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
    		  
    part_of spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pre-mRNA splicing factor-like protein
    NP_001319859.1
    • EMBRYO DEFECTIVE 2770 (EMB2770); FUNCTIONS IN: binding; INVOLVED IN: nuclear mRNA splicing, via spliceosome, response to cold, response to abiotic stimulus; LOCATED IN: nucleus; EXPRESSED IN: 27 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: RNA-processing protein, HAT helix (InterPro:IPR003107), Tetratricopeptide-like helical (InterPro:IPR011990), PRP1 splicing factor, N-terminal (InterPro:IPR010491), Ubiquitin supergroup (InterPro:IPR019955), Tetratricopeptide repeat-containing (InterPro:IPR013026); BEST Arabidopsis thaliana protein match is: beta-galactosidase 14 (TAIR:AT4G38590.1); Has 3874 Blast hits to 2098 proteins in 386 species: Archae - 98; Bacteria - 366; Metazoa - 1194; Fungi - 916; Plants - 656; Viruses - 0; Other Eukaryotes - 644 (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
      1516030..1520563 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001340449.1 → NP_001329764.1  pre-mRNA splicing factor-like protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WVN9, Q9ZT71
      UniProtKB/TrEMBL
      A0A178UXT8
      Conserved Domains (6) summary
      smart00386
      Location:808 → 840
      HAT; HAT (Half-A-TPR) repeats
      sd00008
      Location:727 → 754
      TPR_YbbN; TPR repeat [structural motif]
      sd00006
      Location:761 → 788
      TPR; TPR repeat [structural motif]
      pfam06424
      Location:102 → 266
      PRP1_N; PRP1 splicing factor, N-terminal
      pfam13414
      Location:795 → 859
      TPR_11; TPR repeat
      pfam13432
      Location:832 → 895
      TPR_16; Tetratricopeptide repeat

    2. NM_001340448.1 → NP_001319859.1  pre-mRNA splicing factor-like protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WVN9, Q9ZT71
      UniProtKB/TrEMBL
      A0A178UXT8
      Conserved Domains (6) summary
      smart00386
      Location:808 → 840
      HAT; HAT (Half-A-TPR) repeats
      sd00008
      Location:727 → 754
      TPR_YbbN; TPR repeat [structural motif]
      sd00006
      Location:761 → 788
      TPR; TPR repeat [structural motif]
      pfam06424
      Location:102 → 266
      PRP1_N; PRP1 splicing factor, N-terminal
      pfam13414
      Location:795 → 859
      TPR_11; TPR repeat
      pfam13432
      Location:832 → 895
      TPR_16; Tetratricopeptide repeat

    3. NM_116581.2 → NP_192252.1  pre-mRNA splicing factor-like protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_192252.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WVN9, Q9ZT71
      UniProtKB/TrEMBL
      A0A178UXT8
      Conserved Domains (6) summary
      smart00386
      Location:808 → 840
      HAT; HAT (Half-A-TPR) repeats
      sd00008
      Location:727 → 754
      TPR_YbbN; TPR repeat [structural motif]
      sd00006
      Location:761 → 788
      TPR; TPR repeat [structural motif]
      pfam06424
      Location:102 → 266
      PRP1_N; PRP1 splicing factor, N-terminal
      pfam13414
      Location:795 → 859
      TPR_11; TPR repeat
      pfam13432
      Location:832 → 895
      TPR_16; Tetratricopeptide repeat
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ZT71.1

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