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Pre-mRNA-splicing factor 3 [ Arabidopsis thaliana (thale cress) ]

Gene ID: 839699, updated on 18-Sep-2024

Summary

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Official Full Name
Pre-mRNA-splicing factor 3
Primary source
TAIR:AT1G28060
Locus tag
AT1G28060
See related
Araport:AT1G28060
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
F13K9.16; F13K9_16; RDM16; RNA-directed DNA methylation 16
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Genomic context

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Location:
chromosome: 1
Exon count:
7
Sequence:
Chromosome: 1; NC_003070.9 (9778851..9782907)

Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene RING/U-box superfamily protein Neighboring gene B-box type zinc finger protein with CCT domain-containing protein Neighboring gene ATP-dependent RNA helicase Neighboring gene RING finger protein Neighboring gene ncRNA

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. A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis. Huang CF, et al. PLoS Genet, 2013. PMID 24068953, Free PMC Article
  2. 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
  3. Regulation of plant immunity through ubiquitin-mediated modulation of Ca(2+) -calmodulin-AtSR1/CAMTA3 signaling. Zhang L, et al. Plant J, 2014 Apr. PMID 24528504
  4. A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. McWhite CD, et al. Cell, 2020 Apr 16. PMID 32191846, Free PMC Article
  5. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Theologis A, et al. Nature, 2000 Dec 14. PMID 11130712

GeneRIFs: Gene References Into Functions

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

NM_001332796.1
NM_001332797.1
NM_102571.3

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in embryo development ending in seed dormancy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_positive_effect gene silencing by siRNA-directed DNA methylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of U4/U6 x U5 tri-snRNP complex IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm 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
Pre-mRNA-splicing factor 3
NP_001319094.1
  • Pre-mRNA-splicing factor 3; CONTAINS InterPro DOMAIN/s: Pre-mRNA-splicing factor 3 (InterPro:IPR013881); BEST Arabidopsis thaliana protein match is: Pre-mRNA-splicing factor 3 (TAIR:AT3G55930.1); Has 22923 Blast hits to 12760 proteins in 707 species: Archae - 18; Bacteria - 1085; Metazoa - 11525; Fungi - 3053; Plants - 1999; Viruses - 93; Other Eukaryotes - 5150 (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
    9778851..9782907
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001332796.1 → NP_001319094.1  Pre-mRNA-splicing factor 3 [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q8H0S1, Q9C7E7
    UniProtKB/TrEMBL
    A0A178WNB3, A0A5S9W5H6
    Conserved Domains (3) summary
    TIGR01622
    Location:38 → 105
    SF-CC1; splicing factor, CC1-like family
    pfam06544
    Location:657 → 780
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:404 → 631
    PRP3; pre-mRNA processing factor 3 (PRP3)

  2. NM_102571.3 → NP_174127.1  Pre-mRNA-splicing factor 3 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_174127.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q8H0S1, Q9C7E7
    UniProtKB/TrEMBL
    A0A178WNB3, A0A5S9W5H6
    Conserved Domains (3) summary
    TIGR01622
    Location:38 → 105
    SF-CC1; splicing factor, CC1-like family
    pfam06544
    Location:657 → 780
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:404 → 631
    PRP3; pre-mRNA processing factor 3 (PRP3)

  3. NM_001332797.1 → NP_001321377.1  Pre-mRNA-splicing factor 3 [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q8H0S1, Q9C7E7
    UniProtKB/TrEMBL
    A0A178WNB3, A0A5S9W5H6
    Conserved Domains (3) summary
    TIGR01622
    Location:38 → 105
    SF-CC1; splicing factor, CC1-like family
    pfam06544
    Location:657 → 780
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:404 → 631
    PRP3; pre-mRNA processing factor 3 (PRP3)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9C7E7.1

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