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Gene : PCFS4 A. thaliana

Gene ID  ? AT4G04885
Brief Description  PCF11P-similar protein 4  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? PCF11P-similar protein 4 (PCFS4); FUNCTIONS IN: zinc ion binding; INVOLVED IN: positive regulation of flower development, mRNA polyadenylation; LOCATED IN: nucleus, cytoplasm; EXPRESSED IN: shoot apical meristem, sepal, gynoecium, stamen, leaf; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF618 (InterPro:IPR006903), RNA polymerase II, large subunit, CTD (InterPro:IPR006569), Zinc finger, C2H2-type (InterPro:IPR007087), ENTH/VHS (InterPro:IPR008942); BEST Arabidopsis thaliana protein match is: Pre-mRNA cleavage complex II (TAIR:AT1G66500.1).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? Encodes PCFS4 (Pcf11p-similar protein 4), a homolog of yeast polyadenylation factor Protein 1 of Cleavage Factor (Pcf11p). Regulates FCA (AT4G16280) mRNA polyadenylation. Promotes flowering time.  Source: TAIR, Jun 30, 2015.
Name  ? PCF11P-similar protein 4

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2 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
Analysis of differential mRNA processing and expression of a polyadenylation factor mutant pcfs4 using arabidopsis tiling microarray. 21364912
plays a role in regulatory role in transcription and pre-mRNA processing; plays a role in Arabidopsis circadian rhythm 24004414


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12 Flanking Regions

Flank size: from most upstream transcription start site, or most downstream transcription stop site

Region Name Flank Size Direction Length Gene Included? Chromosome Location
AT4G04885 0.5kb upstream 0.5kb upstream 4660   true Chr4: 2471366-2476025
AT4G04885 0.5kb upstream 0.5kb upstream 500   false Chr4: 2471366-2471865
AT4G04885 0.5kb downstream 0.5kb downstream 4660   true Chr4: 2471866-2476525
AT4G04885 0.5kb downstream 0.5kb downstream 500   false Chr4: 2476026-2476525
AT4G04885 1.0kb upstream 1.0kb upstream 5160   true Chr4: 2470866-2476025
AT4G04885 1.0kb upstream 1.0kb upstream 1000   false Chr4: 2470866-2471865
AT4G04885 1.0kb downstream 1.0kb downstream 5160   true Chr4: 2471866-2477025
AT4G04885 1.0kb downstream 1.0kb downstream 1000   false Chr4: 2476026-2477025
AT4G04885 3.0kb upstream 3.0kb upstream 7160   true Chr4: 2468866-2476025
AT4G04885 3.0kb upstream 3.0kb upstream 3000   false Chr4: 2468866-2471865
AT4G04885 3.0kb downstream 3.0kb downstream 7160   true Chr4: 2471866-2479025
AT4G04885 3.0kb downstream 3.0kb downstream 3000   false Chr4: 2476026-2479025


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1 Pathways

Data Source: KEGG

Identifier Name
03015 mRNA surveillance pathway

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12 Data Sets

Name Description Version
BAR Annotations Lookup Mapping(s) between AGI locus and Affy Probeset identifier 10/08/2013
Genome Annotation Araport11 protein-coding, non-coding and transposable element genes Araport11 (06/2016)
RNA-seq expression Measure of gene expression levels (Transcripts per Million, TPM) quantified by Salmon Araport11 (06/2016)
PubMed to gene mapping Curated associations between publications and NCBI Gene records 8/12/2016
GO Annotation from GOC GO annotations assigned by the GO Consortium 8/01/2016
PO Annotation from TAIR Literature-based annotations of genes to Plant Ontology (PO) terms 06/30/2015
Swiss-Prot data set High-quality, manually annotated, non-redundant protein sequence database 2016_07
Panther data set PANTHER paralogs from Arabidopsis 11.0
KEGG pathways data set Wiring diagrams of molecular interactions, reactions, and relations 79.0
GeneRIF Concise phrase describing gene function and publication associated with NCBI Gene records 8/12/2016
IntAct interactions data set Curated binary and complex protein-protein interactions for Arabidopsis thaliana 8/02/2016
BioGRID interaction data set Curated set of genetic and physical interactions for Arabidopsis thaliana 3.4.139