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Gene : AT5G08565 A. thaliana

Gene ID  ? AT5G08565
Brief Description  Transcription initiation Spt4-like protein  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? Transcription initiation Spt4-like protein; FUNCTIONS IN: positive transcription elongation factor activity, zinc ion binding; INVOLVED IN: positive regulation of transcription; LOCATED IN: nucleus; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Transcription initiation Spt4 (InterPro:IPR009287), Transcription initiation Spt4-like (InterPro:IPR016046); BEST Arabidopsis thaliana protein match is: SPT4 homolog 2 (TAIR:AT5G63670.1).  Source: TAIR, Jun 30, 2015.
  • synonyms:
  • SPT4-1

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2 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
SPT4/SPT5 acts as a transcript elongation factor in Arabidopsis, regulating transcription during the elongation stage with particular impact on the expression of certain auxin-related genes. 24497194
Data indicate that SPT4 is a novel component of the plant RNA-directed DNA methylation pathway required for efficient DNA methylation at various loci and shares the locus specificity with SPT5L. 26424658

Genomics

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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
AT5G08565 0.5kb upstream 0.5kb upstream 2078   true Chr5: 2775397-2777474
AT5G08565 0.5kb upstream 0.5kb upstream 500   false Chr5: 2775397-2775896
AT5G08565 0.5kb downstream 0.5kb downstream 2078   true Chr5: 2775897-2777974
AT5G08565 0.5kb downstream 0.5kb downstream 500   false Chr5: 2777475-2777974
AT5G08565 1.0kb upstream 1.0kb upstream 2578   true Chr5: 2774897-2777474
AT5G08565 1.0kb upstream 1.0kb upstream 1000   false Chr5: 2774897-2775896
AT5G08565 1.0kb downstream 1.0kb downstream 2578   true Chr5: 2775897-2778474
AT5G08565 1.0kb downstream 1.0kb downstream 1000   false Chr5: 2777475-2778474
AT5G08565 3.0kb upstream 3.0kb upstream 4578   true Chr5: 2772897-2777474
AT5G08565 3.0kb upstream 3.0kb upstream 3000   false Chr5: 2772897-2775896
AT5G08565 3.0kb downstream 3.0kb downstream 4578   true Chr5: 2775897-2780474
AT5G08565 3.0kb downstream 3.0kb downstream 3000   false Chr5: 2777475-2780474

Proteins

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0 Pathways

Data Source: KEGG

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Expression

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Interactions

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Homology

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9 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 UniProt GO annotations assigned by UniProt 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
GeneRIF Concise phrase describing gene function and publication associated with NCBI Gene records 8/12/2016