help  | faq  | software  | ARAPORT

Gene : SDG25 A. thaliana

Gene ID  ? AT5G42400
Brief Description  SET domain protein 25  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? SET domain protein 25 (SDG25); CONTAINS InterPro DOMAIN/s: SET domain (InterPro:IPR001214), GYF (InterPro:IPR003169); BEST Arabidopsis thaliana protein match is: homologue of trithorax (TAIR:AT2G31650.1).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? Encodes ATXR7 (ARABIDOPSIS TRITHORAX-RELATED7), required for histone H3-K4 methylation and for transcriptional activation of Flowering Locus C.  Source: TAIR, Jun 30, 2015.
Name  ? SET domain protein 25
  • synonyms:
  • ARABIDOPSIS TRITHORAX-RELATED7,
  • ATXR7

Locus History Displayer

Publication Counts Displayer

3 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
Expression of FLC is down-regulated in the sdg25-1 histone methyltransferase mutant, and H3K36 dimethylation is slightly down-regulated at some regions of FLC. 19726574
H3K4 methylases, atxr7, appear to be required for methylation of lysine 4 of histone H3 and for transcriptional activation of FLOWERING LOCUS C. 19855050
ATXR7 is required for the regulation of SNC1 and RPP4 expression, suggesting that MOS9 functions together with ATXR7 to regulate the expression of NB-LRR-encoding Resistance genes. [ATXR7] 23690534

Genomics

Sequence Feature Displayer

Gene Structure Displayer

J Browse Displayer

Overlapping Features Displayer

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
AT5G42400 0.5kb upstream 0.5kb upstream 8231   true Chr5: 16953515-16961745
AT5G42400 0.5kb upstream 0.5kb upstream 500   false Chr5: 16961246-16961745
AT5G42400 0.5kb downstream 0.5kb downstream 8231   true Chr5: 16953015-16961245
AT5G42400 0.5kb downstream 0.5kb downstream 500   false Chr5: 16953015-16953514
AT5G42400 1.0kb upstream 1.0kb upstream 8731   true Chr5: 16953515-16962245
AT5G42400 1.0kb upstream 1.0kb upstream 1000   false Chr5: 16961246-16962245
AT5G42400 1.0kb downstream 1.0kb downstream 8731   true Chr5: 16952515-16961245
AT5G42400 1.0kb downstream 1.0kb downstream 1000   false Chr5: 16952515-16953514
AT5G42400 3.0kb upstream 3.0kb upstream 10731   true Chr5: 16953515-16964245
AT5G42400 3.0kb upstream 3.0kb upstream 3000   false Chr5: 16961246-16964245
AT5G42400 3.0kb downstream 3.0kb downstream 10731   true Chr5: 16950515-16961245
AT5G42400 3.0kb downstream 3.0kb downstream 3000   false Chr5: 16950515-16953514

Proteins

Protein Displayer


Function

Gene Ontology Displayer

0 Pathways

Data Source: KEGG

Gene --> Ontology term

Gene --> Pathways


Expression

Plant Ontology Displayer

Bar Efp Browser Displayer

Array Expression

RNA-seq Expression

Co-expression

Save / Export

 

 

 

 



Interactions

Cytoscape Network Displayer


Homology

Homologue Displayer

Phytomine Ortholog Displayer


Stocks

Alelle Table Displayer

Stock Gene Table Displayer


 

Other

10 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 TAIR GO annotations assigned by TAIR 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
BioGRID interaction data set Curated set of genetic and physical interactions for Arabidopsis thaliana 3.4.139