Annotation of co-expression genes

PH01000561G0620's details annotation

1.Annotation

ICBR annotation: nonsense-mediated decay UPF3, putative, expressed

Blast result AT1G33980 : 1.30E-76
Blast annotation: Smg-4/UPF3 family protein

2.Location

Scaffold: PH01000561
Strand: -

RegionStartEnd
gene460548469084
mRNA460548469084
exon460548461050
exon461434461552
exon461660461725
exon461811462288
exon462368462465
exon463778463880
exon464627464731
exon464822464901
exon465024465122
exon465225465320
exon466731466837
exon467867469084
CDS460928461050
CDS461434461552
CDS461660461725
CDS461811462288
CDS462368462465
CDS463778463880
CDS464627464731
CDS464822464901
CDS465024465122
CDS465225465320
CDS466731466837
CDS467867468006

UCSC genome browser

3.Network

Co-expression Network CategoryGlobal NetworkConditional Network
Co-expression Positive Top300 PCC genelist

MR network genelist 		Top300 PCC genelist

MR network genelist
Co-expression Negative Top300 PCC genelist

MR network genelist 		Top300 PCC genelist

MR network genelist
Predict protein-portein interaction null
miRNA-targets relationshipnull
 

4.Functional module

MethodModule IDFunction Annotation
coexpression networkCFinderM000002extracellular region,
plant-type cell wall organization,
sexual reproduction,
glycerol metabolic process,
coexpression networkCFinderM000013cellulose biosynthetic process,
cellulose synthase (UDP-forming) activity,
response to oxidative stress,
extracellular polysaccharide biosynthetic process,
hydrolase activity, hydrolyzing O-glycosyl compounds,
carbohydrate metabolic process,
coexpression networkCFinderM000103plant-type cell wall organization,
extracellular region,
microtubule-based movement,
microtubule associated complex,
coexpression networkCFinderM000157RNA_transport
mRNA_surveillance_pathway
coexpression networkCFinderM000161Methane_metabolism
Phenylalanine_metabolism
Phenylpropanoid_biosynthesis
response to oxidative stress,
peroxidase activity,
heme binding,
cellulose biosynthetic process,
coexpression networkCFinderM000342ERF Transcription_Regulator(from PlantTFDB)
AP2/ERF-ERF Transcription_Regulator(from iTAK)
coexpression networkCFinderM000378extracellular region,
sexual reproduction,
RNA_transport
mRNA_surveillance_pathway
coexpression networkCFinderM000469CCAAT-binding factor complex,
NF-YA Transcription_Regulator(from PlantTFDB)
response to biotic stimulus,
coexpression networkCFinderM000528RLK-Pelle_RLCK-XIII (from iTAK)
base-excision repair,
Base_excision_repair
DNA-3-methyladenine glycosylase activity,
coexpression networkCFinderM000529RLK-Pelle_Extensin (from iTAK)
RLK-Pelle_RLCK-XIII (from iTAK)
coexpression networkCFinderM000689hydrolase activity, acting on ester bonds,
lipid metabolic process,
hydrolase activity,
RLK-Pelle_Extensin (from iTAK)
lipase activity,
lipid transport,
coexpression networkCFinderM001601GH35 Glycoside_Hydrolases
coexpression networkCFinderM001609RNA_transport
mRNA_surveillance_pathway

5.Cis-elements

Details in 3kb promoter region

6.Expression profilings


7.Gene family

CategoryFamily
nullnull

8.Protein domain

Pfam AccessionPfam AnnotationAlignment StartAlignment Start
PF03467.14Smg4_UPF37167

9.KEGG Pathway

PathwayKEGG OrthologPathway IDKO
RNA transportregulator of nonsense transcripts 3ko03013K14328
mRNA surveillance pathwayregulator of nonsense transcripts 3ko03015K14328

10.Gene Ontology

GO AccessionGO Annotation
GO:0000166nucleotide binding

Maintained by Xuelian Ma - Zhen Su's Lab - China Agricultural University
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