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Gene : emb1644 A. thaliana

Gene ID  ? AT5G27720
Brief Description  Small nuclear ribonucleoprotein family protein  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? embryo defective 1644 (emb1644); CONTAINS InterPro DOMAIN/s: Like-Sm ribonucleoprotein (LSM) domain (InterPro:IPR001163), Like-Sm ribonucleoprotein (LSM)-related domain (InterPro:IPR010920), Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (InterPro:IPR006649); BEST Arabidopsis thaliana protein match is: snRNP core protein SMD3 (TAIR:AT1G76300.1).  Source: TAIR, Jun 30, 2015.
Name  ? embryo defective 1644
  • synonyms:
  • LSM4,
  • SM-like protein 4

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1 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
SKB1 methylates the U6 snRNP LSM4 in response to salt stress and ABA. Loss of LSM4 results in growth retardation and hypersensitivity to salt. 21258002

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
AT5G27720 0.5kb upstream 0.5kb upstream 2619   true Chr5: 9815000-9817618
AT5G27720 0.5kb upstream 0.5kb upstream 500   false Chr5: 9815000-9815499
AT5G27720 0.5kb downstream 0.5kb downstream 2619   true Chr5: 9815500-9818118
AT5G27720 0.5kb downstream 0.5kb downstream 500   false Chr5: 9817619-9818118
AT5G27720 1.0kb upstream 1.0kb upstream 3119   true Chr5: 9814500-9817618
AT5G27720 1.0kb upstream 1.0kb upstream 1000   false Chr5: 9814500-9815499
AT5G27720 1.0kb downstream 1.0kb downstream 3119   true Chr5: 9815500-9818618
AT5G27720 1.0kb downstream 1.0kb downstream 1000   false Chr5: 9817619-9818618
AT5G27720 3.0kb upstream 3.0kb upstream 5119   true Chr5: 9812500-9817618
AT5G27720 3.0kb upstream 3.0kb upstream 3000   false Chr5: 9812500-9815499
AT5G27720 3.0kb downstream 3.0kb downstream 5119   true Chr5: 9815500-9820618
AT5G27720 3.0kb downstream 3.0kb downstream 3000   false Chr5: 9817619-9820618

Proteins

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Function

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2 Pathways

Data Source: KEGG

Identifier Name
03018 RNA degradation
03040 Spliceosome

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Expression

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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 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