PPGR - Gene Detail

Basic Information

Gene ID	SESE_141648.g View in Genome Browser
Position	Scaffold_251294:44801734-44803008 (-) 1274bp
Gene Type	gene
Gene Description (Protein Product)	RNA recognition motif
Organism	Sequoia sempervirens
Also AS	AT4G26650

upstream:

Domain

Database	EntryID	E-Value	Start	end	InterPro ID	Description

Regulation&Interaction

Protein-protein interaction (PPI)

SESE_148046.g contain most of the conserved domains of hsU2AF35, including the psiRRM, one RS domain, two zinc fingers, and the two regions for interacting with U2AF large subunit. Both proteins lack the stretch of glycines present in human U2AF35. The sequences are overall 83 identical, and each Arabidopsis homolog shows approximately 70 similarity to hsU2AF35. U2AF(35) homologs were also identified from maize, rice and other plants with large-scale EST projects. Both genes are expressed in all major tissues, with atU2AF(35)a expressed at a higher level than atU2AF(35)b in most tissues. The expression patterns were different in roots atU2AF(35)b expressed strongly in whole young roots and root tips and atU2AF(35)a limited to root vascular regions

SESE_149125.g contain most of the conserved domains of hsU2AF35, including the psiRRM, one RS domain, two zinc fingers, and the two regions for interacting with U2AF large subunit. Both proteins lack the stretch of glycines present in human U2AF35. The sequences are overall 83 identical, and each Arabidopsis homolog shows approximately 70 similarity to hsU2AF35. U2AF(35) homologs were also identified from maize, rice and other plants with large-scale EST projects. Both genes are expressed in all major tissues, with atU2AF(35)a expressed at a higher level than atU2AF(35)b in most tissues. The expression patterns were different in roots atU2AF(35)b expressed strongly in whole young roots and root tips and atU2AF(35)a limited to root vascular regions

Regulatory gene

SESE_003751.g transcription factor

SESE_004139.g homeobox-leucine zipper protein

SESE_006675.g Zinc finger AN1 and C2H2 domain-containing stress-associated protein

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Annotation

Orthologous Group

Orthologous ID	Species Number	All hits in PereRegDB	Hits of this species	Orthologous Detail

Pathway

GO Term	Description	GO Category
GO:0003674	molecular_function	MF
GO:0003676	nucleic acid binding	MF
GO:0003723	RNA binding	MF
GO:0003727	single-stranded RNA binding	MF
GO:0005488	binding	MF
GO:0005575	cellular_component	CC
GO:0005622	intracellular anatomical structure	CC
GO:0005623	obsolete cell	CC
GO:0005737	cytoplasm	CC
GO:0005844	polysome	CC
GO:0008150	biological_process	BP
GO:0008187	poly-pyrimidine tract binding	MF
GO:0008266	poly(U) RNA binding	MF
GO:0009987	cellular process	BP
GO:0030154	cell differentiation	BP
GO:0032502	developmental process	BP
GO:0032991	protein-containing complex	CC
GO:0044424	obsolete intracellular part	CC
GO:0044464	obsolete cell part	CC
GO:0048468	cell development	BP
GO:0048856	anatomical structure development	BP
GO:0048863	stem cell differentiation	BP
GO:0048864	stem cell development	BP
GO:0048869	cellular developmental process	BP
GO:0097159	organic cyclic compound binding	MF
GO:1901363	heterocyclic compound binding	MF
GO:1990904	ribonucleoprotein complex	CC

KEGG Term	Name	Description
map03015	mRNA surveillance pathway	The mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go decay (NGD). NMD is a mechanism that eliminates mRNAs containing premature translation-termination codons (PTCs). In vertebrates, PTCs trigger efficient NMD when located upstream of an exon junction complex (EJC). Upf3, together with Upf1 and Upf2, may signal the presence of the PTC to the 5'end of the transcript, resulting in decapping and rapid exonucleolytic digestion of the mRNA. In the NSD pathway, which targets mRNAs lacking termination codons, the ribosome is believed to translate through the 3' untranslated region and stall at the end of the poly(A) tail. NSD involves an eRF3-like protein, Ski7p, which is hypothesized to bind the empty A site of the ribosome and recruit the exosome to degrade the mRNA from the 3' end. NGD targets mRNAs with stalls in translation elongation for endonucleolytic cleavage in a process involving the Dom34 and Hbs1 proteins.