Basic Information
Gene Structure
Domain
Regulation&
Interaction
Annotation
Orthologus Group
Pathway
Basic Information
Gene ID
gene-IMY05_011G0112200
View in Genome Browser
Position
CM029809.1:14863610-14868586 (+)
4976bp
Gene Type
gene
Gene Description (Protein Product)
"rnps1
Organism
Salix suchowensis
Also AS AT1G16610

Gene Structure

upstream:
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Domain
Database EntryID E-Value Start end InterPro ID Description

Regulation&Interaction
Protein-protein interaction (PPI)
gene-IMY05_C4843000300 U1 small nuclear ribonucleoprotein of 70kDa MW N terminal
gene-IMY05_014G0103900 RNA recognition motif
gene-IMY05_014G0103600 pre-mRNA-splicing factor
Regulatory gene
gene-IMY05_001G0005900 Trihelix transcription factor
gene-IMY05_001G0028100 Zinc finger protein
gene-IMY05_001G0057000 Homeobox-leucine zipper protein

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Annotation

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


Pathway
Go Pathway KEGG Pathway
GO Term Description GO Category
GO:0000375 RNA splicing, via transesterification reactions BP
GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile BP
GO:0000398 mRNA splicing, via spliceosome BP
GO:0005575 cellular_component CC
GO:0005622 intracellular anatomical structure CC
GO:0005623 obsolete cell CC
GO:0005634 nucleus CC
GO:0005654 nucleoplasm CC
GO:0005730 nucleolus CC
GO:0006139 nucleobase-containing compound metabolic process BP
GO:0006396 RNA processing BP
GO:0006397 mRNA processing BP
GO:0006725 cellular aromatic compound metabolic process BP
GO:0006807 nitrogen compound metabolic process BP
GO:0007154 cell communication BP
GO:0007165 signal transduction BP
GO:0008150 biological_process BP
GO:0008152 metabolic process BP
GO:0008380 RNA splicing BP
GO:0009743 response to carbohydrate BP
GO:0009756 carbohydrate mediated signaling BP
GO:0009987 cellular process BP
GO:0010033 response to organic substance BP
GO:0010182 sugar mediated signaling pathway BP
GO:0010467 gene expression BP
GO:0016070 RNA metabolic process BP
GO:0016071 mRNA metabolic process BP
GO:0016604 nuclear body CC
GO:0016607 nuclear speck CC
GO:0023052 signaling BP
GO:0031974 membrane-enclosed lumen CC
GO:0031981 nuclear lumen CC
GO:0034641 cellular nitrogen compound metabolic process BP
GO:0042221 response to chemical BP
GO:0043170 macromolecule metabolic process BP
GO:0043226 organelle CC
GO:0043227 membrane-bounded organelle CC
GO:0043228 non-membrane-bounded organelle CC
GO:0043229 intracellular organelle CC
GO:0043231 intracellular membrane-bounded organelle CC
GO:0043232 intracellular non-membrane-bounded organelle CC
GO:0043233 organelle lumen CC
GO:0044237 cellular metabolic process BP
GO:0044238 primary metabolic process BP
GO:0044422 obsolete organelle part CC
GO:0044424 obsolete intracellular part CC
GO:0044428 obsolete nuclear part CC
GO:0044446 obsolete intracellular organelle part CC
GO:0044451 obsolete nucleoplasm part CC
GO:0044464 obsolete cell part CC
GO:0046483 heterocycle metabolic process BP
GO:0050789 regulation of biological process BP
GO:0050794 regulation of cellular process BP
GO:0050896 response to stimulus BP
GO:0051716 cellular response to stimulus BP
GO:0065007 biological regulation BP
GO:0070013 intracellular organelle lumen CC
GO:0070887 cellular response to chemical stimulus BP
GO:0071310 cellular response to organic substance BP
GO:0071322 cellular response to carbohydrate stimulus BP
GO:0071704 organic substance metabolic process BP
GO:0090304 nucleic acid metabolic process BP
GO:1901360 organic cyclic compound metabolic process BP
GO:1901700 response to oxygen-containing compound BP
GO:1901701 cellular response to oxygen-containing compound BP
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.
map03013 RNA transport RNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) via mobile export receptors. The majority of RNAs, such as tRNAs, rRNAs, and U snRNAs, are transported by specific export receptors, which belong to the karyopherin-beta family proteins. A feature of karyopherins is their regulation by the small GTPase Ran. However, general mRNA export is mechanistically different. Nuclear export of mRNAs is functionally coupled to different steps in gene expression processes, such as transcription, splicing, 3'-end formation and even translation.