Basic Information
Gene Structure
Domain
Regulation&
Interaction
Annotation
Orthologus Group
Expresssion
Pathway
Basic Information
Gene ID
PH02Gene40694
View in Genome Browser
Position
hic_scaffold_23:35388093-35391433 (-)
3340bp
Gene Type
gene
Gene Description (Protein Product)
LSM domain
Organism
Phyllostachys edulis
Also AS AT3G14080

Gene Structure

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

Regulation&Interaction
Protein-protein interaction (PPI)
PH02Gene46550 LSM domain
PH02Gene49186 snRNP Sm proteins
PH02Gene42143 Catalyzes the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S- specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX
Regulatory gene
PH02Gene00769 TCP family transcription factor
PH02Gene00783 tesmin TSO1-like CXC
PH02Gene01001 ethylene-responsive transcription factor

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Annotation

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

Expression Profile
DataSet Number of Samples expressed(TPM>1) Mean Min Max Standard deviation(SD) Coeffcient variation(CV)


Pathway
Go Pathway KEGG Pathway
GO Term Description GO Category
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay BP
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA BP
GO:0000339 RNA cap binding MF
GO:0000932 P-body CC
GO:0000956 nuclear-transcribed mRNA catabolic process BP
GO:0001101 response to acid chemical BP
GO:0003674 molecular_function MF
GO:0003676 nucleic acid binding MF
GO:0003723 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:0005845 mRNA cap binding complex CC
GO:0006139 nucleobase-containing compound metabolic process BP
GO:0006396 RNA processing BP
GO:0006397 mRNA processing BP
GO:0006401 RNA catabolic process BP
GO:0006402 mRNA catabolic process BP
GO:0006725 cellular aromatic compound metabolic process BP
GO:0006807 nitrogen compound metabolic process BP
GO:0006950 response to stress BP
GO:0006970 response to osmotic stress BP
GO:0006972 hyperosmotic response BP
GO:0008150 biological_process BP
GO:0008152 metabolic process BP
GO:0009056 catabolic process BP
GO:0009057 macromolecule catabolic process BP
GO:0009266 response to temperature stimulus BP
GO:0009409 response to cold BP
GO:0009414 response to water deprivation BP
GO:0009415 response to water BP
GO:0009628 response to abiotic stimulus BP
GO:0009631 cold acclimation BP
GO:0009651 response to salt stress BP
GO:0009892 negative regulation of metabolic process BP
GO:0009987 cellular process BP
GO:0010035 response to inorganic substance BP
GO:0010467 gene expression BP
GO:0010468 regulation of gene expression BP
GO:0010605 negative regulation of macromolecule metabolic process BP
GO:0010629 negative regulation of gene expression BP
GO:0016070 RNA metabolic process BP
GO:0016071 mRNA metabolic process BP
GO:0019222 regulation of metabolic process BP
GO:0019439 aromatic compound catabolic process BP
GO:0032991 protein-containing complex CC
GO:0034518 RNA cap binding complex CC
GO:0034641 cellular nitrogen compound metabolic process BP
GO:0034655 nucleobase-containing compound catabolic process BP
GO:0035770 ribonucleoprotein granule CC
GO:0036464 cytoplasmic ribonucleoprotein granule CC
GO:0042221 response to chemical BP
GO:0042538 hyperosmotic salinity response BP
GO:0043170 macromolecule metabolic process BP
GO:0043226 organelle CC
GO:0043228 non-membrane-bounded organelle CC
GO:0043229 intracellular organelle CC
GO:0043232 intracellular non-membrane-bounded organelle CC
GO:0044237 cellular metabolic process BP
GO:0044238 primary metabolic process BP
GO:0044248 cellular catabolic process BP
GO:0044260 cellular macromolecule metabolic process BP
GO:0044265 cellular macromolecule catabolic process BP
GO:0044270 cellular nitrogen compound catabolic process BP
GO:0044424 obsolete intracellular part CC
GO:0044444 obsolete cytoplasmic part CC
GO:0044464 obsolete cell part CC
GO:0046483 heterocycle metabolic process BP
GO:0046700 heterocycle catabolic process BP
GO:0048519 negative regulation of biological process BP
GO:0050789 regulation of biological process BP
GO:0050896 response to stimulus BP
GO:0060255 regulation of macromolecule metabolic process BP
GO:0065007 biological regulation BP
GO:0071704 organic substance metabolic process BP
GO:0090304 nucleic acid metabolic process BP
GO:0097159 organic cyclic compound binding MF
GO:0120114 Sm-like protein family complex CC
GO:1901360 organic cyclic compound metabolic process BP
GO:1901361 organic cyclic compound catabolic process BP
GO:1901363 heterocyclic compound binding MF
GO:1901575 organic substance catabolic process BP
GO:1901700 response to oxygen-containing compound BP
GO:1990726 Lsm1-7-Pat1 complex CC
GO:1990904 ribonucleoprotein complex CC
KEGG Term Name Description
map03018 RNA degradation The correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay exist and both pathways are initiated by poly(A) shortening of the mRNA. In the 5' to 3' pathway, this is followed by decapping which then permits the 5' to 3' exonucleolytic degradation of transcripts. In the 3' to 5' pathway, the exosome, a large multisubunit complex, plays a key role. The exosome exists in archaeal cells, too. In bacteria, endoribonuclease E, a key enzyme involved in RNA decay and processing, organizes a protein complex called degradosome. RNase E or R interacts with the phosphate-dependent exoribonuclease polynucleotide phosphorylase, DEAD-box helicases, and additional factors in the RNA-degrading complex.