Basic Information
Gene Structure
Domain
Regulation&
Interaction
Annotation
Orthologus Group
Pathway
Basic Information
Gene ID
Poman.15G061400.v1.1
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Position
Chr15:9565265-9566468 (+)
1203bp
Gene Type
gene
Gene Description (Protein Product)
nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription
Organism
Populus nigra x maximowiczii
Also AS Poman.15G061400AT4G32175Potri.015G075400.v4.1

Gene Structure

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

Regulation&Interaction
Protein-protein interaction (PPI)
Poman.18G035100.v1.1 Exosome complex exonuclease RRP46
Poman.17G077900.v1.1 U3 small nucleolar ribonucleoprotein protein
Poman.16G043400.v1.1 Exosome complex

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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:0000018 regulation of DNA recombination BP
GO:0000175 3'-5'-RNA exonuclease activity MF
GO:0000176 nuclear exosome (RNase complex) CC
GO:0000177 cytoplasmic exosome (RNase complex) CC
GO:0000178 exosome (RNase complex) CC
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay BP
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay BP
GO:0000291 nuclear-transcribed mRNA catabolic process, exonucleolytic BP
GO:0000459 exonucleolytic trimming involved in rRNA processing BP
GO:0000460 maturation of 5.8S rRNA BP
GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) BP
GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) BP
GO:0000469 cleavage involved in rRNA processing BP
GO:0000785 chromatin CC
GO:0000956 nuclear-transcribed mRNA catabolic process BP
GO:0001775 cell activation BP
GO:0002164 larval development BP
GO:0002200 somatic diversification of immune receptors BP
GO:0002204 somatic recombination of immunoglobulin genes involved in immune response BP
GO:0002208 somatic diversification of immunoglobulins involved in immune response BP
GO:0002250 adaptive immune response BP
GO:0002252 immune effector process BP
GO:0002263 cell activation involved in immune response BP
GO:0002285 lymphocyte activation involved in immune response BP
GO:0002312 B cell activation involved in immune response BP
GO:0002366 leukocyte activation involved in immune response BP
GO:0002376 immune system process BP
GO:0002377 immunoglobulin production BP
GO:0002381 immunoglobulin production involved in immunoglobulin-mediated immune response BP
GO:0002440 production of molecular mediator of immune response BP
GO:0002443 leukocyte mediated immunity BP
GO:0002449 lymphocyte mediated immunity BP
GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains BP
GO:0002520 immune system development BP
GO:0002562 somatic diversification of immune receptors via germline recombination within a single locus BP
GO:0002637 regulation of immunoglobulin production BP
GO:0002639 positive regulation of immunoglobulin production BP
GO:0002682 regulation of immune system process BP
GO:0002684 positive regulation of immune system process BP
GO:0002694 regulation of leukocyte activation BP
GO:0002696 positive regulation of leukocyte activation BP
GO:0002697 regulation of immune effector process BP
GO:0002699 positive regulation of immune effector process BP
GO:0002700 regulation of production of molecular mediator of immune response BP
GO:0002702 positive regulation of production of molecular mediator of immune response BP
GO:0002703 regulation of leukocyte mediated immunity BP
GO:0002705 positive regulation of leukocyte mediated immunity BP
GO:0002706 regulation of lymphocyte mediated immunity BP
GO:0002708 positive regulation of lymphocyte mediated immunity BP
GO:0002712 regulation of B cell mediated immunity BP
GO:0002714 positive regulation of B cell mediated immunity BP
GO:0002819 regulation of adaptive immune response BP
GO:0002821 positive regulation of adaptive immune response BP
GO:0002822 regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains BP
GO:0002824 positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains BP
GO:0002889 regulation of immunoglobulin mediated immune response BP
GO:0002891 positive regulation of immunoglobulin mediated immune response BP
GO:0003674 molecular_function MF
GO:0003676 nucleic acid binding MF
GO:0003723 RNA binding MF
GO:0003824 catalytic activity MF
GO:0004518 nuclease activity MF
GO:0004527 exonuclease activity MF
GO:0004532 exoribonuclease activity MF
GO:0004540 ribonuclease activity MF
GO:0005488 binding MF
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:0005694 chromosome CC
GO:0005730 nucleolus CC
GO:0005737 cytoplasm CC
GO:0005829 cytosol CC
GO:0006139 nucleobase-containing compound metabolic process BP
GO:0006259 DNA metabolic process BP
GO:0006304 DNA modification BP
GO:0006310 DNA recombination BP
GO:0006364 rRNA processing BP
GO:0006396 RNA processing BP
GO:0006399 tRNA metabolic process BP
GO:0006401 RNA catabolic process BP
GO:0006402 mRNA catabolic process BP
GO:0006403 RNA localization BP
GO:0006725 cellular aromatic compound metabolic process BP
GO:0006807 nitrogen compound metabolic process BP
GO:0006955 immune response BP
GO:0007275 multicellular organism development BP
GO:0008150 biological_process BP
GO:0008152 metabolic process BP
GO:0008298 intracellular mRNA localization BP
GO:0008408 3'-5' exonuclease activity MF
GO:0009056 catabolic process BP
GO:0009057 macromolecule catabolic process BP
GO:0009791 post-embryonic development BP
GO:0009892 negative regulation of metabolic process BP
GO:0009893 positive regulation of metabolic process BP
GO:0009894 regulation of catabolic process BP
GO:0009987 cellular process BP
GO:0010467 gene expression BP
GO:0010468 regulation of gene expression BP
GO:0010604 positive regulation of macromolecule metabolic process BP
GO:0010605 negative regulation of macromolecule metabolic process BP
GO:0010608 post-transcriptional regulation of gene expression BP
GO:0010629 negative regulation of gene expression BP
GO:0016064 immunoglobulin mediated immune response BP
GO:0016070 RNA metabolic process BP
GO:0016071 mRNA metabolic process BP
GO:0016072 rRNA metabolic process BP
GO:0016073 snRNA metabolic process BP
GO:0016074 sno(s)RNA metabolic process BP
GO:0016075 rRNA catabolic process BP
GO:0016078 tRNA catabolic process BP
GO:0016180 snRNA processing BP
GO:0016444 somatic cell DNA recombination BP
GO:0016445 somatic diversification of immunoglobulins BP
GO:0016447 somatic recombination of immunoglobulin gene segments BP
GO:0016787 hydrolase activity MF
GO:0016788 hydrolase activity, acting on ester bonds MF
GO:0016796 exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters MF
GO:0016896 RNA exonuclease activity, producing 5'-phosphomonoesters MF
GO:0019219 regulation of nucleobase-containing compound metabolic process BP
GO:0019222 regulation of metabolic process BP
GO:0019439 aromatic compound catabolic process BP
GO:0019724 B cell mediated immunity BP
GO:0022613 ribonucleoprotein complex biogenesis BP
GO:0030097 hemopoiesis BP
GO:0030145 manganese ion binding MF
GO:0031123 RNA 3'-end processing BP
GO:0031125 rRNA 3'-end processing BP
GO:0031126 sno(s)RNA 3'-end processing BP
GO:0031323 regulation of cellular metabolic process BP
GO:0031325 positive regulation of cellular metabolic process BP
GO:0031329 regulation of cellular catabolic process BP
GO:0031974 membrane-enclosed lumen CC
GO:0031981 nuclear lumen CC
GO:0032501 multicellular organismal process BP
GO:0032502 developmental process BP
GO:0032991 protein-containing complex CC
GO:0033036 macromolecule localization BP
GO:0034427 nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' BP
GO:0034470 ncRNA processing BP
GO:0034472 snRNA 3'-end processing BP
GO:0034475 U4 snRNA 3'-end processing BP
GO:0034641 cellular nitrogen compound metabolic process BP
GO:0034655 nucleobase-containing compound catabolic process BP
GO:0034660 ncRNA metabolic process BP
GO:0034661 ncRNA catabolic process BP
GO:0035166 post-embryonic hemopoiesis BP
GO:0035167 larval lymph gland hemopoiesis BP
GO:0035327 euchromatin CC
GO:0042113 B cell activation BP
GO:0042254 ribosome biogenesis BP
GO:0043144 sno(s)RNA processing BP
GO:0043167 ion binding MF
GO:0043169 cation binding MF
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:0043412 macromolecule modification BP
GO:0043487 regulation of RNA stability BP
GO:0043488 regulation of mRNA stability BP
GO:0043628 regulatory ncRNA 3'-end processing BP
GO:0043632 modification-dependent macromolecule catabolic process BP
GO:0043633 polyadenylation-dependent RNA catabolic process BP
GO:0043634 polyadenylation-dependent ncRNA catabolic process BP
GO:0043928 exonucleolytic catabolism of deadenylated mRNA BP
GO:0044085 cellular component biogenesis BP
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:0044422 obsolete organelle part CC
GO:0044424 obsolete intracellular part CC
GO:0044427 obsolete chromosomal part CC
GO:0044428 obsolete nuclear part CC
GO:0044444 obsolete cytoplasmic part CC
GO:0044446 obsolete intracellular organelle part CC
GO:0044464 obsolete cell part CC
GO:0045006 DNA deamination BP
GO:0045190 isotype switching BP
GO:0045191 regulation of isotype switching BP
GO:0045321 leukocyte activation BP
GO:0045830 positive regulation of isotype switching BP
GO:0045911 positive regulation of DNA recombination BP
GO:0045935 positive regulation of nucleobase-containing compound metabolic process BP
GO:0046483 heterocycle metabolic process BP
GO:0046649 lymphocyte activation BP
GO:0046700 heterocycle catabolic process BP
GO:0046872 metal ion binding MF
GO:0046914 transition metal ion binding MF
GO:0048513 animal organ development BP
GO:0048518 positive regulation of biological process BP
GO:0048519 negative regulation of biological process BP
GO:0048522 positive regulation of cellular process BP
GO:0048534 hematopoietic or lymphoid organ development BP
GO:0048542 lymph gland development BP
GO:0048569 post-embryonic animal organ development BP
GO:0048583 regulation of response to stimulus BP
GO:0048584 positive regulation of response to stimulus BP
GO:0048731 system development BP
GO:0048732 gland development BP
GO:0048856 anatomical structure development BP
GO:0050776 regulation of immune response BP
GO:0050778 positive regulation of immune response BP
GO:0050789 regulation of biological process BP
GO:0050793 regulation of developmental process BP
GO:0050794 regulation of cellular process BP
GO:0050864 regulation of B cell activation BP
GO:0050865 regulation of cell activation BP
GO:0050867 positive regulation of cell activation BP
GO:0050871 positive regulation of B cell activation BP
GO:0050896 response to stimulus BP
GO:0051052 regulation of DNA metabolic process BP
GO:0051054 positive regulation of DNA metabolic process BP
GO:0051094 positive regulation of developmental process BP
GO:0051171 regulation of nitrogen compound metabolic process BP
GO:0051173 positive regulation of nitrogen compound metabolic process BP
GO:0051179 localization BP
GO:0051239 regulation of multicellular organismal process BP
GO:0051240 positive regulation of multicellular organismal process BP
GO:0051249 regulation of lymphocyte activation BP
GO:0051251 positive regulation of lymphocyte activation BP
GO:0051252 regulation of RNA metabolic process BP
GO:0051641 cellular localization BP
GO:0060255 regulation of macromolecule metabolic process BP
GO:0061013 regulation of mRNA catabolic process BP
GO:0065007 biological regulation BP
GO:0065008 regulation of biological quality BP
GO:0070013 intracellular organelle lumen CC
GO:0070478 nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay BP
GO:0070481 nuclear-transcribed mRNA catabolic process, non-stop decay BP
GO:0070651 nonfunctional rRNA decay BP
GO:0070727 cellular macromolecule localization BP
GO:0071025 RNA surveillance BP
GO:0071027 nuclear RNA surveillance BP
GO:0071028 nuclear mRNA surveillance BP
GO:0071029 nuclear ncRNA surveillance BP
GO:0071031 nuclear mRNA surveillance of mRNA 3'-end processing BP
GO:0071033 nuclear mRNA surveillance BP
GO:0071034 CUT catabolic process BP
GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process BP
GO:0071038 nuclear polyadenylation-dependent tRNA catabolic process BP
GO:0071042 nuclear polyadenylation-dependent mRNA catabolic process BP
GO:0071043 CUT metabolic process BP
GO:0071046 nuclear polyadenylation-dependent ncRNA catabolic process BP
GO:0071047 polyadenylation-dependent mRNA catabolic process BP
GO:0071049 nuclear mRNA surveillance BP
GO:0071051 polyadenylation-dependent snoRNA 3'-end processing BP
GO:0071704 organic substance metabolic process BP
GO:0071840 cellular component organization or biogenesis BP
GO:0080090 regulation of primary metabolic process BP
GO:0090304 nucleic acid metabolic process BP
GO:0090305 nucleic acid phosphodiester bond hydrolysis BP
GO:0090501 RNA phosphodiester bond hydrolysis BP
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic BP
GO:0097159 organic cyclic compound binding MF
GO:0140098 catalytic activity, acting on RNA MF
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:1902494 catalytic complex CC
GO:1903311 regulation of mRNA metabolic process BP
GO:1905354 exoribonuclease complex CC
GO:2000026 regulation of multicellular organismal development BP
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.