Basic Information
Gene Structure
Domain
Regulation&
Interaction
Annotation
Orthologus Group
Pathway
Basic Information
Gene ID
SESE_121408.g
View in Genome Browser
Position
Scaffold_167773:221993293-221995368 (+)
2075bp
Gene Type
gene
Gene Description (Protein Product)
U4atac snRNA binding
Organism
Sequoia sempervirens
Also AS AT4G22380

Gene Structure

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

Regulation&Interaction
Protein-protein interaction (PPI)
SESE_123116.g Small nuclear ribonucleoprotein
SESE_122796.g Nucleolar protein
SESE_139106.g Fibrillarin
Regulatory gene
SESE_000862.g Zinc finger CCCH domain-containing protein
SESE_007476.g dof zinc finger protein
SESE_022567.g dof zinc finger 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:0000003 reproduction BP
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:0000470 maturation of LSU-rRNA BP
GO:0000491 small nucleolar ribonucleoprotein complex assembly BP
GO:0000492 box C/D snoRNP assembly BP
GO:0001651 dense fibrillar component CC
GO:0001775 cell activation BP
GO:0002252 immune effector process BP
GO:0002263 cell activation involved in immune response BP
GO:0002274 myeloid leukocyte activation BP
GO:0002275 myeloid cell activation involved in immune response BP
GO:0002283 neutrophil activation involved in immune response BP
GO:0002366 leukocyte activation involved in immune response BP
GO:0002376 immune system process BP
GO:0002443 leukocyte mediated immunity BP
GO:0002444 myeloid leukocyte mediated immunity BP
GO:0002446 neutrophil mediated immunity BP
GO:0003674 molecular_function MF
GO:0003676 nucleic acid binding MF
GO:0003723 RNA binding MF
GO:0003729 mRNA binding MF
GO:0005488 binding MF
GO:0005515 protein binding MF
GO:0005575 cellular_component CC
GO:0005576 extracellular region CC
GO:0005615 extracellular space CC
GO:0005622 intracellular anatomical structure CC
GO:0005623 obsolete cell CC
GO:0005634 nucleus CC
GO:0005654 nucleoplasm CC
GO:0005681 spliceosomal complex CC
GO:0005684 U2-type spliceosomal complex CC
GO:0005690 U4atac snRNP CC
GO:0005730 nucleolus CC
GO:0005732 sno(s)RNA-containing ribonucleoprotein complex CC
GO:0005737 cytoplasm CC
GO:0005829 cytosol CC
GO:0005886 plasma membrane CC
GO:0006139 nucleobase-containing compound metabolic process BP
GO:0006364 rRNA processing BP
GO:0006396 RNA processing BP
GO:0006397 mRNA processing BP
GO:0006417 regulation of translation BP
GO:0006725 cellular aromatic compound metabolic process BP
GO:0006807 nitrogen compound metabolic process BP
GO:0006810 transport BP
GO:0006887 exocytosis BP
GO:0006955 immune response BP
GO:0007154 cell communication BP
GO:0007165 signal transduction BP
GO:0007166 cell surface receptor signaling pathway BP
GO:0007167 enzyme-linked receptor protein signaling pathway BP
GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway BP
GO:0007275 multicellular organism development BP
GO:0007338 single fertilization BP
GO:0007399 nervous system development BP
GO:0007422 peripheral nervous system development BP
GO:0007517 muscle organ development BP
GO:0008150 biological_process BP
GO:0008152 metabolic process BP
GO:0008283 cell population proliferation BP
GO:0008380 RNA splicing BP
GO:0009566 fertilization BP
GO:0009653 anatomical structure morphogenesis BP
GO:0009887 animal organ morphogenesis BP
GO:0009888 tissue development BP
GO:0009889 regulation of biosynthetic process BP
GO:0009891 positive regulation of biosynthetic process BP
GO:0009893 positive regulation of metabolic process BP
GO:0009987 cellular process BP
GO:0010467 gene expression BP
GO:0010468 regulation of gene expression BP
GO:0010556 regulation of macromolecule biosynthetic process BP
GO:0010557 positive regulation of macromolecule biosynthetic process BP
GO:0010604 positive regulation of macromolecule metabolic process BP
GO:0010608 post-transcriptional regulation of gene expression BP
GO:0010628 positive regulation of gene expression BP
GO:0012505 endomembrane system CC
GO:0016020 membrane CC
GO:0016043 cellular component organization BP
GO:0016070 RNA metabolic process BP
GO:0016071 mRNA metabolic process BP
GO:0016072 rRNA metabolic process BP
GO:0016192 vesicle-mediated transport BP
GO:0017069 snRNA binding MF
GO:0019222 regulation of metabolic process BP
GO:0019838 growth factor binding MF
GO:0019899 enzyme binding MF
GO:0019953 sexual reproduction BP
GO:0022414 reproductive process BP
GO:0022607 cellular component assembly BP
GO:0022613 ribonucleoprotein complex biogenesis BP
GO:0022618 ribonucleoprotein complex assembly BP
GO:0023052 signaling BP
GO:0030141 secretory granule CC
GO:0030490 maturation of SSU-rRNA BP
GO:0030515 snoRNA binding MF
GO:0030532 small nuclear ribonucleoprotein complex CC
GO:0030621 U4 snRNA binding MF
GO:0030622 U4atac snRNA binding MF
GO:0030684 preribosome CC
GO:0031323 regulation of cellular metabolic process BP
GO:0031325 positive regulation of cellular metabolic process BP
GO:0031326 regulation of cellular biosynthetic process BP
GO:0031328 positive regulation of cellular biosynthetic process BP
GO:0031410 cytoplasmic vesicle CC
GO:0031428 box C/D RNP complex CC
GO:0031974 membrane-enclosed lumen CC
GO:0031981 nuclear lumen CC
GO:0031982 vesicle CC
GO:0032040 small-subunit processome CC
GO:0032268 regulation of protein metabolic process BP
GO:0032270 positive regulation of protein metabolic process BP
GO:0032501 multicellular organismal process BP
GO:0032502 developmental process BP
GO:0032940 secretion by cell BP
GO:0032991 protein-containing complex CC
GO:0034248 regulation of amide metabolic process BP
GO:0034250 positive regulation of amide metabolic process BP
GO:0034470 ncRNA processing BP
GO:0034511 U3 snoRNA binding MF
GO:0034512 box C/D RNA binding MF
GO:0034622 protein-containing complex assembly BP
GO:0034641 cellular nitrogen compound metabolic process BP
GO:0034660 ncRNA metabolic process BP
GO:0036230 granulocyte activation BP
GO:0042119 neutrophil activation BP
GO:0042254 ribosome biogenesis BP
GO:0042273 ribosomal large subunit biogenesis BP
GO:0042274 ribosomal small subunit biogenesis 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:0043299 leukocyte degranulation BP
GO:0043312 neutrophil degranulation BP
GO:0043933 protein-containing complex organization BP
GO:0044085 cellular component biogenesis BP
GO:0044237 cellular metabolic process BP
GO:0044238 primary metabolic process BP
GO:0044421 obsolete extracellular region part CC
GO:0044422 obsolete organelle part CC
GO:0044424 obsolete intracellular part CC
GO:0044428 obsolete nuclear part CC
GO:0044433 obsolete cytoplasmic vesicle part CC
GO:0044444 obsolete cytoplasmic part CC
GO:0044446 obsolete intracellular organelle part CC
GO:0044452 obsolete nucleolar part CC
GO:0044464 obsolete cell part CC
GO:0044703 multi-organism reproductive process BP
GO:0045055 regulated exocytosis BP
GO:0045321 leukocyte activation BP
GO:0045727 positive regulation of translation BP
GO:0046483 heterocycle metabolic process BP
GO:0046540 U4/U6 x U5 tri-snRNP complex CC
GO:0046903 secretion BP
GO:0048008 platelet-derived growth factor receptor signaling pathway BP
GO:0048407 platelet-derived growth factor binding MF
GO:0048513 animal organ development BP
GO:0048518 positive regulation of biological process BP
GO:0048522 positive regulation of cellular process BP
GO:0048644 muscle organ morphogenesis BP
GO:0048729 tissue morphogenesis BP
GO:0048731 system development BP
GO:0048856 anatomical structure development BP
GO:0050789 regulation of biological process BP
GO:0050794 regulation of cellular process BP
GO:0050896 response to stimulus BP
GO:0051117 ATPase binding MF
GO:0051171 regulation of nitrogen compound metabolic process BP
GO:0051173 positive regulation of nitrogen compound metabolic process BP
GO:0051179 localization BP
GO:0051234 establishment of localization BP
GO:0051246 regulation of protein metabolic process BP
GO:0051247 positive regulation of protein metabolic process BP
GO:0051704 obsolete multi-organism process BP
GO:0051716 cellular response to stimulus BP
GO:0060255 regulation of macromolecule metabolic process BP
GO:0060415 muscle tissue morphogenesis BP
GO:0061061 muscle structure development BP
GO:0065003 protein-containing complex assembly BP
GO:0065007 biological regulation BP
GO:0070013 intracellular organelle lumen CC
GO:0071005 U2-type precatalytic spliceosome CC
GO:0071011 precatalytic spliceosome CC
GO:0071704 organic substance metabolic process BP
GO:0071826 ribonucleoprotein complex subunit organization BP
GO:0071840 cellular component organization or biogenesis BP
GO:0071944 cell periphery CC
GO:0080090 regulation of primary metabolic process BP
GO:0090304 nucleic acid metabolic process BP
GO:0097159 organic cyclic compound binding MF
GO:0097525 spliceosomal snRNP complex CC
GO:0097526 spliceosomal tri-snRNP complex CC
GO:0097708 intracellular vesicle CC
GO:0099503 secretory vesicle CC
GO:0101002 ficolin-1-rich granule CC
GO:0120114 Sm-like protein family complex CC
GO:1901360 organic cyclic compound metabolic process BP
GO:1901363 heterocyclic compound binding MF
GO:1904813 ficolin-1-rich granule lumen CC
GO:1990904 ribonucleoprotein complex CC
GO:2000112 regulation of cellular macromolecule biosynthetic process BP
KEGG Term Name Description
map03040 Spliceosome After transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, the spliceosome. The standard spliceosome is made up of five small nuclear ribonucleoproteins (snRNPs), U1, U2, U4, U5, and U6 snRNPs, and several spliceosome-associated proteins (SAPs). Spliceosomes are not a simple stable complex, but a dynamic family of particles that assemble on the mRNA precursor and help fold it into a conformation that allows transesterification to proceed. Various spliceosome forms (e.g. A-, B- and C-complexes) have been identified.
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.
map03008 Ribosome biogenesis in eukaryotes Ribosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It requires hundreds of factors not present in the mature particle. In the absence of these proteins, ribosome biogenesis is stalled and cell growth is terminated even under optimal growth conditions. The primary pre-rRNA transcript is assembled into the 90S pre-ribosome, which contains both 40S and 60S assembly factors. Within this complex, the pre-rRNA is cleaved. pre-60S ribosomes are subjected to several sequential processing steps in the nucleoplasm involving numerous assembly intermediates before it is exported to the cytoplasm and matured into the 60S ribosomal subunit. The pre-40S ribosome is matured to the small ribosomal subunit in the cytoplasm by cleavage.