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Description : (at3g13300 : 338.0) Encodes VCS (VARICOSE). Involved in mRNA decapping. VCS forms a mRNA decapping complex with DCP1 (At1g08370) and DCP2 (At5g13570). Unlike DCP2, VCS itself does not have mRNA decapping activity in vitro. DCP1, DCP2 and VCS colocalize in cytoplasmic loci, which are putative Arabidopsis mRNA processing bodies. Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. These mutants also share a similar lethal phenotype at the seedling cotyledon stage, with disorganized veins, swollen root hairs, and altered epidermal cell morphology. VCS is also required for leaf development.; VARICOSE (VCS); FUNCTIONS IN: protein homodimerization activity, nucleotide binding; INVOLVED IN: mRNA catabolic process, deadenylation-independent decapping of nuclear-transcribed mRNA, leaf morphogenesis; LOCATED IN: cytosol, nucleus, cytoplasmic mRNA processing body; EXPRESSED IN: whole plant, guard cell, cultured cell; CONTAINS InterPro DOMAIN/s: WD40 repeat-like-containing domain (InterPro:IPR011046), WD40 repeat 2 (InterPro:IPR019782), WD40-repeat-containing domain (InterPro:IPR017986), WD40/YVTN repeat-like-containing domain (InterPro:IPR015943), WD40 repeat (InterPro:IPR001680), WD40 repeat, subgroup (InterPro:IPR019781); BEST Arabidopsis thaliana protein match is: varicose-related (TAIR:AT3G13290.1); Has 885 Blast hits to 799 proteins in 264 species: Archae - 2; Bacteria - 218; Metazoa - 230; Fungi - 185; Plants - 114; Viruses - 4; Other Eukaryotes - 132 (source: NCBI BLink). & (reliability: 676.0) & (original description: no original description)
Gene families : OG_42_0001770 (Orthogroups_2024-Update) Phylogenetic Tree(s): OG0001770_tree
Note:Only the main profile, including all conditions, is shown. Additional statistics and tissue specific profiles are available here.
| Type | Description | Actions |
|---|---|---|
| Neighborhood | Picea release: MA_10431534g0030 | |
| Cluster | HCCA clusters: Cluster_137 |
| Target | Alias | Description | ECC score | Gene Family Method | Actions |
|---|---|---|---|---|---|
| Bradi1g43097 | No alias | varicose-related | 0.03 | Orthogroups_2024-Update | |
| Bradi3g56517 | No alias | varicose-related | 0.04 | Orthogroups_2024-Update | |
| Cre12.g553100 | No alias | varicose-related | 0.02 | Orthogroups_2024-Update | |
| Glyma.09G016800 | No alias | Transducin/WD40 repeat-like superfamily protein | 0.03 | Orthogroups_2024-Update | |
| Glyma.15G122400 | No alias | varicose-related | 0.04 | Orthogroups_2024-Update | |
| Mp3g11710.1 | No alias | scaffold component VCS of mRNA decapping complex | 0.04 | Orthogroups_2024-Update | |
| PSME_00010984-RA | No alias | (at3g13300 : 912.0) Encodes VCS (VARICOSE). Involved... | 0.04 | Orthogroups_2024-Update | |
| Potri.016G002100 | No alias | Transducin/WD40 repeat-like superfamily protein | 0.04 | Orthogroups_2024-Update | |
| Pp1s124_170V6 | No alias | MDC11.13; transducin family protein / WD-40 repeat... | 0.03 | Orthogroups_2024-Update | |
| Seita.4G131500.1 | No alias | scaffold component *(VCS) of mRNA decapping complex | 0.04 | Orthogroups_2024-Update | |
| Sobic.004G256500.1 | No alias | scaffold component *(VCS) of mRNA decapping complex | 0.04 | Orthogroups_2024-Update | |
| evm.model.tig00001038.27 | No alias | (at3g13290 : 87.8) varicose-related (VCR); FUNCTIONS IN:... | 0.01 | Orthogroups_2024-Update |
| Type | GO Term | Name | Evidence | Source |
|---|---|---|---|---|
No GO annotation available for this sequence |
| Type | GO Term | Name | Evidence | Source |
|---|---|---|---|---|
| CC | GO:0000148 | 1,3-beta-D-glucan synthase complex | IEP | Predicted GO |
| MF | GO:0000155 | phosphorelay sensor kinase activity | IEP | Predicted GO |
| CC | GO:0000159 | protein phosphatase type 2A complex | IEP | Predicted GO |
| CC | GO:0000428 | DNA-directed RNA polymerase complex | IEP | Predicted GO |
| MF | GO:0003676 | nucleic acid binding | IEP | Predicted GO |
| MF | GO:0003723 | RNA binding | IEP | Predicted GO |
| MF | GO:0003843 | 1,3-beta-D-glucan synthase activity | IEP | Predicted GO |
| MF | GO:0004673 | protein histidine kinase activity | IEP | Predicted GO |
| MF | GO:0004842 | ubiquitin-protein transferase activity | IEP | Predicted GO |
| CC | GO:0005665 | RNA polymerase II, core complex | IEP | Predicted GO |
| BP | GO:0005991 | trehalose metabolic process | IEP | Predicted GO |
| BP | GO:0005992 | trehalose biosynthetic process | IEP | Predicted GO |
| BP | GO:0006074 | (1->3)-beta-D-glucan metabolic process | IEP | Predicted GO |
| BP | GO:0006075 | (1->3)-beta-D-glucan biosynthetic process | IEP | Predicted GO |
| BP | GO:0006139 | nucleobase-containing compound metabolic process | IEP | Predicted GO |
| BP | GO:0006351 | transcription, DNA-templated | IEP | Predicted GO |
| BP | GO:0006354 | DNA-templated transcription, elongation | IEP | Predicted GO |
| BP | GO:0006364 | rRNA processing | IEP | Predicted GO |
| BP | GO:0006366 | transcription by RNA polymerase II | IEP | Predicted GO |
| BP | GO:0006368 | transcription elongation from RNA polymerase II promoter | IEP | Predicted GO |
| BP | GO:0006396 | RNA processing | IEP | Predicted GO |
| BP | GO:0006725 | cellular aromatic compound metabolic process | IEP | Predicted GO |
| CC | GO:0008023 | transcription elongation factor complex | IEP | Predicted GO |
| CC | GO:0008287 | protein serine/threonine phosphatase complex | IEP | Predicted GO |
| BP | GO:0009058 | biosynthetic process | IEP | Predicted GO |
| BP | GO:0009059 | macromolecule biosynthetic process | IEP | Predicted GO |
| BP | GO:0009119 | ribonucleoside metabolic process | IEP | Predicted GO |
| BP | GO:0009312 | oligosaccharide biosynthetic process | IEP | Predicted GO |
| BP | GO:0009987 | cellular process | IEP | Predicted GO |
| BP | GO:0015969 | guanosine tetraphosphate metabolic process | IEP | Predicted GO |
| BP | GO:0016051 | carbohydrate biosynthetic process | IEP | Predicted GO |
| BP | GO:0016070 | RNA metabolic process | IEP | Predicted GO |
| BP | GO:0016072 | rRNA metabolic process | IEP | Predicted GO |
| BP | GO:0016192 | vesicle-mediated transport | IEP | Predicted GO |
| MF | GO:0016307 | phosphatidylinositol phosphate kinase activity | IEP | Predicted GO |
| BP | GO:0016569 | covalent chromatin modification | IEP | Predicted GO |
| BP | GO:0016570 | histone modification | IEP | Predicted GO |
| CC | GO:0016593 | Cdc73/Paf1 complex | IEP | Predicted GO |
| MF | GO:0016775 | phosphotransferase activity, nitrogenous group as acceptor | IEP | Predicted GO |
| BP | GO:0018130 | heterocycle biosynthetic process | IEP | Predicted GO |
| MF | GO:0019208 | phosphatase regulator activity | IEP | Predicted GO |
| BP | GO:0019438 | aromatic compound biosynthetic process | IEP | Predicted GO |
| MF | GO:0019787 | ubiquitin-like protein transferase activity | IEP | Predicted GO |
| MF | GO:0019888 | protein phosphatase regulator activity | IEP | Predicted GO |
| CC | GO:0030684 | preribosome | IEP | Predicted GO |
| CC | GO:0030880 | RNA polymerase complex | IEP | Predicted GO |
| CC | GO:0032040 | small-subunit processome | IEP | Predicted GO |
| BP | GO:0032774 | RNA biosynthetic process | IEP | Predicted GO |
| CC | GO:0032991 | protein-containing complex | IEP | Predicted GO |
| BP | GO:0034035 | purine ribonucleoside bisphosphate metabolic process | IEP | Predicted GO |
| BP | GO:0034637 | cellular carbohydrate biosynthetic process | IEP | Predicted GO |
| BP | GO:0034641 | cellular nitrogen compound metabolic process | IEP | Predicted GO |
| BP | GO:0034645 | cellular macromolecule biosynthetic process | IEP | Predicted GO |
| BP | GO:0034654 | nucleobase-containing compound biosynthetic process | IEP | Predicted GO |
| BP | GO:0042278 | purine nucleoside metabolic process | IEP | Predicted GO |
| BP | GO:0044237 | cellular metabolic process | IEP | Predicted GO |
| BP | GO:0044249 | cellular biosynthetic process | IEP | Predicted GO |
| BP | GO:0044271 | cellular nitrogen compound biosynthetic process | IEP | Predicted GO |
| CC | GO:0044428 | nuclear part | IEP | Predicted GO |
| CC | GO:0044451 | nucleoplasm part | IEP | Predicted GO |
| CC | GO:0044464 | cell part | IEP | Predicted GO |
| BP | GO:0046128 | purine ribonucleoside metabolic process | IEP | Predicted GO |
| BP | GO:0046351 | disaccharide biosynthetic process | IEP | Predicted GO |
| BP | GO:0046483 | heterocycle metabolic process | IEP | Predicted GO |
| CC | GO:0055029 | nuclear DNA-directed RNA polymerase complex | IEP | Predicted GO |
| CC | GO:0061695 | transferase complex, transferring phosphorus-containing groups | IEP | Predicted GO |
| BP | GO:0090304 | nucleic acid metabolic process | IEP | Predicted GO |
| BP | GO:0097659 | nucleic acid-templated transcription | IEP | Predicted GO |
| CC | GO:0098796 | membrane protein complex | IEP | Predicted GO |
| CC | GO:0098797 | plasma membrane protein complex | IEP | Predicted GO |
| BP | GO:1901068 | guanosine-containing compound metabolic process | IEP | Predicted GO |
| BP | GO:1901360 | organic cyclic compound metabolic process | IEP | Predicted GO |
| BP | GO:1901362 | organic cyclic compound biosynthetic process | IEP | Predicted GO |
| BP | GO:1901576 | organic substance biosynthetic process | IEP | Predicted GO |
| CC | GO:1902494 | catalytic complex | IEP | Predicted GO |
| CC | GO:1903293 | phosphatase complex | IEP | Predicted GO |
| CC | GO:1990234 | transferase complex | IEP | Predicted GO |
No InterPro domains available for this sequence
| No external refs found! |