Gene Details:

• Gene ID: AT3G13300
• Gene Symbol: VCS
• Gene Name: VARICOSE
• Description: Transducin/WD40 repeat-like superfamily protein;(source:Araport11)
• TAIR Accession:
• Genome: Araport11_genome_release
• Species: Arabidopsis thaliana

Transcripts:

• AT3G13300.1     AT3G13300.2     AT3G13300.3

Plant Ontology Annotations:

• PO:0000003  — whole plant — planta entera (Spanish, exact), 植物体全体 (Japanese, exact), clonal colony (related), colony (related), bush (narrow), frutex (narrow), frutices (narrow), gametophyte (narrow), herb (narrow), liana (narrow), prothalli (narrow), prothallium (narrow), prothallus (narrow), seedling (narrow), shrub (narrow), sporophyte (narrow), suffrutex (narrow), suffrutices (narrow), tree (narrow), vine (narrow), woody clump (narrow), genet (broad), ramet (broad)

Germplasm Phenotype:

• CS66952  — No visible phenotype.
• CS66954  — No visible phenotype.
• CS66956  — No visible phenotype.
• CS66958  — No visible phenotype.
• CS66960  — No visible phenotype.
• CS66962  — No visible phenotype.
• CS66963  — No visible phenotype.
• CS66965  — No visible phenotype.
• CS66967  — No visible phenotype.
• CS66971  — No visible phenotype.
• CS66972  — No visible phenotype.
• VCS:vcs-7  — In the progeny of selfed heterozygous mutants, the homozygous vcs-7 embryos were also clearly distinguished from their siblings based on their SAM morphology (seven vcs-7 embryos out of 25 embryos examined). These vcs-7 embryos contained small dense cells in the SAM region; however, this region was not dome-shaped, nor were the cells organized into distinct layers.
• VCS:vcs1/VCS:vcs7  — The transheterozygote was indistinguishable from vcs-1; it produced green organs, a longer root, and leaves that expanded to become broad and pointed.
• vcs-1  — 29°C-grown vcs apices contained multiple clusters of small densely staining cells dispersed across the apical region and often in close proximity to leaf-like structures, but no typical SAM.
• vcs-1  — Accumulates extra ectopic tracheary elements within their cotyledons and the upper hypocotyl.
• vcs-1  — Smaller than the wild type, and produced narrow, asymmetric leaves when grown at 22°C. All five mutant alleles showed identical phenotypic responses to growth temperature. When grown at 16°C, vcs mutants resembled the wild-type controls except their leaves were pointed at the apex, and prolonged growth revealed defects in apical dominance. By contrast, growth at 29°C resulted in a strongly enhanced phenotype. These high temperature-grown mutants were chlorotic, leaves were narrow and epinastic, and prolonged growth resulted in a callus-like growth at the apex. vcs roots appeared similar to those of wild type, except that at high temperature root hairs occasionally appeared swollen. vcs also produced decreased numbers of lateral roots.
• vcs-1  — The wild-type SAM was similar in size and organ phyllotaxy regardless of growth temperature. By contrast, the vcs SAM was smaller than the wild type; this defect was most severe in the 29°C-grown vcs plants, where the SAM appeared small and flat.
• vcs-1  — When grown at 22°C, vcs-1 mutants were green, had slightly longer roots, and produced narrow, pointed leaves.
• vcs-2  — 29°C-grown vcs apices contained multiple clusters of small densely staining cells dispersed across the apical region and often in close proximity to leaf-like structures, but no typical SAM.
• vcs-2  — Accumulates extra ectopic tracheary elements within their cotyledons and the upper hypocotyl.
• vcs-2  — Smaller than the wild type, and produced narrow, asymmetric leaves when grown at 22°C. All five mutant alleles showed identical phenotypic responses to growth temperature. When grown at 16°C, vcs mutants resembled the wild-type controls except their leaves were pointed at the apex, and prolonged growth revealed defects in apical dominance. By contrast, growth at 29°C resulted in a strongly enhanced phenotype. These high temperature-grown mutants were chlorotic, leaves were narrow and epinastic, and prolonged growth resulted in a callus-like growth at the apex. vcs roots appeared similar to those of wild type, except that at high temperature root hairs occasionally appeared swollen. vcs also produced decreased numbers of lateral roots.
• vcs-2  — The wild-type SAM was similar in size and organ phyllotaxy regardless of growth temperature. By contrast, the vcs SAM was smaller than the wild type; this defect was most severe in the 29°C-grown vcs plants, where the SAM appeared small and flat.
• vcs-3  — 29°C-grown vcs apices contained multiple clusters of small densely staining cells dispersed across the apical region and often in close proximity to leaf-like structures, but no typical SAM.
• vcs-3  — Accumulates extra ectopic tracheary elements within their cotyledons and the upper hypocotyl.
• vcs-3  — Smaller than the wild type, and produced narrow, asymmetric leaves when grown at 22°C. All five mutant alleles showed identical phenotypic responses to growth temperature. When grown at 16°C, vcs mutants resembled the wild-type controls except their leaves were pointed at the apex, and prolonged growth revealed defects in apical dominance. By contrast, growth at 29°C resulted in a strongly enhanced phenotype. These high temperature-grown mutants were chlorotic, leaves were narrow and epinastic, and prolonged growth resulted in a callus-like growth at the apex. vcs roots appeared similar to those of wild type, except that at high temperature root hairs occasionally appeared swollen. vcs also produced decreased numbers of lateral roots.
• vcs-3  — The wild-type SAM was similar in size and organ phyllotaxy regardless of growth temperature. By contrast, the vcs SAM was smaller than the wild type; this defect was most severe in the 29°C-grown vcs plants, where the SAM appeared small and flat.
• vcs-4  — 29°C-grown vcs apices contained multiple clusters of small densely staining cells dispersed across the apical region and often in close proximity to leaf-like structures, but no typical SAM.
• vcs-4  — Accumulates extra ectopic tracheary elements within their cotyledons and the upper hypocotyl.
• vcs-4  — Smaller than the wild type, and produced narrow, asymmetric leaves when grown at 22°C. All five mutant alleles showed identical phenotypic responses to growth temperature. When grown at 16°C, vcs mutants resembled the wild-type controls except their leaves were pointed at the apex, and prolonged growth revealed defects in apical dominance. By contrast, growth at 29°C resulted in a strongly enhanced phenotype. These high temperature-grown mutants were chlorotic, leaves were narrow and epinastic, and prolonged growth resulted in a callus-like growth at the apex. vcs roots appeared similar to those of wild type, except that at high temperature root hairs occasionally appeared swollen. vcs also produced decreased numbers of lateral roots.
• vcs-4  — The wild-type SAM was similar in size and organ phyllotaxy regardless of growth temperature. By contrast, the vcs SAM was smaller than the wild type; this defect was most severe in the 29°C-grown vcs plants, where the SAM appeared small and flat.
• vcs-5  — 29°C-grown vcs apices contained multiple clusters of small densely staining cells dispersed across the apical region and often in close proximity to leaf-like structures, but no typical SAM.
• vcs-5  — Accumulates extra ectopic tracheary elements within their cotyledons and the upper hypocotyl.
• vcs-5  — Smaller than the wild type, and produced narrow, asymmetric leaves when grown at 22°C. All five mutant alleles showed identical phenotypic responses to growth temperature. When grown at 16°C, vcs mutants resembled the wild-type controls except their leaves were pointed at the apex, and prolonged growth revealed defects in apical dominance. By contrast, growth at 29°C resulted in a strongly enhanced phenotype. These high temperature-grown mutants were chlorotic, leaves were narrow and epinastic, and prolonged growth resulted in a callus-like growth at the apex. vcs roots appeared similar to those of wild type, except that at high temperature root hairs occasionally appeared swollen. vcs also produced decreased numbers of lateral roots.
• vcs-5  — The wild-type SAM was similar in size and organ phyllotaxy regardless of growth temperature. By contrast, the vcs SAM was smaller than the wild type; this defect was most severe in the 29°C-grown vcs plants, where the SAM appeared small and flat.
• vcs-6  — Fork-like appearance of cotyledon secondary veins similar to that of vcs-7.
• vcs-6  — Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. The homozygous progeny of 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-7  — Cotyledons of wild-type and vcs-1 plants contain a primary vein and four secondary veins that form between two and four closed loops, whereas in vcs-7, the cotyledon secondary veins were mostly free-ending, resulting in a fork-like appearance.
• vcs-7  — Growth of vcs-7 at 16°C resulted in only modest suppression of growth.
• vcs-7  — Mutants produced cotyledons that expanded slowly and accumulated anthocyanins around their margins, hypocotyls that were short and slightly swollen, and root hairs that were short and swollen. These traits were similar to those we reported previously for vcs-1 grown at 29°C. The vcs-7 mutant also showed cotyledon vein pattern defects.
• vcs-7  — The SAM of the vcs-7 3-d-old seedlings varied: some were modestly rounded and layered, whereas others were more similar to the tdt embryonic SAM; however, none had leaf primordia.
• vcs-7  — When grown at 22°C, vcs-7 mutants had short roots, small chlorotic cotyledons, and typically failed to produce leaf primordia.
• vcs-7 tdt-1  — Appears similar to the single mutants.

Function-related keywords:

• whole plant

Literature:

• VARICOSE, a WD-domain protein, is required for leaf blade development.   DOI:  10.1242/dev.00909 ;  PMID:  14660546
• Intron retention is a major phenomenon in alternative splicing in Arabidopsis.   DOI:  10.1111/j.1365-313X.2004.02172.x ;  PMID:  15341630
• Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development.   DOI:  10.1105/tpc.106.047605 ;  PMID:  17158604
• Components of the Arabidopsis mRNA decapping complex are required for early seedling development.   DOI:  10.1105/tpc.106.047621 ;  PMID:  17513503
• Site-specific phosphorylation profiling of Arabidopsis proteins by mass spectrometry and peptide chip analysis.   DOI:  10.1021/pr8000173 ;  PMID:  18433157
• Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.   DOI:  10.1104/pp.108.121038 ;  PMID:  18650403
• Arabidopsis decapping 5 is required for mRNA decapping, P-body formation, and translational repression during postembryonic development.   DOI:  10.1105/tpc.109.070078 ;  PMID:  19855049
• The role of decapping proteins in the miRNA accumulation in Arabidopsis thaliana.   DOI:  10.4161/rna.19877 ;  PMID:  22614834
• 5' to 3' mRNA Decay Contributes to the Regulation of Arabidopsis Seed Germination by Dormancy.   DOI:  10.1104/pp.16.01933 ;  PMID:  28126845
• Arabidopsis mRNA decay landscape arises from specialized RNA decay substrates, decapping-mediated feedback, and redundancy.   DOI:  10.1073/pnas.1712312115 ;  PMID:  29386391
• Protein and metabolite composition of Arabidopsis stress granules.   DOI:  10.1111/nph.15690 ;  PMID:  30664249
• SnRK2 Protein Kinases and mRNA Decapping Machinery Control Root Development and Response to Salt.   DOI:  10.1104/pp.19.00818 ;  PMID:  31570508
• Non-TZF Protein AtC3H59/ZFWD3 Is Involved in Seed Germination, Seedling Development, and Seed Development, Interacting with PPPDE Family Protein Desi1 in Arabidopsis.   DOI:  10.3390/ijms22094738 ;  PMID:  33947021
• A NYN domain protein directly interacts with DECAPPING1 and is required for phyllotactic pattern.   DOI:  10.1093/plphys/kiab529 ;  PMID:  34791434
• Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development.   DOI:  10.1105/tpc.106.047605 ;  PMID:  17158604
• Site-specific phosphorylation profiling of Arabidopsis proteins by mass spectrometry and peptide chip analysis.   DOI:  10.1021/pr8000173 ;  PMID:  18433157
• Site-specific phosphorylation profiling of Arabidopsis proteins by mass spectrometry and peptide chip analysis.   DOI:  10.1021/pr8000173 ;  PMID:  18433157

Sequences: