Show all genes, phenotypes and metabolites for which the QTL profile correlates with that of the query profile above the set cut-off, the query trait is in the first row.
Strongly correlating QTL profiles could indicate common regulation.
Encodes a RNA binding protein ELF9 (EARLY FLOWERING9). Loss of ELF9 function in the Wassilewskija ecotype causes early flowering in short days. ELF9 reduces SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CO1) transcript levels%2C possibly via nonsense-mediated mRNA decay.
Encodes a transcriptional factor TFIIIA required for transcription of 5S rRNA gene. 5S rRNA is the smallest constituent of the ribosome. Work on one of the gene models AT1G72050.2 showed that it encodes a protein with nine Cys(2)-His(2)-type zinc fingers%2C a characteristic feature of TFIIIA proteins. AT1G72050.2 also contains a 23 amino acid spacer between fingers 1 and 2%2C a 66 amino acid spacer between fingers 4 and 5%2C and a 50 amino acid non-finger C-terminal tail. in vitro assay demonstrated that AT1g72050.2 binds to 5S rDNA and efficiently stimulates the transcription of 5S rRNA. AT1g72050.2 also binds to 5S rRNA in vitro. AT1g72050.2 is located at several nuclear foci including the nucleolus and is absent from the cytoplasm.
Nucleotide/sugar transporter family protein%3B CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF6%2C transmembrane (InterPro:IPR000620)%2C Protein of unknown function DUF250 (InterPro:IPR004853)%3B BEST Arabidopsis thaliana protein match is: Nucleotide-sugar transporter family protein (TAIR:AT5G25400.1)%3B Has 2283 Blast hits to 2278 proteins in 296 species: Archae - 6%3B Bacteria - 116%3B Metazoa - 574%3B Fungi - 390%3B Plants - 969%3B Viruses - 0%3B Other Eukaryotes - 228 (source: NCBI BLink).
Encodes a protein that is found in not only the eif3 complex but also in association with subunits of the COP9 signalosome. eIF3e appears to be subjected to proteasome-dependent degradation that requires the PCI domain of eIF3e. The level of eIF3e present in cells appears to affect the rate of translation.
This gene is predicted to encode a protein involved in the exon junction complex. Though there is a predicted RNA binding motif%2C in the Drosophila ortholog (33%25 identity)%2C this motif mediates interactions with Mago and is not available for RNA binding. The Arabidopsis Y14 protein appears to be predominantly nucleolar%2C but there is also some evidence for its presence in the cytoplasm.
encodes a serine-threonine protein kinase whose expression increases in response to abscisic acid%2C cold%2C drought%2C high salt%2C and wounding conditions. The gene is expressed in developing seeds and seedlings. Lines carrying a T-DNA insertions have reduced germination efficiency and expression of cold%2C high-salt%2C and abscisic acid marker genes are altered%2C but not drought-response markers.
Encodes AtLa1%2C a member of the highly abundant phosphoprotein La proteins. Predominantly localized to the nucleoplasm and was also detected in the nucleolar cavity. Has RNA binding activity. Required for normal ribosome biogenesis and embryogenesis.
Encodes an isoamylase-like protein. Mutant studies show that the gene is strongly involved in starch breakdown. A GUS-protein fusion product was shown to localize to the surface of chloroplastic structures reminiscent of starch granules. In the mutants%2C the chloroplastic %26#945%3B-amylase AMY3 is upregulated.
Encodes a member of the TBL (TRICHOME BIREFRINGENCE-LIKE) gene family containing a plant-specific DUF231 (domain of unknown function) domain. TBL gene family has 46 members%2C two of which (TBR/AT5G06700 and TBL3/AT5G01360) have been shown to be involved in the synthesis and deposition of secondary wall cellulose%2C presumably by influencing the esterification state of pectic polymers. A nomenclature for this gene family has been proposed (Volker Bischoff %26 Wolf Scheible%2C 2010%2C personal communication).
Encodes a protein disulfide isomerase-like (PDIL) protein%2C a member of a multigene family within the thioredoxin (TRX) superfamily. This protein also belongs to the adenosine 5'-phosphosulfate reductase-like (APRL) group.
catalytic subunit of cyclin dependent kinase 1. physically interact with cyclin-dependent kinases (CDKs) and play an essential%2C but yet not entirely resolved%2C role in the regulation of the cell cycle
Encodes a member of KPP-like gene family%2C homolog of KPP (kinase partner protein) gene in tomato. Also a member of the RopGEF (guanine nucleotide exchange factor) family%2C containing the novel PRONE domain (plant-specific Rop nucleotide exchanger)%2C which is exclusively active towards members of the Rop subfamily.
Protein of unknown function (DUF1685)%3B FUNCTIONS IN: molecular_function unknown%3B INVOLVED IN: biological_process unknown%3B EXPRESSED IN: 11 plant structures%3B EXPRESSED DURING: 6 growth stages%3B CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF1685 (InterPro:IPR012881)%3B BEST Arabidopsis thaliana protein match is: Protein of unknown function (DUF1685) (TAIR:AT2G15590.2)%3B Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12%3B Bacteria - 1396%3B Metazoa - 17338%3B Fungi - 3422%3B Plants - 5037%3B Viruses - 0%3B Other Eukaryotes - 2996 (source: NCBI BLink).
This gene is predicted to encode a protein that functions as a Golgi apparatus structural component known as a golgin in mammals and yeast. A fluorescently-tagged version of GC1 co-localizes with Golgi markers%2C and this localization appears to be replicated using the C-terminal (558-715 aa) portion of the protein.
CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF3741 (InterPro:IPR022212)%3B BEST Arabidopsis thaliana protein match is: Phosphatidylinositol N-acetyglucosaminlytransferase subunit P-related (TAIR:AT2G45900.1)%3B Has 703 Blast hits to 632 proteins in 148 species: Archae - 5%3B Bacteria - 69%3B Metazoa - 168%3B Fungi - 50%3B Plants - 149%3B Viruses - 4%3B Other Eukaryotes - 258 (source: NCBI BLink).
Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family%3B CONTAINS InterPro DOMAIN/s: Late embryogenesis abundant protein%2C group 2 (InterPro:IPR004864)%3B BEST Arabidopsis thaliana protein match is: hydroxyproline-rich glycoprotein family protein (TAIR:AT3G52460.1)%3B Has 868 Blast hits to 868 proteins in 31 species: Archae - 2%3B Bacteria - 0%3B Metazoa - 2%3B Fungi - 0%3B Plants - 862%3B Viruses - 0%3B Other Eukaryotes - 2 (source: NCBI BLink).
ADCS encodes a protein that has two functional domains. The N-terminal domain has glutamine amidotransferase activity while the C-terminal domain has aminodeoxychorismate synthase (ADCS) activity. These two domains act together to catalyze the transformation of chorismate to 4-amino-4-deoxychorismate. This reaction is required for 4-aminobenzoate (pABA) production and ultimately for folate biosynthesis. The putative target peptide of ADCS can direct GFP to the chloroplast.
Encodes one of the 36 carboxylate clamp (CC)-tetratricopeptide repeat (TPR) proteins (Prasad 2010%2C Pubmed ID: 20856808) with potential to interact with Hsp90/Hsp70 as co-chaperones.
Encodes a chloroplastic lipocalin AtCHL. Located in thylakoid lumen. Involved in the protection of thylakoidal membrane lipids against reactive oxygen species%2C especially singlet oxygen%2C produced upon excess light.
Phosphoinositide-specific phospholipase C (PI-PLC)%2C catalyzes hydrolysis of phosphatidylinositol 4%2C5-bisphosphate into inositol 1%2C4%2C5-trisphosphate and diacylglycerol.
protein kinase 1B (PK1B)%3B FUNCTIONS IN: protein serine/threonine kinase activity%2C protein kinase activity%2C kinase activity%2C ATP binding%3B INVOLVED IN: protein amino acid phosphorylation%2C N-terminal protein myristoylation%3B LOCATED IN: plasma membrane%3B EXPRESSED IN: 22 plant structures%3B EXPRESSED DURING: 13 growth stages%3B CONTAINS InterPro DOMAIN/s: Protein kinase%2C ATP binding site (InterPro:IPR017441)%2C Protein kinase%2C catalytic domain (InterPro:IPR000719)%2C Serine-threonine/tyrosine-protein kinase (InterPro:IPR001245)%2C Protein kinase-like domain (InterPro:IPR011009)%2C Serine/threonine-protein kinase%2C active site (InterPro:IPR008271)%3B BEST Arabidopsis thaliana protein match is: Protein kinase superfamily protein (TAIR:AT1G07570.1)%3B Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798%3B Bacteria - 22429%3B Metazoa - 974%3B Fungi - 991%3B Plants - 531%3B Viruses - 0%3B Other Eukaryotes - 9610 (source: NCBI BLink).
A member of heat shock protein 90 (HSP90) gene family. Expressed in all tissues and abundant in root apical meristem%2C pollen and tapetum. Expression is NOT heat-induced but induced by IAA and NaCl. Interacts with HsfA1d in the cytosol and the nucleus and negatively regulates HsfA1d. Did not bind to AtHsfA4c.
Encodes formylglycinamidine ribonucleotide synthase an enzyme involved in de novo purine biosynthesis. PUR4 is localizes to the chloroplast and mitochondria. Loss of PUR4 function affects male but not female gametophyte development.
Encodes a plastid isoform of the enzyme phosphoglucomutase involved in controlling photosynthetic carbon flow. Effective petiole movement against the direction of the gravity requires functional PGM activity that is required for full development of amyloplasts.
Encodes an expansin. Naming convention from the Expansin Working Group (Kende et al%2C Plant Mol Bio). Involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana.
Encodes the large subunit of ADP-glucose pyrophosphorylase%2C the enzyme which catalyzes the first and limiting step in starch biosynthesis. The large subunit plays a regulatory role whereas the small subunit (ApS) is the catalytic isoform. Four isoforms of the large subunit (ApL1-4) have been described.
Encodes a protein disulfide isomerase-like (PDIL) protein%2C a member of a multigene family within the thioredoxin (TRX) superfamily. Unlike several other PDI family members%2C transcript levels for this gene are not up-regulated in response to three different chemical inducers of ER stress (dithiothreitol%2C beta-mercaptoethanol%2C and tunicamycin).
A member of a large family of seven-transmembrane domain proteins specific to plants%2C homologs of the barley mildew resistance locus o (MLO) protein. The Arabidopsis genome contains 15 genes encoding MLO proteins%2C with localization in plasma membrane. Phylogenetic analysis revealed four clades of closely-related AtMLO genes. ATMLO1 belongs to the clade II%2C with ATMLO13 and ATMLO15. The gene is expressed during early seedling growth%2C in root and cotyledon vascular system%2C in pollen and in papillae%2C as shown by GUS activity patterns. The expression of several phylogenetically closely-related AtMLO genes showed similar or overlapping tissue specificity and analogous responsiveness to external stimuli%2C suggesting functional redundancy%2C co-function%2C or antagonistic function(s).
Encodes a plastid-localized arogenate dehydratase involved in phenylalanine biosynthesis. Not less than six genes encoding ADT were identi%26#64257%3Bed in the Arabidopsis genome: ADT1 [At1g11790]%3B ADT2 [At3g07630]%3B ADT3 [At2g27820]%3B ADT4 [At3g44720]%3B ADT5 [At5g22630]%3B and ADT6 [At1g08250].
Encodes an RNA helicase that may be a component of the Exon Junction Complex. Subcellular localization is modulated by stress. Under normal conditions it is localized to the nuceloplasm but under hyopoxic conditions it localizes to the nucleolus and splicing speckles.
Encodes a nucleolar localized WD-40 repeat protein that is preferentially expressed in dividing cells and is required for regulated division planes and embryo development.
Encodes a protein that likely has dihydropicolinate synthase activity based on its mutant phenotype of decreased lysine levels and increased aspartate levels. The mutant also has increased levels of threonine. The enzyme is predicted to localize to the chloroplast.
Encodes a cytosolic ascorbate peroxidase APX6. Ascorbate peroxidases are enzymes that scavenge hydrogen peroxide in plant cells. Eight types of APX have been described for Arabidopsis: three cytosolic (APX1%2C APX2%2C APX6)%2C two chloroplastic types (stromal sAPX%2C thylakoid tAPX)%2C and three microsomal (APX3%2C APX4%2C APX5) isoforms.
Homolog of yeast retromer subunit VPS5. Part of a retromer-like protein complex involved in endosome to lysosome protein transport. In roots it co-localizes with the PIN2 auxin efflux carrier. Involved in endocytic sorting of membrane proteins including PIN2%2C BOR1 and BRI1.
Encodes a homolog of the human ATM gene%2C which is mutated in ataxia telangiectasia%2C a chromosome instability disorder. Characterization of mutants suggest a role homologous recombination for DNA damage repair in response to ionizing radiation as well as during meiosis. The protein has kinase domains and shows kinase activity in orthologs. There is also evidence that ATM might be involved in the telomerase-independent process known as Alternative Lengthening of Telomeres.
Encodes a protein disulfide isomerase-like (PDIL) protein%2C a member of a multigene family within the thioredoxin (TRX) superfamily. Unlike several other PDI family members%2C transcript levels for this gene are not up-regulated in response to three different chemical inducers of ER stress (dithiothreitol%2C beta-mercaptoethanol%2C and tunicamycin).
Encodes PSL4%2C beta-subunit of endoplasmic reticulum-resident glucosidase II%2C which is essential for stable accumulation and quality control of the elf18 receptor EFR but not the flg22 receptor FLS2.
Encodes an F-box protein. Based on genetic analysis appears to be functionally redundant with VFB1%2C2%2Cand 4. When levels of all 4 genes are reduced plants show defects in growth and reduced levels of auxin response genes.
EMBRYO DEFECTIVE 2756 (EMB2756)%3B INVOLVED IN: response to cadmium ion%2C embryo development ending in seed dormancy%3B EXPRESSED IN: 25 plant structures%3B EXPRESSED DURING: 13 growth stages%3B CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF616 (InterPro:IPR006852)%3B BEST Arabidopsis thaliana protein match is: Protein of unknown function (DUF616) (TAIR:AT4G09630.1)%3B Has 593 Blast hits to 590 proteins in 103 species: Archae - 14%3B Bacteria - 45%3B Metazoa - 74%3B Fungi - 32%3B Plants - 255%3B Viruses - 0%3B Other Eukaryotes - 173 (source: NCBI BLink).
Contains an N-terminal tripartite nucleotide binding site and a C-terminal tandem array of leucine-rich repeats. Confers resistance to Pseudomonas syringae strains that carry the avirulence genes avrB and avrRpm1.
encodes a chloroplast pyruvate kinase beta subunit. The enzyme is less active than the other chloroplast pyruvate kinase beta subunit encoded by AT5G52920. Involved in seed oil biosynthesis. Can partially complement the AT5G52920 mutant.
Encodes a MAP kinase protein. MPK12 interacts with the IBR5 protein phosphatase in vitro and in vivo%2C and it can be dephosphorylated and inactivated by IBR5. MPK12 appears to be a negative regulator of auxin signlaing. MPK12 RNAi lines are hypersensitive to auxin in root elongation and transcriptional response assays%2C but they appear to have normal sensitivity to ABA. MPK12 is a nuclear protein and its kinase activity is increased following auxin treatment. MPK12 transcripts are widely expressed in seedlings%2C but MPK12 expression is stronger in guard cells than in other cell types in mature plants.
Encodes BOBBER1 (BOB1)%2C a non-canonical small heat shock protein required for both development and thermotolerance. BOB1 is cytoplasmic at basal temperatures but forms heat shock granules containing canonical small heat shock proteins at high temperatures.
Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002). Induced by Salicylic acid. Independent of NPR1 for their induction by salicylic acid.
Encodes a mitochondrial transcription termination factor (mTERF) family protein. The gene product is targeted to the chloroplast and mutants are affected in chloroplast development. Mutants%2C named as twirt1 (twr-1)%2C display altered root meristem function resulting in short roots. Mutation also affects shoot meristem function.
encodes a plastid lipoamide dehydrogenase%2C subunit of the pyruvate dehydrogenase complex which provides acetyl-CoA for de novo fatty acid biosynthesis. The gene is highly expressed in developing seeds.
Encodes a protein that is involved in mRNA processing and localized to cytoplasmic p-bodies. Double mutants with CCR4a show decreased sensitivity to high concentrations of sucrose. Involved in starch and sucrose metabolism.
Encodes a pseudo-response regulator whose mutation affects various circadian-associated biological events such as flowering time in the long-day photoperiod conditions%2C red light sensitivity of seedlings during early photomorphogenesis%2C and the period of free-running rhythms of certain clock-controlled genes including CCA1 and APRR1/TOC1 in constant white light. Acts as transcriptional repressor of CCA1 and LHY.
Encodes one of the two RPT2 (26S proteasome subunit RPT2) paralogs: RPT2a (At4g29040) and RPT2b (At2g20140). RPT2b can not complement the rpt2a mutant phenotype. rpt2a rpt2b double mutants are embryo lethal.
Represents a homolog of the yeast MDN gene%2C which encodes a non-ribosomal protein involved in the maturation and assembly of the 60S ribosomal subunit. In Arabidopsis%2C it is essential for female gametogenesis progression.
Encodes SMALLER WITH VARIABLE BRANCHES (SVB)%2C a protein with a conserved domain of unknown function (DUF538). The trichomes of the SVB mutants are smaller and exhibit branches of variable length and number.
encodes U2B%2C which is a component of the U2 snRNP complex. Its precise role in pre-mRNA splicing is still unknown. It has been suggested that U2B0 may not be required for the splicing reaction itself but may have a role in U2 snRNP biogenesis. Deletion analysis of the U2B0 gene fusion has identified the N-terminal RNP-80 motif as sufficient for localization to the coiled body and the nucleus.
Encodes AKT1%2C a member of the Shaker family inward rectifying potassium channel predominantly expressed in predominantly in root hairs and root endodermis. This family includes five groups based on phylogenetic analysis (FEBS Letters (2007) 581: 2357): I (inward rectifying channel): AKT1 (AT2G26650)%2C AKT5 (AT4G32500) and SPIK (also known as AKT6%2C AT2G25600)%3B II (inward rectifying channel): KAT1 (AT5G46240) and KAT2 (AT4G18290)%3B III (weakly inward rectifying channel): AKT2 (AT4G22200)%3B IV (regulatory subunit involved in inwardly rectifying conductance formation): KAT3 (also known as AtKC1%2C AT4G32650)%3B V (outward rectifying channel): SKOR (AT3G02850) and GORK (AT5G37500).
epidermis-specific%2C encodes KCS10%2C a putative 3-ketoacyl-CoA synthase. probably involved in the synthesis of long-chain lipids found in the cuticle.
Encodes RARE1 (Required for accD RNA Editing 1)%2C a trans-factor essential for C-to-U editing of the chloroplast accD transcript. RARE1 carries 15 PPR (pentatricopeptide repeat) motifs%2C an E/E+ and a DYW domain (C-terminal tripeptide).
Sulfur acceptor that interacts with and activates the cysteine desulfurases%2C AtSufS in plastids and AtNifS1 in mitochondria%2C and both activations are vital during embryogenesis. Dual localization in mitochondria and chloroplasts. Involved in Fe-S cluster biogenesis in mitochondria and plastids. Expressed in all major tissues%2C with higher expression in green parts. Its expression is light-dependent and regulated at the mRNA level. Activates the cysteine desulfurase activity of CpNifS for chloroplastic iron-sulfur cluster biogenesis.
Ribosomal protein L10 family protein%3B FUNCTIONS IN: structural constituent of ribosome%3B INVOLVED IN: translational elongation%2C response to salt stress%2C translation%3B LOCATED IN: cytosolic ribosome%2C ribosome%2C membrane%3B EXPRESSED IN: 23 plant structures%3B EXPRESSED DURING: 13 growth stages%3B CONTAINS InterPro DOMAIN/s: Ribosomal protein 60S (InterPro:IPR001813)%2C Ribosomal protein L10 (InterPro:IPR001790)%3B BEST Arabidopsis thaliana protein match is: Ribosomal protein L10 family protein (TAIR:AT3G09200.1)%3B Has 1983 Blast hits to 1980 proteins in 500 species: Archae - 322%3B Bacteria - 1%3B Metazoa - 680%3B Fungi - 420%3B Plants - 226%3B Viruses - 0%3B Other Eukaryotes - 334 (source: NCBI BLink).
Encodes an Arabidopsis Transmembrane nine (TMN) protein. Transmembrane nine (TM9) proteins are localized in the secretory pathway of eukaryotic cells and are involved in cell adhesion and phagocytosis.
Leucine-rich repeat protein kinase family protein%3B FUNCTIONS IN: protein kinase activity%2C kinase activity%3B INVOLVED IN: protein amino acid phosphorylation%3B LOCATED IN: endomembrane system%3B EXPRESSED IN: 21 plant structures%3B EXPRESSED DURING: 13 growth stages%3B CONTAINS InterPro DOMAIN/s: Protein kinase%2C ATP binding site (InterPro:IPR017441)%2C Protein kinase%2C catalytic domain (InterPro:IPR000719)%2C Serine-threonine/tyrosine-protein kinase (InterPro:IPR001245)%2C Protein kinase-like domain (InterPro:IPR011009)%2C Serine/threonine-protein kinase%2C active site (InterPro:IPR008271)%3B BEST Arabidopsis thaliana protein match is: Leucine-rich repeat protein kinase family protein (TAIR:AT2G37050.3)%3B Has 172111 Blast hits to 130582 proteins in 4641 species: Archae - 151%3B Bacteria - 14946%3B Metazoa - 47791%3B Fungi - 11011%3B Plants - 76783%3B Viruses - 518%3B Other Eukaryotes - 20911 (source: NCBI BLink).
Predicted to encode a PR (pathogenesis-related) peptide that belongs to the PR-6 proteinase inhibitor family. Six putative PR-6-type protein encoding genes are found in Arabidopsis: At2g38900%2C At2g38870%2C At5g43570%2C At5g43580%2C At3g50020 and At3g46860.
Encodes a member of the MYB family of transcriptional regulators. MYB5 act as a negative regulator of trichome branching and play a role in the correct formation of the seed coat and possibly the formation the underlying endosperm layers. Loss of function mutations have defects in seed coat mucilage and columella cells as well as trichome defects (smaller and reduced number of branches).
Encodes a CCHC zinc finger protein that may function as a step II splicing factor. In an epigenetic allele of SMP1 (in which SMP1 and SMP2 mRNA is reduced) organs are smaller and contain fewer cells.
Protein of unknown function%2C DUF547%3B CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF547 (InterPro:IPR006869)%3B BEST Arabidopsis thaliana protein match is: Protein of unknown function%2C DUF547 (TAIR:AT5G66600.2)%3B Has 867 Blast hits to 688 proteins in 125 species: Archae - 4%3B Bacteria - 86%3B Metazoa - 75%3B Fungi - 16%3B Plants - 587%3B Viruses - 0%3B Other Eukaryotes - 99 (source: NCBI BLink).
One of several nuclear-encoded ClpPs (caseinolytic protease). Contains a highly conserved catalytic triad of Ser-type proteases (Ser-His-Asp). The name reflects nomenclature described in Adam et. al (2001).
Protein phosphatase 2C family protein%3B FUNCTIONS IN: protein serine/threonine phosphatase activity%2C catalytic activity%3B INVOLVED IN: N-terminal protein myristoylation%3B LOCATED IN: cellular_component unknown%3B EXPRESSED IN: 17 plant structures%3B EXPRESSED DURING: 6 growth stages%3B CONTAINS InterPro DOMAIN/s: Protein phosphatase 2C-related (InterPro:IPR001932)%2C Protein phosphatase 2C (InterPro:IPR015655)%2C Protein phosphatase 2C%2C N-terminal (InterPro:IPR014045)%3B BEST Arabidopsis thaliana protein match is: Protein phosphatase 2C family protein (TAIR:AT1G16220.1)%3B Has 5543 Blast hits to 5523 proteins in 290 species: Archae - 2%3B Bacteria - 8%3B Metazoa - 1342%3B Fungi - 594%3B Plants - 2451%3B Viruses - 5%3B Other Eukaryotes - 1141 (source: NCBI BLink).
Encodes a homologue of the ATR-interacting protein ATRIP. Mutant (named sensitive to UV2 or suv2) is UVB-hypersensitive and defective in DNA damage response.
BEST Arabidopsis thaliana protein match is: copper ion binding (TAIR:AT4G32610.1)%3B Has 43784 Blast hits to 26928 proteins in 1799 species: Archae - 86%3B Bacteria - 6347%3B Metazoa - 15971%3B Fungi - 5398%3B Plants - 1931%3B Viruses - 259%3B Other Eukaryotes - 13792 (source: NCBI BLink).
Encodes ribosomal protein L5 that binds to 5S ribosomal RNA and in involved in its export from the nucleus to the cytoplasm. Identified in a screen for enhancers of as1. as1/pgy double mutants show defects in leaf vascular patterning and adaxial cell fate. Double mutant analysis indicates pgy genes function in the same pathway as REV%2C KAN1 and KAN2.
SHB1 encodes a nuclear and cytosolic protein that has motifs homologous with SYG1 protein family members. Acts in cryptochrome signaling. Overexpression of SHB1 enhanced the expression of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) under red light and promoted proteasome-mediated degradation of phytochrome A and hypocotyl elongation under far-red light. A knockout allele suppressed LONG HYPOCOTYL IN FAR-RED LIGHT1 (HFR1) expression and showed several deetiolation phenotypes. Acts upstream of HFR1. Regulates seed development.
Protein of unknown function (DUF630 and DUF632)%3B FUNCTIONS IN: molecular_function unknown%3B INVOLVED IN: N-terminal protein myristoylation%3B LOCATED IN: cellular_component unknown%3B EXPRESSED IN: shoot apex%2C embryo%2C flower%3B EXPRESSED DURING: petal differentiation and expansion stage%2C D bilateral stage%3B CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF630 (InterPro:IPR006868)%2C Protein of unknown function DUF632 (InterPro:IPR006867)%3B BEST Arabidopsis thaliana protein match is: Protein of unknown function (DUF630 and DUF632) (TAIR:AT2G17110.1)%3B Has 3752 Blast hits to 2914 proteins in 298 species: Archae - 59%3B Bacteria - 209%3B Metazoa - 1260%3B Fungi - 213%3B Plants - 622%3B Viruses - 0%3B Other Eukaryotes - 1389 (source: NCBI BLink).
Encodes one of four UDP-glucose dehydrogenase UGD) genes. Mutation of this gene in combination with UGD3 leads to swollen plant cell walls and severe developmental defects associated with changes in pectic polysaccharides.
Protein of unknown function%2C DUF593%3B CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF593 (InterPro:IPR007656)%3B BEST Arabidopsis thaliana protein match is: Protein of unknown function%2C DUF593 (TAIR:AT4G30830.1)%3B Has 1121 Blast hits to 1059 proteins in 203 species: Archae - 5%3B Bacteria - 110%3B Metazoa - 379%3B Fungi - 69%3B Plants - 280%3B Viruses - 2%3B Other Eukaryotes - 276 (source: NCBI BLink).
Encodes a protein with hydroxymethylglutaryl-CoA synthase activity which was characterized by phenotypical complementation of the S. cerevisiae mutant.
Encodes a leaf-type ferredoxin:NADP(H) oxidoreductase. It is present in both chloroplast stroma and thylakoid membranes but is more abundant in the stroma
This gene belongs to the CO (CONSTANS) gene family. This gene family is divided in three subgroups: groups III%2C to which COL9 belongs%2C is characterised by one B-box (supposed to regulate protein-protein interactions) and a second diverged zinc finger. COL9 downregulates expression of CO (CONSTANS) as well as FT and SOC1 which are known regulatory targets of CO.
Ribosomal protein L22p/L17e family protein%3B FUNCTIONS IN: structural constituent of ribosome%3B INVOLVED IN: translation%3B LOCATED IN: ribosome%2C cytosolic large ribosomal subunit%2C plasma membrane%2C chloroplast%2C vacuole%3B EXPRESSED IN: 23 plant structures%3B EXPRESSED DURING: 13 growth stages%3B CONTAINS InterPro DOMAIN/s: Ribosomal protein L22/L17 (InterPro:IPR001063)%2C Ribosomal protein L22/L17%2C eukaryotic/archaeal (InterPro:IPR005721)%2C Ribosomal protein L22/L17%2C conserved site (InterPro:IPR018260)%3B BEST Arabidopsis thaliana protein match is: Ribosomal protein L22p/L17e family protein (TAIR:AT1G67430.1)%3B Has 2094 Blast hits to 2094 proteins in 650 species: Archae - 321%3B Bacteria - 492%3B Metazoa - 519%3B Fungi - 182%3B Plants - 156%3B Viruses - 0%3B Other Eukaryotes - 424 (source: NCBI BLink).
Encodes a calmodulin-regulated Ca(2+)-ATPase that improves salt tolerance in yeast. Localized to the vacuole. Lesion mimic phenotype when mutation in the gene is combined with a mutation in ACA11. Lesion mimic phenotype of double knockout can be suppressed by nutritional supplements that increase anion levels (e.g. 15 mM Nitrate%2C Chloride%2C or Phosphate).
Encodes PAT2%2C a putative beta-subunit of adaptor protein complex 3 (AP-3) that can partially complement the corresponding yeast mutant. Mediates the biogenesis and function of lytic vacuoles.
member of SYP2 Gene Family. Over-expression of the gene in tobacco protoplasts leads to a disruption of vacuolar transport from the prevacuolar compartment (PVC) to the vacuole%2C but not from the Golgi apparatus to the plasma membrane.
Encodes a protein of the RAD51B family involved in double stranded DNA repair. Homozygous mutant plants show increased sensitivity to mitomycin which induces DS breaks.
Encodes a protein with similarity to RAF MAP kinases. Based on loss of function phenotype%2C RAF11 appears to be involved in mediating ABA responses such as dormancy and environmental stress. Expressed in most plant tissues but excluded from root tips and young leaves.
Encodes a member of an eight-gene family (SMAX1 and SMAX1-like) that has weak similarity to AtHSP101%2C a ClpB chaperonin required for thermotolerance.
Arabidopsis protein of unknown function (DUF241)%3B CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF241%2C plant (InterPro:IPR004320)%3B BEST Arabidopsis thaliana protein match is: Arabidopsis protein of unknown function (DUF241) (TAIR:AT4G35720.1)%3B Has 444 Blast hits to 436 proteins in 12 species: Archae - 0%3B Bacteria - 0%3B Metazoa - 0%3B Fungi - 0%3B Plants - 444%3B Viruses - 0%3B Other Eukaryotes - 0 (source: NCBI BLink).
pentatricopeptide (PPR) repeat-containing protein%3B CONTAINS InterPro DOMAIN/s: Pentatricopeptide repeat (InterPro:IPR002885)%3B BEST Arabidopsis thaliana protein match is: Pentatricopeptide repeat (PPR-like) superfamily protein (TAIR:AT1G09900.1)%3B Has 43076 Blast hits to 12816 proteins in 267 species: Archae - 3%3B Bacteria - 25%3B Metazoa - 283%3B Fungi - 440%3B Plants - 41291%3B Viruses - 2%3B Other Eukaryotes - 1032 (source: NCBI BLink).
GO
domain
Definition
P-value
nucleolus
cellular_component
"A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN:0198506732]
3.44e-09
cytosol
cellular_component
"The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC:hgd, GOC:jl]
1.04e-05
small-subunit processome
cellular_component
"A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins." [GOC:krc, GOC:vw, PMID:12068309, PMID:12957375, PMID:15120992, PMID:15590835]
1.04e-05
RNA methylation
biological_process
"Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor." [GOC:hjd]
2.49e-05
cullin deneddylation
biological_process
"The modification of cullins by removal of ubiquitin-like protein NEDD8 (RUB1)." [PMID:17307927]
4.74e-05
ribosome biogenesis
biological_process
"A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis." [GOC:ma]
4.74e-05
rRNA processing
biological_process
"Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules." [GOC:curators]
1.01e-04
pyrimidine ribonucleotide biosynthetic process
biological_process
"The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
1.01e-04
ncRNA metabolic process
biological_process
"The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs)." [GOC:mah]
1.01e-04
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
biological_process
"Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript." [GOC:curators]
1.63e-04
photomorphogenesis
biological_process
"The control of plant growth, development, and differentiation by the duration and nature of light, independent of photosynthesis." [GOC:lr]
1.63e-04
protein import into nucleus
biological_process
"The directed movement of a protein from the cytoplasm to the nucleus." [GOC:jl]
"A complex of several polypeptides that plays at least two important roles in protein synthesis: First, eIF3 binds to the 40S ribosome and facilitates loading of the Met-tRNA/eIF2.GTP ternary complex to form the 43S preinitiation complex. Subsequently, eIF3 apparently assists eIF4 in recruiting mRNAs to the 43S complex. The eIF3 complex contains five conserved core subunits, and may contain several additional proteins; the non-core subunits are thought to mediate association of the complex with specific sets of mRNAs." [PMID:15904532]
1.75e-03
ribonucleoprotein complex assembly
biological_process
"The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex." [GOC:jl]
1.75e-03
transcription factor activity, sequence-specific DNA binding
molecular_function
"Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:curators, GOC:txnOH]
2.43e-03
seed development
biological_process
"The process whose specific outcome is the progression of the seed over time, from its formation to the mature structure. A seed is a propagating organ formed in the sexual reproductive cycle of gymnosperms and angiosperms, consisting of a protective coat enclosing an embryo and food reserves." [GOC:jid, PO:0009010]
4.35e-03
cytoplasm
cellular_component
"All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684]
4.89e-03
RNA processing
biological_process
"Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules." [GOC:mah]
4.89e-03
RNA secondary structure unwinding
biological_process
"The process in which a secondary structure of RNA are broken or 'melted'." [PMID:17169986]
4.89e-03
ribosomal large subunit biogenesis
biological_process
"A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a large ribosomal subunit; includes transport to the sites of protein synthesis." [GOC:jl]
4.89e-03
ncRNA processing
biological_process
"Any process that results in the conversion of one or more primary non-coding RNA (ncRNA) transcripts into one or more mature ncRNA molecules." [GOC:mah]
4.97e-03
nucleic acid binding
molecular_function
"Interacting selectively and non-covalently with any nucleic acid." [GOC:jl]
6.23e-03
translation initiation factor activity
molecular_function
"Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide." [ISBN:0198506732]
6.23e-03
fruit development
biological_process
"The process whose specific outcome is the progression of the fruit over time, from its formation to the mature structure. The fruit is a reproductive body of a seed plant." [GOC:sm]
6.46e-03
mRNA export from nucleus
biological_process
"The directed movement of mRNA from the nucleus to the cytoplasm." [GOC:ma]
1.09e-02
embryo development
biological_process
"The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu]
1.09e-02
seed maturation
biological_process
"A process in seed development that occurs after embryogenesis by which a quiescent state is established in a seed. Seed maturation is characterized by storage compound accumulation, acquisition of desiccation tolerance, growth arrest and the entry into a dormancy period of variable length that is broken upon germination." [PMID:16096971]
1.25e-02
ATP-dependent RNA helicase activity
molecular_function
"Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix." [EC:3.6.1.3, GOC:jl]
1.42e-02
mRNA splicing, via spliceosome
biological_process
"The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced." [GOC:krc, ISBN:0198506732, ISBN:0879695897]
2.57e-02
aminoacyl-tRNA ligase activity
molecular_function
"Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP." [ISBN:0198506732]
3.14e-02
nucleotide binding
molecular_function
"Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC:mah, ISBN:0198547684]
3.32e-02
translation
biological_process
"The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators]
3.39e-02
translational initiation
biological_process
"The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X]
4.29e-02
embryo development ending in seed dormancy
biological_process
"The process whose specific outcome is the progression of the embryo over time, from zygote formation to the end of seed dormancy. An example of this process is found in Arabidopsis thaliana." [GOC:go_curators, GOC:mtg_sensu]
4.29e-02
post-embryonic development
biological_process
"The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development." [GOC:go_curators]
4.47e-02
acid phosphatase activity
molecular_function
"Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum." [EC:3.1.3.2]
4.58e-02
reproductive structure development
biological_process
"The reproductive developmental process whose specific outcome is the progression of structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures." [GOC:dph, GOC:isa_complete, GOC:jid]