Biological process to genes

Query process ID GO:0048316
Process name 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.
Organism Arabidopsis thaliana

Click Gene ID to show a list of co-expressed genes.

ECC Gene ID Repr. ID Gene name Functional description O.I. H.G. Other DB
XAt1g21750838779ATPDIL1-1 (PDI-LIKE 1-1)Encodes a protein disulfide isomerase-like (PDIL) protein, a member of a multigene family within the thioredoxin (TRX) superfamily; isoform contains non-consensus GA donor splice site at intron 9. Transcript levels for this gene are up-regulated in response to three different chemical inducers of ER stress (dithiothreitol, beta-mercaptoethanol, and tunicamycin). Neither AtIRE1-2 nor AtbZIP60 appear to be required for this response.O.I.H.G.
XAt1g27080839597NRT1.6 (NITRATE TRANSPORTER 1.6)Encodes a protein with low-affinity nitrate transporter activity that is expressed in the vascular tissue of the funiculus and the silique. This plasma membrane-localized enzyme is predicted to have 12 transmembrane domains. Plants lacking NRT1.6 have reduced levels of nitrate in their seeds and have increased levels of early embryonic developmental defects and seed abortion.O.I.H.G.
XAt1g49320841355BURP domain-containing proteinF:molecular_function unknown;P:unknown;C:endomembrane system;PO.I.H.G.
XAt1g53130841747GRI (GRIM REAPER)Encodes GRIM REAPER (GRI), involved in the regulation of cell death induced by extracellular ROS (reactive oxygen species). Secreted into the extracellular space.O.I.H.G.
XAt1g63990842702SPO11-2 (SPORULATION 11-2)Encodes AtSPO11-2, one of the three Arabidopsis homologues of the archaeal DNA topoisomerase VIA subunit (topo VIA). Required for meiotic recombination. Plants homozygous for atspo11-2 exhibit a severe sterility phenotype. Both male and female meiosis are severely disrupted in the atspo11-2 mutant, and this is associated with severe defects in synapsis during the first meiotic division and reduced meiotic recombination. AtSPO11-1 and AtSPO11-2 have overlapping functions (i.e. both required for meiotic recombination) whereas AtSPO11-3 functions in DNA replication. Required for double-strand break induction.O.I.H.G.
XAt1g67990843127TSM1Encodes a tapetum-specific O-methyltransferase. In vitro enzyme assay indicated activity with caffeoyl-CoA, caffeoyl glucose, chlorogenic acid and polyamine conjugates. RNAi mutants had impaired silique development and seed setting.O.I.H.G.
XAt1g71890843520SUC5Encodes a sucrose transporter that is expressed in the endosperm. Mutants have delayed accumulation of fatty acids and embryo maturation.O.I.H.G.
XAt2g16500816149ADC1 (ARGININE DECARBOXYLASE 1)encodes a arginine decarboxylase (ADC), a rate-limiting enzyme that catalyzes the first step of polyamine (PA) biosynthesis via ADC pathway in Arabidopsis thaliana. Arabidopsis genome has two ADC paralogs, ADC1 and ADC2. Double mutant analysis showed that ADC genes are essential for the production of PA, and are required for normal seed development. Promoter region of ADC1 contains 742-bp AT-rich transposable element, called AtATE, that belongs to the MITE families of repetitive elements.O.I.H.G.
XAt2g17420816248NTRA (NADPH-DEPENDENT THIOREDOXIN REDUCTASE A)NADPH-dependent thioredoxin reductase, major cytosolic isoformO.I.H.G.
XAt2g36270818199ABI5 (ABA INSENSITIVE 5)Encodes a member of the basic leucine zipper transcription factor family, involved in ABA signalling during seed maturation and germination. The Arabidopsis abscisic acid (ABA)-insensitive abi5 mutants have pleiotropic defects in ABA response, including decreased sensitivity to ABA inhibition of germination and altered expression of some ABA-regulated genes. Comparison of seed and ABA-inducible vegetative gene expression in wild-type and abi5-1 plants indicates that ABI5 regulates a subset of late embryogenesis-abundant genes during both developmental stages.O.I.H.G.
XAt2g40170818608GEA6 (LATE EMBRYOGENESIS ABUNDANT 6)Encodes a group 1 LEA gene that is activated by direct binding of ABI5 to its promoter and is involved in response to ABA. Is required for normal seed development. Involved in regulating the timing of dessication tolerance and rate of water loss during seed maturation.O.I.H.G.
XAt2g40220818614ABI4 (ABA INSENSITIVE 4)encodes a member of the DREB subfamily A-3 of ERF/AP2 transcription factor family (ABI4). The protein contains one AP2 domain. There is only one member in this family. Involved in abscisic acid (ABA) signal transduction, ABA-mediated glucose response, and hexokinase-dependent sugar responses. Expressed most abundantly in developing siliques and to a lesser degree in seedlings.O.I.H.G.
XAt2g44190819026EDE1 (ENDOSPERM DEFECTIVE 1)Encodes a novel microtubule binding protein that preferentially associates with nuclear microtubules during mitosis and is essential during the mitotic and cytokinetic stages that generate the endosperm and embryo.O.I.H.G.
XAt3g04120819567GAPC1 (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE C SUBUNIT 1)encodes cytosolic GADPH (C subunit) involved in the glycolytic pathway but also interacts with H2O2 potentially placing it in a signalling cascade induced by ROS.O.I.H.G.
XAt3g23070821881RNA bindingF:RNA binding;P:unknown;C:chloroplast;PMOFBAVO.I.H.G.
XAt3g49600824122UBP26 (UBIQUITIN-SPECIFIC PROTEASE 26)Encodes a ubiquitin-specific protease which catalyzes deubiquitination of histone H2B and is required for heterochromatin silencing.Loss of function mutations display autonomous endosperm development and embryo arrest. Loss of function also results in an increase in expression of the PcG complex target gene PHE1.O.I.H.G.
XAt3g54650824630FBL17F:ubiquitin-protein ligase activity;P:embryonic development, generative cell mitosis, seed development, pollen development, ubiquitin-dependent protein catabolic process;C:chloroplast;MPOFBO.I.H.G.
XAt4g02460827997PMS1 (POSTMEIOTIC SEGREGATION 1)Encodes a protein similar to PMS1 in yeast, a member of the family of eukaryotic MutL homologs. The protein appears to play a role in DNA mismatch repair and in the suppression of somatic homeologous recombination.O.I.H.G.
XAt4g09140826493MLH1 (MUTL-HOMOLOGUE 1)Encodes a protein with similarity to Mut1 DNA mismatch repair protein, from E.coli. The protein is expressed during prophase I of meiosis, colocalizes with MLH3 throughout pachytene and is dependent on MLH3 for proper localization.O.I.H.G.
XAt4g14510827098RNA bindingF:RNA binding;P:biological_process unknown;C:chloroplast;POMFBVAO.I.H.G.
XAt4g34710829623ADC2 (ARGININE DECARBOXYLASE 2)encodes a arginine decarboxylase (ADC), a rate-limiting enzyme that catalyzes the first step of polyamine (PA) biosynthesis via ADC pathway in Arabidopsis thaliana. Arabidopsis genome has two ADC paralogs, ADC1 and ADC2. ADC2 is stress-inducible (osmotic stress). Double mutant analysis showed that ADC genes are essential for the production of PA, and are required for normal seed development. Overexpression causes phenotypes similar to GA-deficient plants and these plants show reduced levels of GA due to lower expression levels of AtGA20ox1, AtGA3ox3 and AtGA3ox1.O.I.H.G.
XAt4g35420829695dihydroflavonol 4-reductase family / dihydrokaempferol 4-reductase familyF:coenzyme binding, binding, catalytic activity;P:cellular metabolic process, metabolic process;C:endomembrane system;BOPFMAVO.I.H.G.
XAt4g35460829698NTRB (NADPH-DEPENDENT THIOREDOXIN REDUCTASE B)NADPH-dependent thioredoxin reductase 1 (NTR1. Similar to E.coli NTR and has conserved NADPH binding domains.O.I.H.G.
XAt4g36920829845AP2 (APETALA 2)Encodes a floral homeotic gene, a member of the AP2/EREBP (ethylene responsive element binding protein) class of transcription factors and is involved in the specification of floral organ identity, establishment of floral meristem identity, suppression of floral meristem indeterminancy, and development of the ovule and seed coat. AP2 also has a role in controlling seed mass. Dominant negative allele I28, revealed a function in meristem maintenance-mutant meristems are smaller than normal siblings. AP2 appears to act on the WUS-CLV pathway in an AG independent manner.O.I.H.G.
XAt4g38680830024GRP2 (GLYCINE RICH PROTEIN 2)Encodes a glycine-rich protein that binds nucleic acids and promotes DNA melting. Its transcript and protein levels are up-regulated in response to cold treatment with protein levels peaking earlier in shoots (~10-14 days) than in roots (~21 days). It is normally expressed in meristematic regions and developing tissues where cell division occurs. RNAi and antisense lines with lower levels of CSP2/GRP2 transcripts flower earlier than wild type plants and have some defects in anther and seed development.O.I.H.G.
XAt5g17400831606ER-ANT1 (ENDOPLASMIC RETICULUM-DENINE NUCLEOTIDE TRANSPORTER 1)This gene is predicted to encode an ER-localized adenine nucleotide transporter with six putative transmembrane helices. It appears to act as a ATP:ADP antiporter when expressed in E.coli plasma membranes. Transcript levels for several ER-localized chaperones (e.g. BIP1/2) and other ATP-requiring ER proteins (e.g. CPK2) are reduced in er-ant1 knock-out lines, suggesting a lack of adequate ATP transport into the ER in these mutants. They also have reduced seed oil and seed protein levels.O.I.H.G.
XAt5g23260832390TT16 (TRANSPARENT TESTA16)Encodes a MADS box protein. Regulates proanthocyanidin biosynthesis in the inner-most cell layer of the seed coat. Also controls cell shape of the inner-most cell layer of the seed coat. Also shown to be necessary for determining the identity of the endothelial layer within the ovule.O.I.H.G.
XAt5g43940834417HOT5 (sensitive to hot temperatures 5)Encodes a glutathione-dependent formaldehyde dehydrogenase (also known as class III type alcohol dehydrogenase) reduces S-nitrosoglutathione (GSNO), the condensation product of glutathione and NO, that is a naturally occurring NO reservoir and also a reactive nitrogen intermediate. Gene expression is reduced by wounding and induced by salicylic acid. Is required for the acclimation of plants to high temperature and for fertility.O.I.H.G.
XAt5g52520835328OVA6 (OVULE ABORTION 6)F:proline-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:regulation of photosynthesis, seed development, embryo sac development, ovule development, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast, chloroplast stroma;BOAMFPO.I.H.G.
XAt5g52920835369PKP-BETA1 (PLASTIDIC PYRUVATE KINASE BETA SUBUNIT 1)encodes a dominant chloroplast pyruvate kinase beta subunit. Important for seed oil biosynthesis. Ubiquitously expressed, with significantly increased expression in maturing seeds. The mutant plant has wrinkled seeds, with a 50-70% reduction in seed fatty acid content.O.I.H.G.
XAt5g58230835935MSI1 (MULTICOPY SUPRESSOR OF IRA1)Encodes a WD-40 repeat containing protein that functions in chromatin assembly as part of the CAF1 and FIE complex. Mutants exhibit parthenogenetic development that includes proliferation of unfertilized endosperm and embryos. In heterozygous plants 50% of embryos abort. Of the aborted embryos the early aborted class are homozygous and the later aborting lass are heterozygotes in which the defective allele is maternally transmitted. Other phenotypes include defects in ovule morphogenesis and organ initiation,as well as increased levels of heterochromatic DNA. MSI1 is needed for the transition to flowering. In Arabidopsis, the three CAF-1 subunits are encoded by FAS1, FAS2 and, most likely, MSI1, respectively. Mutations in FAS1 or FAS2 lead to increased frequency of homologous recombination and T-DNA integration in Arabidopsis. In the ovule, the MSI1 transcripts are accumulated at their highest level before fertilization and gradually decrease after fertilization. MSI is biallelically expressed, the paternall allele is expressed in the endosperm and embryo and is not imprinted. MSI1 forms a complex with RBR1 that is required for activation of the imprinted genes FIS2 and FWA. This activation is mediated by MSI1/RBR1 mediated repression of MET1.O.I.H.G.



The upper GO terms

Process ID Gene number Process name
GO:000979115The 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.
GO:001015425The 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.
GO:00325010Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
GO:00486080The 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.



The lower GO terms

Process ID Gene number Process name
GO:00097930The 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.
GO:000996013The process whose specific outcome is the progression of the endosperm over time, from its formation to the mature structure. The endosperm is formed during fertilization and provides nutrients to the developing embryo.
GO:00102148The process whose specific outcome is the progression of the seed coat over time, from its formation to the mature structure.
GO:00103444The cellular process by which an seed oilbody is synthesized, aggregates, and bonds together. Seed oilbodies are simple organelles comprising a matrix of triglyceride surrounded by a phospholipid monolayer embedded and covered with unique proteins called oleosins. Seed oilbodies supply the energy requirements for the growth of the seedling after germination.
GO:00104312A 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.
GO:00483171The process by which the anatomical structures of the seed are generated and organized. Morphogenesis pertains to the creation of form.
GO:00800011The process by which seed mucilage expands through hydration and breaks the outer cell wall that encapsulates the whole seed upon imbibition. Mucilage, mainly composed of pectins, is formed during seed development and deposited into the apoplast underneath the outer wall of the seed coat.
GO:00801120The increase in size or mass of a seed. Seed is a propagating organ formed in the reproductive cycle of gymnosperms and angiosperms, derived from the ovule and enclosing an embryo.





Comparison with co-expressed genes



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