Biological process to genes

Query process ID GO:0009845
Process name The physiological and developmental changes that occur in a seed commencing with water uptake (imbibition) and terminating with the elongation of the embryonic axis.
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
XAt1g03120839571ATRAB28Atrab28 plays a role in the ion cell balance during late embryogenesis and germination.O.I.H.G.
XAt1g09090837430ATRBOHB (respiratory burst oxidase homolog B)F:in 7 functions;P:response to heat, defense response;C:integral to membrane, membrane;MPFOBAO.I.H.G.
XAt1g43620840946UDP-glucose:sterol glucosyltransferase, putativeF:transferase activity, transferring glycosyl groups;P:lipid glycosylation, carbohydrate metabolic process, metabolic process;C:plasma membrane, vacuole;BMFPOVO.I.H.G.
XAt1g62750842573SCO1 (SNOWY COTYLEDON 1)Nuclear encoded protein consists of the five domains conserved in EF-G proteins, with two GTP-binding sites in the first domain, and an additional transit peptide at the N-terminus. Localized in chloroplasts. Point mutation results in a delay in the onset of germination. At early developmental stage embryos still contain undifferentiated proplastids. The greening of cotyledons is severely impaired in light-grown mutant sco1 seedlings, whereas the following true leaves develop normally as in wild-type plants.O.I.H.G.
XAt1g80340844374GA3OX2 (GIBBERELLIN 3-OXIDASE 2)Encodes a protein with gibberellin 3 β-hydroxylase activity. The protein was heterologously expressed in E. coli and shown to catalyze the hydroxylation of both GA9 and GA20.O.I.H.G.
XAt2g26300817170GP ALPHA 1 (G PROTEIN ALPHA SUBUNIT 1)Encodes an alpha subunit of a heterotrimeric GTP-binding protein. The active GTP-bound form of GPA1 binds to the GTG1 and GTG2 abscisic acid (ABA) receptors and appears to affect their GTPase and GTP-binding activity, and hence, ABA binding abilities. GPA1 is a positive regulator in ABA-mediated inhibition of stomatal opening. Plants with recessive mutant alleles have complex phenotypes including: reduced brassinolide response, reduced cell divisions, round leaves, short hypocotyls. It is likely to be involved in the signaling events that trigger unfolded protein response-associated cell death. GPA1 is also involved in sugar signaling.O.I.H.G.
XAt2g27300817273NTL8 (NTM1-LIKE 8)F:transcription factor activity;P:multicellular organismal development, response to salt stress, seed germination;C:plasma membrane;PO.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.
XAt2g46590819271DAG2 (DOF AFFECTING GERMINATION 2)encodes a protein containing Dof zinc finger motifs. expression is limited to vascular system of the mother plant. recessive mutation is inherited as maternal-effect and expression is not detected in the embryo. mutants are defective in seed germination. mutants are more dependent on light and cold treatment and less sensitive to gibberellin during seed germination.O.I.H.G.
XAt3g03090821117AtVGT1 (Arabidopsis thaliana vacuolar glucose transporter 1)Encodes a vacuolar membrane-localized glucose transporter that can also transport fructose. Mutations in these gene have effects on seed germination and time to flowering.O.I.H.G.
XAt3g07130819899PAP15 (PURPLE ACID PHOSPHATASE 15)F:protein serine/threonine phosphatase activity, acid phosphatase activity;P:biological_process unknown;C:endomembrane system;BPOMFAO.I.H.G.
XAt3g15730820816PLDALPHA1 (PHOSPHOLIPASE D ALPHA 1)Encodes phospholipase D alpha 1 (PLD alpha 1). Positive regulator of abscisic acid (ABA) mediated stomatal movements. PLD alpha 1 plays an important role in seed deterioration and aging in Arabidopsis.O.I.H.G.
XAt3g22942825532AGG2 (G-PROTEIN GAMMA SUBUNIT 2)heterotrimeric G-protein gamma subunit 2(AGG2)O.I.H.G.
XAt3g27660822388OLEO4 (OLEOSIN 4)Encodes oleosin4 (Plant Cell, 2006, 18:1961), a protein found in oil bodies, involved in seed lipid accumulation. Functions in freezing tolerance of seeds. Note: also referred to as OLE3 in Plant Journal 2008, 55:798.O.I.H.G.
XAt3g48330823991PIMT1 (PROTEIN-L-ISOASPARTATE METHYLTRANSFERASE 1)encodes protein-L-isoaspartate methyltransferase. Important for maintaining viability as the seed ages. Involved in germination.O.I.H.G.
XAt3g54810824646zinc finger (GATA type) family proteinEncodes a protein containing a GATA type zinc finger domain that is expressed in the embryo axis and involved in germination. Mutants have a reduced rate of germination even when stratified.O.I.H.G.
XAt3g61850825358DAG1 (dof affecting germination 1)Zinc finger transcription factor of the Dof family involved in the control of seed germination.O.I.H.G.
XAt3g63420825517AGG1 (Arabidopsis Ggamma-subunit 1)heterotrimeric G protein gamma-subunit (AGG1) mRNA,O.I.H.G.
XAt4g03560825655ATTPC1 (TWO-PORE CHANNEL 1)Encodes a depolarization-activated Ca(2+) channel. Anti-sense experiments with this gene as well as Sucrose-H(+) symporters and complementation of yeast sucrose uptake mutant cch1 suggest that this protein mediates a voltage-activated Ca(2+ )influx. Mutants lack detectable SV channel activity suggesting TPC1 is essential component of the SV channel. Patch clamp analysis of loss of function mutation indicates TPC1 does not affect Ca2+ signaling in response to abiotic and biotic stress.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.
XAt4g13850827019GR-RBP2 (GLYCINE-RICH RNA-BINDING PROTEIN 2)Encodes a glycine-rich RNA-binding protein. Gene expression is induced by cold.O.I.H.G.
XAt4g18010827526AT5PTASE2 (MYO-INOSITOL POLYPHOSPHATE 5-PHOSPHATASE 2)Encodes an inositol polyphosphate 5-phosphatase that appears to have Type I activity. It can dephosphorylate IP3(inositol(1,4,5)P3) and IP4 (inositol(1,3,4,5)P4), but it does not appear to be active against phosphatidylinositol 4,5 bisphosphate. Overexpression of this gene renders plants insensitive to ABA in germination and growth assays.O.I.H.G.
XAt4g21540828239SPHK1 (SPHINGOSINE KINASE 1)Encodes a sphingosine kinase, also has enzyme activity towards other plant long-chain sphingoid bases. Involved in guard cell ABA signalling and seed germination.O.I.H.G.
XAt4g24210828522SLY1 (SLEEPY1)F-box protein that is involved in GA signaling. Regulates seed germination. Component of E3 ubiquitin complex. Interacts with DELLA proteins.O.I.H.G.
XAt4g25140828617OLEO1 (OLEOSIN 1)Encodes oleosin1, a protein found in oil bodies, involved in seed lipid accumulation. Suppression of OLEO1 (and OLEO2) resulted in an aberrant phenotype of embryo cells that contain unusually large oilbodies that are not normally observed in seeds. Changes in the size of oilbodies caused disruption of storage organelles, altering accumulation of lipids and proteins and causing delay in germination. Functions in freezing tolerance of seeds.O.I.H.G.
XAt4g29010829022AIM1 (ABNORMAL INFLORESCENCE MERISTEM)Functions in beta-oxidation of fatty acids, similar to CuMFP with L-3-hydroxyacyl-CoA hydrolyase , L-3-hydroxyacyl-dehydrogenase, D-3-hydroxyacyl-CoA epimerase, and 3, 2-enoyl-CoA isomerase activitiesO.I.H.G.
XAt4g34460829597AGB1 (GTP BINDING PROTEIN BETA 1)Encodes the heterotrimeric G-protein beta subunit and is involved in organ shape. A significant fraction of the protein is found in the ER. Mutants carrying null alleles express similar fruit phenotypes, as seen in er plants, but differ from er in that the stem is only slightly shorter than that in the wild type, the pedicel is slightly longer than that in the wild type, and the leaves are rounder than those in er mutants. Gene is expressed in all tissues examined, with highest expression level found in siliques. It is involved in resistance to Plectosphaerella cucumerina. The predicted protein has two DWD motifs. It can bind to DDB1a in Y2H assays and may be involved in the formation of a CUL4-based E3 ubiquitin ligaseO.I.H.G.
XAt5g01540831722LECRKA4.1 (LECTIN RECEPTOR KINASE A4.1)Encodes LecRKA4.1, a member of the lectin receptor kinase subfamily A4 (LecRKA4.1 At5g01540; LecRKA4.2 At5g01550; LecRKA4.3 At5g01560). Together with other members of the subfamily, functions redundantly in the negative regulation of ABA response in seed germination.O.I.H.G.
XAt5g01550831700LECRKA4.2 (LECTIN RECEPTOR KINASE A4.1)Encodes LecRKA4.2, a member of the lectin receptor kinase subfamily A4 (LecRKA4.1 At5g01540; LecRKA4.2 At5g01550; LecRKA4.3 At5g01560). Together with other members of the subfamily, functions redundantly in the negative regulation of ABA response in seed germination.O.I.H.G.
XAt5g01560830345LECRKA4.3 (LECTIN RECEPTOR KINASE A4.3)Encodes LecRKA4.3, a member of the lectin receptor kinase subfamily A4 (LecRKA4.1 At5g01540; LecRKA4.2 At5g01550; LecRKA4.3 At5g01560). Together with other members of the subfamily, functions redundantly in the negative regulation of ABA response in seed germination.O.I.H.G.
XAt5g09810830841ACT7 (ACTIN 7)Member of Actin gene family.Mutants are defective in germination and root growth.O.I.H.G.
XAt5g37260833700RVE2 (REVEILLE 2)Encodes a MYB family transcription factor Circadian 1 (CIR1). Involved in circadian regulation in Arabidopsis.O.I.H.G.
XAt5g40420834040OLEO2 (OLEOSIN 2)Encodes oleosin2, a protein found in oil bodies, involved in seed lipid accumulation. Suppression of OLEO1 (and OLEO2) resulted in an aberrant phenotype of embryo cells that contain unusually large oilbodies that are not normally observed in seeds. Changes in the size of oilbodies caused disruption of storage organelles, altering accumulation of lipids and proteins and causing delay in germination. Functions in freezing tolerance of seeds.O.I.H.G.
XAt5g42890834300SCP2 (STEROL CARRIER PROTEIN 2)F:sterol carrier activity, oxidoreductase activity;P:glyoxylate metabolic process, intracellular lipid transport, fatty acid beta-oxidation, seed germination;C:peroxisome;MFOPBO.I.H.G.
XAt5g57390835845AIL5 (AINTEGUMENTA-LIKE 5)Encodes a member of the AP2 family of transcriptional regulators.May be involved in germination and seedling growth. Mutants are resistant to ABA analogs and are resistant to high nitrogen concentrations.O.I.H.G.
SAt1g03880839383CRU2 (CRUCIFERIN 2)Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds.O.I.H.G.
SAt2g27380817282ATEPR1Encodes an extensin like gene involved in seed germination.O.I.H.G.
NAt3g13540820556ATMYB5 (MYB DOMAIN PROTEIN 5)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).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:00325010Any biological process, occurring at the level of a multicellular organism, pertinent to its function.



The lower GO terms

Process ID Gene number Process name
GO:00486230The process by which a seed germinates before being shed from the parent plant.
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.





Comparison with co-expressed genes



Back to the CoP portal site

Back to the KAGIANA project homepage