SOC1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0009409 response to cold	IEP PMID:16507079 Quantitative effects of vernalization on FLC and SOC1 expres...	KEEP AS NON CORE	Summary: The source supports SOC1 transcript induction by vernalization/cold in reciprocal relationship to FLC repression. This is useful evidence that SOC1 is an output of cold-dependent flowering regulation, but it does not make cold response the core function of the protein. Reason: SOC1 is a flowering-time transcription factor whose expression responds to vernalization. The response-to-cold annotation should be retained as a non-core regulatory input rather than treated as a stress-response function. Supporting Evidence: PMID:16507079 SUPPRESSOR OF OVER-EXPRESSION OF CO 1 (SOC1), a downstream target of FLC, is quantitatively induced by vernalization in a reciprocal manner to FLC.
GO:0009908 flower development	TAS PMID:10995392 The AGAMOUS-LIKE 20 MADS domain protein integrates floral in...	MODIFY	Summary: The paper identifies AGL20/SOC1 as an integrator of flowering pathways. That evidence is about floral induction and phase transition, not the broader developmental process of building flowers. Reason: Replace the broad flower development term with the more specific process supported for SOC1: vegetative to reproductive phase transition of meristem. Proposed replacements: vegetative to reproductive phase transition of meristem Supporting Evidence: PMID:10995392 Our results indicate that AGL20 is an important integrator of three pathways controlling flowering in Arabidopsis.
GO:0009911 positive regulation of flower development	IMP PMID:10834834 Distinct roles of CONSTANS target genes in reproductive deve...	MODIFY	Summary: SOC1 is required for CONSTANS-mediated promotion of flowering, supporting a positive role in floral induction. The term is broad and implies flower development generally rather than the meristem phase transition. Reason: The experimental result supports SOC1 as a promotive component of the flowering-time transition. GO:0010228 is more precise than positive regulation of flower development. Proposed replacements: vegetative to reproductive phase transition of meristem Supporting Evidence: PMID:10834834 Two of these genes, SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) and FLOWERING LOCUS T (FT), are required for CO to promote flowering
GO:0009911 positive regulation of flower development	IMP PMID:11123798 A MADS domain gene involved in the transition to flowering i...	MODIFY	Summary: The source supports late flowering in agl20 mutants and activation of AGL20 in shoot apical meristems during transition to flowering. This is strong evidence for the floral transition but not for broad flower development. Reason: Replace the broad positive regulation of flower development term with the specific meristem phase-transition process directly supported by SOC1/AGL20 mutant and expression evidence. Proposed replacements: vegetative to reproductive phase transition of meristem Supporting Evidence: PMID:11123798 AGL20 (AGAMOUS LIKE 20) is a MADS domain gene from Arabidopsis that is activated in shoot apical meristems during the transition to flowering.
GO:0010077 maintenance of inflorescence meristem identity	IGI PMID:20626659 Arabidopsis BLADE-ON-PETIOLE1 and 2 promote floral meristem ...	UNDECIDED	Summary: The accessible cached text for this paper focuses on BOP1/2, LFY, AP1, and AGL24. It does not mention SOC1 directly, and the full text is not available locally to verify the IGI annotation or the specific genetic interaction context. Reason: SOC1 can promote inflorescence/floral-transition programs, but this specific annotation to maintenance of inflorescence meristem identity cannot be checked from the available abstract-level cache. Supporting Evidence: PMID:20626659 [Cached abstract does not mention SOC1; full text is needed to assess this IGI annotation.]
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA GO_REF:0000002	ACCEPT	Summary: SOC1 is a MADS-box transcription factor, and direct studies show SOC1 binding to regulatory DNA regions such as the LFY promoter and CArG-box regions at TFS1. Reason: This sequence-specific RNA polymerase II regulatory-region DNA-binding activity is consistent with conserved MADS-box domains and with direct SOC1 promoter-binding evidence. Supporting Evidence: PMID:18466303 Here, we show that SOC1 directly binds to the distal and proximal region of the LFY promoter where critical cis-elements are located. file:interpro/panther/PTHR48019/PTHR48019-metadata.yaml The MADS-box/MEF2 family proteins are transcription factors that play crucial roles in various developmental processes across a wide range of organisms.
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA GO_REF:0000033	ACCEPT	Summary: The IBA annotation matches SOC1's conserved MADS-domain DNA-binding role and is supported by gene-specific ChIP/promoter evidence for LFY and TFS1 regulatory regions. Reason: SOC1 is a sequence-specific cis-regulatory DNA-binding transcription factor acting on RNA polymerase II-transcribed genes. Supporting Evidence: PMID:30946745 ChIP-qPCR analysis of SOC1 (B) and SVP (C) on CArG-boxes at TFS1 in 35S::SOC1:GR soc1 plants after DEX treatment. PMID:18466303 SOC1 directly binds to the distal and proximal region of the LFY promoter where critical cis-elements are located.
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific	IPI PMID:30946745 Floral regulators FLC and SOC1 directly regulate expression ...	ACCEPT	Summary: Richter et al. place SOC1 as a MADS-box transcription factor that directly activates TFS1 and opposes Polycomb repression by recruiting REF6 and BRM. This supports RNA polymerase II-specific DNA-binding transcription factor activity. Reason: SOC1 independently enables transcription factor activity through its MADS-domain DNA binding and transcriptional regulatory function at flowering-transition targets. Supporting Evidence: PMID:30946745 SOC1 opposes PRC function at TFS1 through recruitment of the histone demethylase RELATIVE OF EARLY FLOWERING 6 (REF6) and the SWI/SNF chromatin remodeler ATPase BRAHMA (BRM). file:ARATH/SOC1/SOC1-deep-research-falcon.md Primary molecular role is a sequence-specific transcriptional regulator promoting floral transition; SOC1 integrates endogenous and environmental flowering inputs and activates floral meristem identity programs
GO:0003677 DNA binding	IEA GO_REF:0000002	MODIFY	Summary: SOC1 clearly binds DNA, but the generic DNA binding term loses the important specificity that SOC1 is a MADS-domain RNA polymerase II cis-regulatory transcription factor. Reason: Replace generic DNA binding with RNA polymerase II cis-regulatory region sequence-specific DNA binding, which captures the MADS-box regulatory DNA-binding activity. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:18466303 SOC1 directly binds to the distal and proximal region of the LFY promoter where critical cis-elements are located.
GO:0003700 DNA-binding transcription factor activity	IEA GO_REF:0000002	MODIFY	Summary: The generic transcription factor activity term is directionally correct but less specific than the RNA polymerase II-specific activity supported for plant MADS-box transcription factors. Reason: SOC1 regulates RNA polymerase II-transcribed developmental genes, so GO:0000981 is the better molecular-function term. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: file:ARATH/SOC1/SOC1-uniprot.txt Transcription activator active in flowering time control.
GO:0003700 DNA-binding transcription factor activity	TAS PMID:10995392 The AGAMOUS-LIKE 20 MADS domain protein integrates floral in...	MODIFY	Summary: The paper supports SOC1/AGL20 as a MADS-domain flowering regulator. The molecular-function term should be the RNA polymerase II-specific transcription factor activity rather than the broader legacy term. Reason: SOC1 acts as a MADS-box RNA polymerase II transcription factor in flowering control, and GO:0000981 captures that specificity. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:10995392 A MADS-domain gene, AGAMOUS-LIKE 20 (AGL20), was identified as a dominant FRI suppressor in activation tagging mutagenesis.
GO:0003700 DNA-binding transcription factor activity	ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a...	MODIFY	Summary: The source is a genome-wide transcription factor family analysis and is consistent with SOC1 being a transcription factor, but the annotation should use the more precise RNA polymerase II-specific term. Reason: SOC1 is not merely any DNA-binding transcription factor; it is a eukaryotic MADS-domain regulator of RNA polymerase II target genes. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:11118137 Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors
GO:0003700 DNA-binding transcription factor activity	ISS PMID:11123798 A MADS domain gene involved in the transition to flowering i...	MODIFY	Summary: SOC1/AGL20 is described as a MADS-domain gene involved in floral induction. The activity is correct in essence but should be updated to the RNA polymerase II-specific transcription factor term. Reason: The more precise molecular-function term is GO:0000981. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:11123798 AGL20 (AGAMOUS LIKE 20) is a MADS domain gene from Arabidopsis that is activated in shoot apical meristems during the transition to flowering.
GO:0003700 DNA-binding transcription factor activity	ISS PMID:12837945 Molecular and phylogenetic analyses of the complete MADS-box...	MODIFY	Summary: The MADS-box family analysis supports SOC1 family membership and transcription factor inference, but the generic term is less informative than RNA polymerase II-specific DNA-binding transcription factor activity. Reason: Update the broad term to GO:0000981, consistent with SOC1's conserved MADS-domain role in regulation of RNA polymerase II target genes. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:12837945 MADS-box transcription factors are key regulators of several plant development processes.
GO:0005515 protein binding	IPI PMID:11439126 APETALA1 and SEPALLATA3 interact to promote flower developme...	UNDECIDED	Summary: The annotation is based on reported interactions with AP1/CAL in GOA, but the locally cached abstract does not identify SOC1 as an interactor. The paper's full text is not available locally to verify the specific SOC1 interaction rows. Reason: Protein binding is too generic for curation, but this specific source cannot be assessed from the cached abstract. If full text confirms SOC1 heterodimerization with AP1/CAL, the preferred replacement would be protein heterodimerization activity. Supporting Evidence: PMID:11439126 [Cached abstract does not identify SOC1 among the yeast two-hybrid interactors; full text is needed to verify the annotation.]
GO:0005515 protein binding	IPI PMID:15805477 Comprehensive interaction map of the Arabidopsis MADS Box tr...	MODIFY	Summary: The MADS-box interactome paper supports specific heterodimer formation among MADS transcription factors, including SOC1 partners represented in GOA. Generic protein binding under-describes the MADS complex-forming activity. Reason: Replace protein binding with protein heterodimerization activity for SOC1's MADS-domain partner interactions. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:15805477 A matrix-based yeast two-hybrid screen of >100 members of this family revealed a collection of specific heterodimers and a few homodimers.
GO:0005515 protein binding	IPI PMID:18466303 SOC1 translocated to the nucleus by interaction with AGL24 d...	MODIFY	Summary: SOC1 interaction with AGL24 is a key mechanism for nuclear localization and LFY activation. The evidence supports heterodimerization rather than the uninformative protein binding term. Reason: Replace protein binding with protein heterodimerization activity for the SOC1-AGL24 MADS-domain complex. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:18466303 heterodimerization of SOC1 and AGL24 is a key mechanism in activating LFY expression.
GO:0005515 protein binding	IPI PMID:20129060 Pin1At encoding a peptidyl-prolyl cis/trans isomerase regula...	MARK AS OVER ANNOTATED	Summary: Pin1At interacts with phosphorylated SOC1 and AGL24 and regulates flowering through prolyl cis/trans isomerization of these transcription factors. This is biologically relevant, but generic protein binding is not an informative SOC1 molecular-function annotation. Reason: The interaction is best retained in interaction/protein-modification records. GO:0005515 does not describe SOC1's actual activity, and no more specific SOC1-enabled MF term is justified by this interaction. Supporting Evidence: PMID:20129060 Pin1At interacts with the phosphorylated AGL24 and SOC1 in vitro and with AGL24 and SOC1 in vivo
GO:0005515 protein binding	IPI PMID:21798944 Evidence for network evolution in an Arabidopsis interactome...	MARK AS OVER ANNOTATED	Summary: This proteome-wide binary interactome supports high-throughput SOC1 interaction records but not a precise molecular activity beyond physical association. Reason: Generic protein binding from high-throughput interactome mapping should not be treated as a curated core molecular function for SOC1. Supporting Evidence: PMID:21798944 We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana
GO:0005515 protein binding	IPI PMID:24714165 Phytoplasma effector SAP54 hijacks plant reproduction by deg...	REMOVE	Summary: SAP54 binds and destabilizes several Type II MADS-box transcription factors, including SOC1. This pathogen-effector interaction is real, but protein binding is not an informative intrinsic SOC1 function. Reason: The GO annotation overstates a pathogen-effector target interaction as a host gene product activity. This should remain an interaction/pathogenesis record and be removed from SOC1 molecular-function annotations rather than retained as generic protein binding. Supporting Evidence: PMID:24714165 Peptides associated with Type II MTFs MAF1, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), SEP1, SEP2, and AP1 were recovered in samples immunoprecipitated with GFP-SAP54 but not with GFP alone
GO:0005515 protein binding	IPI PMID:31540691 OXIDATIVE STRESS 3 regulates drought-induced flowering throu...	MARK AS OVER ANNOTATED	Summary: OXS3 binds SOC1 and modulates drought-associated flowering output through AP1 promoter repression. The specific biology is regulatory, but the protein binding term remains too generic for SOC1's molecular function. Reason: This interaction is non-core and should not be curated as generic protein binding. Existing SOC1 annotations to transcription factor activity and MADS heterodimerization better capture its function. Supporting Evidence: PMID:31540691 OXS3 could bind SOC1 in vitro and in vivo.
GO:0046983 protein dimerization activity	IEA GO_REF:0000002	ACCEPT	Summary: SOC1 is a MADS-box protein that functions through partner complex formation. Direct evidence supports heterodimerization with AGL24, and broader MADS-family data support dimeric/quartet regulatory complexes. Reason: Protein dimerization is a core molecular mechanism for SOC1 transcription factor function, although partner-specific annotations should preferably use heterodimerization when evidence identifies the partner. Supporting Evidence: file:ARATH/SOC1/SOC1-uniprot.txt Forms a heterodimer with AGL24 through MADS-box domain. PMID:18466303 heterodimerization of SOC1 and AGL24 is a key mechanism in activating LFY expression.
GO:0006355 regulation of DNA-templated transcription	IEA GO_REF:0000002	MODIFY	Summary: SOC1 regulates transcription, but the existing term is broader than needed for a eukaryotic MADS-box transcription factor. Reason: Replace with regulation of transcription by RNA polymerase II, which matches SOC1's nuclear transcriptional regulatory role. Proposed replacements: regulation of transcription by RNA polymerase II Supporting Evidence: file:ARATH/SOC1/SOC1-uniprot.txt Transcription activator active in flowering time control.
GO:0006357 regulation of transcription by RNA polymerase II	IBA GO_REF:0000033	ACCEPT	Summary: SOC1 is a conserved MADS-box transcription factor and direct studies show it regulates RNA polymerase II target genes during floral transition. Reason: This biological process term appropriately captures SOC1's transcriptional regulatory role. Supporting Evidence: PMID:30946745 Furthermore, SOC1 directly activates the transcription of TFS1.
GO:0009739 response to gibberellin	IEP PMID:18466303 SOC1 translocated to the nucleus by interaction with AGL24 d...	KEEP AS NON CORE	Summary: SOC1 participates in gibberellin-dependent flowering output through interaction with AGL24, but gibberellin response is an upstream hormonal input into the flowering network rather than SOC1's core molecular function. Reason: Retain as non-core pathway context. The strongest locally accessible GA-specific statement is in PMID:18339670 rather than the cached abstract for PMID:18466303, so the annotation should not be treated as a primary SOC1 function. Supporting Evidence: PMID:18339670 the effect of gibberellins on flowering under short-day conditions was mediated by the interaction between AGL24 and SOC1.
GO:0045893 positive regulation of DNA-templated transcription	IEP PMID:18339670 Direct interaction of AGL24 and SOC1 integrates flowering si...	MODIFY	Summary: SOC1 directly upregulates AGL24 at the shoot apex in a positive-feedback loop. The annotation is correct in essence but should use the RNA polymerase II-specific positive regulation term. Reason: Replace the broad DNA-templated transcription term with positive regulation of transcription by RNA polymerase II. Proposed replacements: positive regulation of transcription by RNA polymerase II Supporting Evidence: PMID:18339670 ChIP assay using a functional SOC1-9myc-tagged line and promoter mutagenesis analysis also revealed in vivo binding of SOC1-9myc to the regulatory regions of AGL24 and upregulation of AGL24 at the shoot apex by SOC1.
GO:0045944 positive regulation of transcription by RNA polymerase II	IEA GO_REF:0000002	ACCEPT	Summary: SOC1 is described as a transcription activator and has gene-specific evidence for activation of AGL24, LFY, and TFS1-associated floral transition programs. Reason: Positive regulation of RNA polymerase II transcription is a core aspect of SOC1's activity as a floral-transition transcription factor. Supporting Evidence: file:ARATH/SOC1/SOC1-uniprot.txt Transcription activator active in flowering time control. PMID:30946745 SOC1 directly activates the transcription of TFS1.
GO:0050793 regulation of developmental process	IEA GO_REF:0000117	MODIFY	Summary: SOC1 regulates developmental timing, but this ARBA term is far too broad for a well-studied flowering pathway integrator. Reason: Replace with vegetative to reproductive phase transition of meristem, the specific developmental process repeatedly supported by SOC1 genetics and expression. Proposed replacements: vegetative to reproductive phase transition of meristem Supporting Evidence: PMID:11123798 AGL20 is involved in flowering time control.
GO:0005634 nucleus	IEA GO_REF:0000002	ACCEPT	Summary: SOC1's MADS transcription factor role requires nuclear activity, and direct localization experiments show AGL24-dependent nuclear relocation. Reason: Nuclear localization is well supported for functional SOC1 transcription factor complexes. Supporting Evidence: PMID:18466303 The full-length SOC1 protein locates in the cytoplasm if expressed alone in protoplast transient expression assay, but relocates to the nucleus if expressed with AGAMOUS-LIKE 24 (AGL24)
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: UniProt maps SOC1 to the nucleus based on curated subcellular-location evidence, consistent with direct SOC1-AGL24 localization experiments and transcription factor activity. Reason: The nucleus is the primary site of SOC1's transcriptional regulatory function. Supporting Evidence: file:ARATH/SOC1/SOC1-uniprot.txt Nucleus {ECO:0000255\|PROSITE-ProRule:PRU00251, ECO:0000269\|PubMed:18466303, ECO:0000269\|PubMed:31540691}.
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: AtSubP prediction is weaker than direct localization evidence, but the predicted nuclear localization agrees with SOC1's experimentally supported nuclear role. Reason: Although the original evidence is computational, the term is supported by independent experimental localization and transcription-factor function. Supporting Evidence: PMID:18466303 The full-length SOC1 protein locates in the cytoplasm if expressed alone in protoplast transient expression assay, but relocates to the nucleus if expressed with AGAMOUS-LIKE 24 (AGL24)
GO:0005634 nucleus	IDA PMID:18466303 SOC1 translocated to the nucleus by interaction with AGL24 d...	ACCEPT	Summary: SOC1 relocates to the nucleus when co-expressed with AGL24, consistent with partner-dependent nuclear action of SOC1-AGL24 MADS complexes. Reason: Direct localization assays support nucleus as the functional site of SOC1 transcription factor activity. Supporting Evidence: PMID:18466303 The full-length SOC1 protein locates in the cytoplasm if expressed alone in protoplast transient expression assay, but relocates to the nucleus if expressed with AGAMOUS-LIKE 24 (AGL24)
GO:0005634 nucleus	IDA PMID:31540691 OXIDATIVE STRESS 3 regulates drought-induced flowering throu...	ACCEPT	Summary: The cached abstract supports OXS3-SOC1 binding but does not describe localization. UniProt records OXS3 interaction with SOC1 in the nucleus, and other direct SOC1 localization evidence supports the nuclear term. Reason: The term is correct for SOC1, but the source-specific localization detail is not present in the abstract-level cached publication. Supporting Evidence: file:ARATH/SOC1/SOC1-uniprot.txt Interacts with OXS3 in the nucleus (PubMed:31540691). PMID:31540691 OXS3 could bind SOC1 in vitro and in vivo.
GO:0005737 cytoplasm	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: SOC1 can be detected in the cytoplasm when expressed alone, while AGL24 interaction promotes relocation to the nucleus. Reason: Cytoplasmic localization is experimentally observed, but the core site of SOC1 function is the nucleus. Retain as a context-dependent/non-core localization. Supporting Evidence: PMID:18466303 The full-length SOC1 protein locates in the cytoplasm if expressed alone in protoplast transient expression assay, but relocates to the nucleus if expressed with AGAMOUS-LIKE 24 (AGL24)
GO:0005737 cytoplasm	IDA PMID:18466303 SOC1 translocated to the nucleus by interaction with AGL24 d...	KEEP AS NON CORE	Summary: Direct assays show cytoplasmic localization of full-length SOC1 when expressed alone in protoplasts, followed by nuclear relocalization in the presence of AGL24. Reason: The cytoplasm term is supported as an observed localization state, but it is not the primary compartment for SOC1's transcriptional function. Supporting Evidence: PMID:18466303 The full-length SOC1 protein locates in the cytoplasm if expressed alone in protoplast transient expression assay, but relocates to the nucleus if expressed with AGAMOUS-LIKE 24 (AGL24)

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