FLC K-box region and MADS-box transcription factor family protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: FLC
Official Full Name: K-box region and MADS-box transcription factor family protein
Primary source: TAIR:AT5G10140
Locus tag: AT5G10140
See related: Araport:AT5G10140
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Arabidopsis thaliana (ecotype: Columbia)
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as: AGAMOUS-like 25; AGL25; FLF; FLOWERING LOCUS C; FLOWERING LOCUS F; MADS BOX PROTEIN FLOWERING LOCUS F; REDUCED STEM BRANCHING 6; RSB6; T31P16.130; T31P16_130
Summary: MADS-box protein encoded by FLOWERING LOCUS C - transcription factor that functions as a repressor of floral transition and contributes to temperature compensation of the circadian clock. Expression is downregulated during cold treatment. Vernalization, FRI and the autonomous pathway all influence the state of FLC chromatin. Both maternal and paternal alleles are reset by vernalization, but their earliest activation differs in timing and location. Histone H3 trimethylation at lysine 4 and histone acetylation are associated with active FLC expression, whereas histone deacetylation and histone H3 dimethylation at lysines 9 and 27 are involved in FLC repression. Expression is also repressed by two small RNAs (30- and 24-nt) complementary to the FLC sense strand 3? to the polyA site. The small RNAs are most likely derived from an antisense transcript of FLC. Interacts with SOC1 and FT chromatin in vivo. Member of a protein complex.
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Genomic context

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See FLC in Genome Data Viewer

Location:: chromosome: 5

Exon count:: 8

Sequence:: Chromosome: 5; NC_003076.8 (3173382..3179448, complement)

Chromosome 5 - NC_003076.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003076.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SISTER OF FCA physically associates with SKB1 to regulate flowering time in Arabidopsis thaliana.
Title: SISTER OF FCA physically associates with SKB1 to regulate flowering time in Arabidopsis thaliana.
Genome-wide association study identifies a novel BMI1A QTL allele that confers FLC expression diversity in Arabidopsis thaliana.
Title: Genome-wide association study identifies a novel BMI1A QTL allele that confers FLC expression diversity in Arabidopsis thaliana.
COOLAIR and PRC2 function in parallel to silence FLC during vernalization.
Title: COOLAIR and PRC2 function in parallel to silence FLC during vernalization.
FLZ13 interacts with FLC and ABI5 to negatively regulate flowering time in Arabidopsis.
Title: FLZ13 interacts with FLC and ABI5 to negatively regulate flowering time in Arabidopsis.
Causal role of a promoter polymorphism in natural variation of the Arabidopsis floral repressor gene FLC.
Title: Causal role of a promoter polymorphism in natural variation of the Arabidopsis floral repressor gene FLC.
Regulation of FLC nuclear import by coordinated action of the NUP62-subcomplex and importin beta SAD2.
Title: Regulation of FLC nuclear import by coordinated action of the NUP62-subcomplex and importin β SAD2.
The P-body component DECAPPING5 and the floral repressor SISTER OF FCA regulate FLOWERING LOCUS C transcription in Arabidopsis.
Title: The P-body component DECAPPING5 and the floral repressor SISTER OF FCA regulate FLOWERING LOCUS C transcription in Arabidopsis.
Integrating analog and digital modes of gene expression at Arabidopsis FLC.
Title: Integrating analog and digital modes of gene expression at Arabidopsis FLC.
FLK is an mRNA m[6]A reader that regulates floral transition by modulating the stability and splicing of FLC in Arabidopsis.
Title: FLK is an mRNA m(6)A reader that regulates floral transition by modulating the stability and splicing of FLC in Arabidopsis.
Distinct responses to autumn and spring temperatures by the key flowering-time regulator FLOWERING LOCUS C.
Title: Distinct responses to autumn and spring temperatures by the key flowering-time regulator FLOWERING LOCUS C.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

NM_001085094.2

Supported by ESTs:

NM_001161231.2

Supported by ESTs:

NM_001203343.1

Supported by ESTs:

NM_121052.3

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info
enables transcription cis-regulatory region binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within negative regulation of flower development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of photoperiodism, flowering	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to temperature stimulus	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to temperature stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within vernalization response	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	ISM Inferred from Sequence Model more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: K-box region and MADS-box transcription factor family protein

NP_001078563.1

FLOWERING LOCUS C (FLC); CONTAINS InterPro DOMAIN/s: Transcription factor, MADS-box (InterPro:IPR002100), Transcription factor, K-box (InterPro:IPR002487); BEST Arabidopsis thaliana protein match is: K-box region and MADS-box transcription factor family protein (TAIR:AT5G65060.1); Has 6850 Blast hits to 6845 proteins in 859 species: Archae - 0; Bacteria - 0; Metazoa - 626; Fungi - 311; Plants - 5839; Viruses - 0; Other Eukaryotes - 74 (source: NCBI BLink).

NP_001154703.1

K-box region and MADS-box transcription factor family protein; CONTAINS InterPro DOMAIN/s: Transcription factor, MADS-box (InterPro:IPR002100), Transcription factor, K-box (InterPro:IPR002487); BEST Arabidopsis thaliana protein match is: K-box region and MADS-box transcription factor family protein (TAIR:AT5G65060.1); Has 6794 Blast hits to 6790 proteins in 825 species: Archae - 0; Bacteria - 0; Metazoa - 626; Fungi - 298; Plants - 5796; Viruses - 0; Other Eukaryotes - 74 (source: NCBI BLink).

NP_001190272.1

FLOWERING LOCUS C (FLC); CONTAINS InterPro DOMAIN/s: Transcription factor, MADS-box (InterPro:IPR002100), Transcription factor, K-box (InterPro:IPR002487); BEST Arabidopsis thaliana protein match is: AGAMOUS-like 31 (TAIR:AT5G65050.1).

NP_196576.1

FLOWERING LOCUS C (FLC); CONTAINS InterPro DOMAIN/s: Transcription factor, MADS-box (InterPro:IPR002100), Transcription factor, K-box (InterPro:IPR002487); BEST Arabidopsis thaliana protein match is: K-box region and MADS-box transcription factor family protein (TAIR:AT1G77080.4); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_003076.8 Reference assembly

Range

3173382..3179448 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_121052.3 → NP_196576.1 K-box region and MADS-box transcription factor family protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_196576.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9S7Q7

UniProtKB/TrEMBL

A0A5S9Y545, G4WUB7, Q5Q9J1, Q5Q9J3

Conserved Domains (1) summary

cd00265
Location:2 → 78

MADS_MEF2_like; MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I ...
NM_001203343.1 → NP_001190272.1 K-box region and MADS-box transcription factor family protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001190272.1

Status: REVIEWED

UniProtKB/TrEMBL

G4WUB7, Q58T14, Q5Q9J3

Conserved Domains (2) summary

cd00265
Location:2 → 78

MADS_MEF2_like; MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I ...

pfam01486
Location:94 → 149

K-box; K-box region
NM_001085094.2 → NP_001078563.1 K-box region and MADS-box transcription factor family protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001078563.1

Status: REVIEWED

UniProtKB/TrEMBL

K0IFX0, Q58T15

Conserved Domains (2) summary

cd00265
Location:2 → 78

MADS_MEF2_like; MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I ...

pfam01486
Location:94 → 163

K-box; K-box region
NM_001161231.2 → NP_001154703.1 K-box region and MADS-box transcription factor family protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001154703.1

Status: REVIEWED

UniProtKB/TrEMBL

A5JM49, K0IFX0

Conserved Domains (1) summary

cd00265
Location:2 → 78

MADS_MEF2_like; MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I ...