PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT3G18990.1

Common Name

K13E13.10, REM39, VRN1

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

Protein Properties

Length: 341aa MW: 39274.7 Da PI: 9.5175

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G18990.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	56.7	4.5e-18	5	95	1	97
EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97 ff +l+ s++ +++rl++p kf+++++ + s+ + l+ ++g +W+v l rk ++++++++GW+eFv+ ++ g ++F+++g+s f v +f AT3G18990.1 5 FFHKLIFSSTIQEKRLRVPDKFVSKFKDE--LSVAVALTVPDGHVWRVGL--RKADNKIWFQDGWQEFVDRYSIRIGYLLIFRYEGNSAF--SVYIF 95 899999***************999755..99*************..********************************9999..88777 PP
2	B3	55.1	1.4e-17	244	337	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97 f vl ps+ + ++++lp fae++ +g++ + ++++ + ++W v++ k gr +++GW eF +n+L egD++vF+l ++++f l+v++f AT3G18990.1 244 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKVQ---LAEKQWPVRC--LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAF 335 677899******************84442.444555...567***..666666779********************99*****999 PP -S CS B3 98 rk 99 r AT3G18990.1 336 RV 337 85 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	7.6E-23	3	97	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	5.1E-22	3	97	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.61E-19	5	96	No hit	No description
Pfam	PF02362	3.0E-15	5	96	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	14.663	5	98	IPR003340	B3 DNA binding domain
SMART	SM01019	2.7E-17	5	98	IPR003340	B3 DNA binding domain
Gene3D	G3DSA:2.40.330.10	4.3E-23	236	337	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	4.32E-22	237	338	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.79E-20	242	336	No hit	No description
Pfam	PF02362	5.2E-16	244	337	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.619	244	338	IPR003340	B3 DNA binding domain
SMART	SM01019	8.1E-22	244	338	IPR003340	B3 DNA binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009909	Biological Process	regulation of flower development
GO:0010048	Biological Process	vernalization response
GO:0005654	Cellular Component	nucleoplasm
GO:0003677	Molecular Function	DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 341 aa Download sequence Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVSKF KDELSVAVAL TVPDGHVWRV GLRKADNKIW 60 FQDGWQEFVD RYSIRIGYLL IFRYEGNSAF SVYIFNLSHS EINYHSTGLM DSAHNHFKRA 120 RLFEDLEDED AEVIFPSSVY PSPLPESTVP ANKGYASSAI QTLFTGPVKA EEPTPTPKIP 180 KKRGRKKKNA DPEEINSSAP RDDDPENRSK FYESASARKR TVTAEERERA INAAKTFEPT 240 NPFFRVVLRP SYLYRGCIMY LPSGFAEKYL SGISGFIKVQ LAEKQWPVRC LYKAGRAKFS 300 QGWYEFTLEN NLGEGDVCVF ELLRTRDFVL KVTAFRVNEY V

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4i1k_A	2e-94	207	341	12	146	B3 domain-containing transcription factor VRN1
4i1k_B	2e-94	207	341	12	146	B3 domain-containing transcription factor VRN1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.27524	0.0	bud\| flower\| root\| seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	256944_at	0.0
Expression Atlas	AT3G18990	-
AtGenExpress	AT3G18990	-
ATTED-II	AT3G18990	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots and at lower levels in aerial parts. {ECO:0000269\|PubMed:12114624}.

Functional Description ? help Back to Top
Source	Description
TAIR	Required for vernalization. Essential for the complete repression of FLC in vernalized plants. Required for the methylation of histone H3
UniProt	Involved in the regulation of vernalization. Acts as transcriptional repressor of FLC, a major target of the vernalization pathway. Binds DNA in vitro in a non-sequence-specific manner. {ECO:0000269\|PubMed:12114624}.

Function -- GeneRIF ? help Back to Top
Preliminary X-ray diffraction data analysis revealed that the VRN1(208-341) crystal diffracted to 2.1 A. [PMID: 19255487] Although VRN1 is sequence-nonspecific in DNA binding, it has a defined DNA-binding surface. [PMID: 23255593]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G18990.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G65480(A), AT2G03220(A), AT4G16845(R), AT5G10140(R)

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q8L3W1

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G18990

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF289052	0.0	AF289052.1 Arabidopsis thaliana reduced vernalization response 1 (VRN1) mRNA, VRN1-Ler allele, complete cds.
GenBank	AK230388	0.0	AK230388.1 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL25-06-L05.
GenBank	BT024731	0.0	BT024731.1 Arabidopsis thaliana At3g18990 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_188529.2	0.0	AP2/B3-like transcriptional factor family protein
Swissprot	Q8L3W1	0.0	VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBL	A0A178VIS1	0.0	A0A178VIS1_ARATH; VRN1
STRING	AT3G18990.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1124	28	103
Representative plant	OGRP2051	14	36

Link Out ? help Back to Top
Phytozome	AT3G18990.1
Entrez Gene	821432
iHOP	AT3G18990
wikigenes	AT3G18990

Publications ? help Back to Top
Sheldon CC,Rouse DT,Finnegan EJ,Peacock WJ,Dennis ES The molecular basis of vernalization: the central role of FLOWERING LOCUS C (FLC). Proc. Natl. Acad. Sci. U.S.A., 2000. 97(7): p. 3753-8 [PMID:10716723] Levy YY,Mesnage S,Mylne JS,Gendall AR,Dean C Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science, 2002. 297(5579): p. 243-6 [PMID:12114624] Prasad K,Kushalappa K,Vijayraghavan U Mechanism underlying regulated expression of RFL, a conserved transcription factor, in the developing rice inflorescence. Mech. Dev., 2003. 120(4): p. 491-502 [PMID:12676326] Yan L, et al. Positional cloning of the wheat vernalization gene VRN1. Proc. Natl. Acad. Sci. U.S.A., 2003. 100(10): p. 6263-8 [PMID:12730378] Sung S,Amasino RM Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature, 2004. 427(6970): p. 159-64 [PMID:14712276] Bastow R, et al. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature, 2004. 427(6970): p. 164-7 [PMID:14712277] Sung S,Amasino RM Vernalization and epigenetics: how plants remember winter. Curr. Opin. Plant Biol., 2004. 7(1): p. 4-10 [PMID:14732435] Loukoianov A,Yan L,Blechl A,Sanchez A,Dubcovsky J Regulation of VRN-1 vernalization genes in normal and transgenic polyploid wheat. Plant Physiol., 2005. 138(4): p. 2364-73 [PMID:16055679] Jean Finnegan E, et al. The downregulation of FLOWERING LOCUS C (FLC) expression in plants with low levels of DNA methylation and by vernalization occurs by distinct mechanisms. Plant J., 2005. 44(3): p. 420-32 [PMID:16236152] Trevaskis B,Hemming MN,Peacock WJ,Dennis ES HvVRN2 responds to daylength, whereas HvVRN1 is regulated by vernalization and developmental status. Plant Physiol., 2006. 140(4): p. 1397-405 [PMID:16500994] Sheldon CC,Finnegan EJ,Dennis ES,Peacock WJ Quantitative effects of vernalization on FLC and SOC1 expression. Plant J., 2006. 45(6): p. 871-83 [PMID:16507079] Mylne JS, et al. LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC. Proc. Natl. Acad. Sci. U.S.A., 2006. 103(13): p. 5012-7 [PMID:16549797] Greb T, et al. The PHD finger protein VRN5 functions in the epigenetic silencing of Arabidopsis FLC. Curr. Biol., 2007. 17(1): p. 73-8 [PMID:17174094] Finnegan EJ,Dennis ES Vernalization-induced trimethylation of histone H3 lysine 27 at FLC is not maintained in mitotically quiescent cells. Curr. Biol., 2007. 17(22): p. 1978-83 [PMID:17980595] Hemming MN,Peacock WJ,Dennis ES,Trevaskis B Low-temperature and daylength cues are integrated to regulate FLOWERING LOCUS T in barley. Plant Physiol., 2008. 147(1): p. 355-66 [PMID:18359843] Li C,Dubcovsky J Wheat FT protein regulates VRN1 transcription through interactions with FDL2. Plant J., 2008. 55(4): p. 543-54 [PMID:18433437] Dortay H, et al. Toward an interaction map of the two-component signaling pathway of Arabidopsis thaliana. J. Proteome Res., 2008. 7(9): p. 3649-60 [PMID:18642946] Ascencio-Ib Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiol., 2008. 148(1): p. 436-54 [PMID:18650403] Swaminathan K,Peterson K,Jack T The plant B3 superfamily. Trends Plant Sci., 2008. 13(12): p. 647-55 [PMID:18986826] Shimada S, et al. A genetic network of flowering-time genes in wheat leaves, in which an APETALA1/FRUITFULL-like gene, VRN1, is upstream of FLOWERING LOCUS T. Plant J., 2009. 58(4): p. 668-81 [PMID:19175767] King G,Hill JM,Martin JL,Mylne JS Expression, purification and preliminary X-ray diffraction studies of VERNALIZATION1(208-341) from Arabidopsis thaliana. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 2009. 65(Pt 3): p. 291-4 [PMID:19255487] Greenup A,Peacock WJ,Dennis ES,Trevaskis B The molecular biology of seasonal flowering-responses in Arabidopsis and the cereals. Ann. Bot., 2009. 103(8): p. 1165-72 [PMID:19304997] Hemming MN,Peacock WJ,Dennis ES,Trevaskis B Integration of seasonal flowering time responses in temperate cereals. Plant Signal Behav, 2008. 3(8): p. 601-2 [PMID:19704811] Amasino R Seasonal and developmental timing of flowering. Plant J., 2010. 61(6): p. 1001-13 [PMID:20409274] Greenup AG, et al. ODDSOC2 is a MADS box floral repressor that is down-regulated by vernalization in temperate cereals. Plant Physiol., 2010. 153(3): p. 1062-73 [PMID:20431086] Matias-Hernandez L, et al. VERDANDI is a direct target of the MADS domain ovule identity complex and affects embryo sac differentiation in Arabidopsis. Plant Cell, 2010. 22(6): p. 1702-15 [PMID:20581305] Elrouby N,Coupland G Proteome-wide screens for small ubiquitin-like modifier (SUMO) substrates identify Arabidopsis proteins implicated in diverse biological processes. Proc. Natl. Acad. Sci. U.S.A., 2010. 107(40): p. 17415-20 [PMID:20855607] Mylne JS,Mas C,Hill JM NMR assignment and secondary structure of the C-terminal DNA binding domain of Arabidopsis thaliana VERNALIZATION1. Biomol NMR Assign, 2012. 6(1): p. 5-8 [PMID:21553305] Kinjo H,Shitsukawa N,Takumi S,Murai K Diversification of three APETALA1/FRUITFULL-like genes in wheat. Mol. Genet. Genomics, 2012. 287(4): p. 283-94 [PMID:22314801] Liang S, et al. Transcriptional Regulations on the Low-Temperature-Induced Floral Transition in an Orchidaceae Species, Dendrobium nobile: An Expressed Sequence Tags Analysis. Comp. Funct. Genomics, 2012. 2012: p. 757801 [PMID:22550428] Jung CH,Wong CE,Singh MB,Bhalla PL Comparative genomic analysis of soybean flowering genes. PLoS ONE, 2012. 7(6): p. e38250 [PMID:22679494] King GJ, et al. The Arabidopsis B3 domain protein VERNALIZATION1 (VRN1) is involved in processes essential for development, with structural and mutational studies revealing its DNA-binding surface. J. Biol. Chem., 2013. 288(5): p. 3198-207 [PMID:23255593] Chen A,Dubcovsky J Wheat TILLING mutants show that the vernalization gene VRN1 down-regulates the flowering repressor VRN2 in leaves but is not essential for flowering. PLoS Genet., 2012. 8(12): p. e1003134 [PMID:23271982] Mantegazza O, et al. Analysis of the arabidopsis REM gene family predicts functions during flower development. Ann. Bot., 2014. 114(7): p. 1507-15 [PMID:25002525] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Kumar A,Singh A,Panigrahy M,Sahoo PK,Panigrahi KCS Carbon nanoparticles influence photomorphogenesis and flowering time in Arabidopsis thaliana. Plant Cell Rep., 2018. 37(6): p. 901-912 [PMID:29541883] Chandler J,Wilson A,Dean C Arabidopsis mutants showing an altered response to vernalization. Plant J., 1996. 10(4): p. 637-44 [PMID:8998499]