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

AT1G50420.1

Common Name

F11F12.22, SCL3, SCL-3

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

GRAS

Protein Properties

Length: 482aa MW: 54152.8 Da PI: 6.3959

Description

scarecrow-like 3

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G50420.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	533.2	8.3e-163	54	479	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlta 98 l++lLl+cA++v+sg+l++a+a+L++ls+laspdgd+mqR+aayfteALa+r+++s+++lykal++++t+++n+see+++++lf+e++Pilk+s+l++ AT1G50420.1 54 LIHLLLTCANHVASGSLQNANAALEQLSHLASPDGDTMQRIAAYFTEALANRILKSWPGLYKALNATQTRTNNVSEEIHVRRLFFEMFPILKVSYLLT 151 689********************************************************************************************* PP GRAS 99 NqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrv 196 N+aIlea+ege++vH+iD+d+s+++QW+aLlqa++sRpegpp+lRiTgv++ +ke le++++rL + Ae+l++pf+fn+ v++rl++l++e+Lrv AT1G50420.1 152 NRAILEAMEGEKMVHVIDLDASEPAQWLALLQAFNSRPEGPPHLRITGVHH----QKEVLEQMAHRLIEEAEKLDIPFQFNP-VVSRLDCLNVEQLRV 244 ***********************************************....9**********************.7********** PP GRAS 197 kpgEalaVnlvlqlhrll.......................................................desvsles..erdevLklvkslsPk 237 k+gEalaV++vlqlh++l ++s++l+s ++d++L+++++lsPk AT1G50420.1 245 KTGEALAVSSVLQLHTFLasdddlmrkncalrfqnnpsgvdlqrvlmmshgsaaearendmsnnngyspsgdsASSLPLPSsgRTDSFLNAIWGLSPK 342 *******************************************************************9977777777779********** PP GRAS 238 vvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaak 335 v+vv+eq++dhn+++++er+le+l++y+alfd+le+k+pr+s++rikvE++l+g+ei+n+++ceg+errerhe+lekW++r++ aGF++vpls++a+ AT1G50420.1 343 VMVVTEQDSDHNGSTLMERLLESLYTYAALFDCLETKVPRTSQDRIKVEKMLFGEEIKNIISCEGFERRERHEKLEKWSQRIDLAGFGNVPLSYYAML 440 ********************************************************************************************** PP GRAS 336 qaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 qa++ll+ +++dgyr++eesg++v++W+drpL+svSaWr AT1G50420.1 441 QARRLLQGCGFDGYRIKEESGCAVICWQDRPLYSVSAWR 479 ************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	60.107	28	459	IPR005202	Transcription factor GRAS
Pfam	PF03514	2.9E-160	54	479	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009739	Biological Process	response to gibberellin
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0043565	Molecular Function	sequence-specific 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:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0006036	anatomy	root epidermis
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: 482 aa Download sequence Send to blast
MVAMFQEDNG TSSVASSPLQ VFSTMSLNRP TLLASSSPFH CLKDLKPEER GLYLIHLLLT 60 CANHVASGSL QNANAALEQL SHLASPDGDT MQRIAAYFTE ALANRILKSW PGLYKALNAT 120 QTRTNNVSEE IHVRRLFFEM FPILKVSYLL TNRAILEAME GEKMVHVIDL DASEPAQWLA 180 LLQAFNSRPE GPPHLRITGV HHQKEVLEQM AHRLIEEAEK LDIPFQFNPV VSRLDCLNVE 240 QLRVKTGEAL AVSSVLQLHT FLASDDDLMR KNCALRFQNN PSGVDLQRVL MMSHGSAAEA 300 RENDMSNNNG YSPSGDSASS LPLPSSGRTD SFLNAIWGLS PKVMVVTEQD SDHNGSTLME 360 RLLESLYTYA ALFDCLETKV PRTSQDRIKV EKMLFGEEIK NIISCEGFER RERHEKLEKW 420 SQRIDLAGFG NVPLSYYAML QARRLLQGCG FDGYRIKEES GCAVICWQDR PLYSVSAWRC 480 RK

Sequence ? help Back to Top

Protein Sequence Length: 482 aa Download sequence Send to blast

MVAMFQEDNG TSSVASSPLQ VFSTMSLNRP TLLASSSPFH CLKDLKPEER GLYLIHLLLT  60
CANHVASGSL QNANAALEQL SHLASPDGDT MQRIAAYFTE ALANRILKSW PGLYKALNAT  120
QTRTNNVSEE IHVRRLFFEM FPILKVSYLL TNRAILEAME GEKMVHVIDL DASEPAQWLA  180
LLQAFNSRPE GPPHLRITGV HHQKEVLEQM AHRLIEEAEK LDIPFQFNPV VSRLDCLNVE  240
QLRVKTGEAL AVSSVLQLHT FLASDDDLMR KNCALRFQNN PSGVDLQRVL MMSHGSAAEA  300
RENDMSNNNG YSPSGDSASS LPLPSSGRTD SFLNAIWGLS PKVMVVTEQD SDHNGSTLME  360
RLLESLYTYA ALFDCLETKV PRTSQDRIKV EKMLFGEEIK NIISCEGFER RERHEKLEKW  420
SQRIDLAGFG NVPLSYYAML QARRLLQGCG FDGYRIKEES GCAVICWQDR PLYSVSAWRC  480
RK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_A	4e-40	37	481	1	380	Protein SCARECROW
5b3h_D	4e-40	37	481	1	380	Protein SCARECROW
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.14826	0.0	flower\| leaf\| root\| vegetative tissue

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	186490011	0.0
Genevisible	261866_at	0.0
Expression Atlas	AT1G50420	-
AtGenExpress	AT1G50420	-
ATTED-II	AT1G50420	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in seedlings, root epidermis, leaves, flowers and siliques. {ECO:0000269\|PubMed:10341448, ECO:0000269\|PubMed:18500650}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a scarecrow-like protein (SCL3) Putative transcription factors interacting with the gene product of VHA-B1 (vacuolar ATPase subunit B1; as shown through yeast two-hybrid assay).
UniProt	Probable transcription factor involved in plant development. {ECO:0000250}.

Function -- GeneRIF ? help Back to Top
A coregulator exchange system between DELLA (as coactivator) and SCL3 (as corepressor) regulates the expression of SCL3. [PMID: 24821766] The balance of the DELLAs and SCL3 protein levels (both are GRAS proteins) regulates downstream gene expression through IDDs binding to DNA. Review. [PMID: 25763707] Data indicate that SEUSS (SEU) gene has distinct genetic interactions with SHORT-ROOT (SHR), SCARECROW (SCR), and SCARECROW-LIKE3 (SCL3) genes. [PMID: 26818732]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G50420.1

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

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT4G37650 (A)

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q9LPR8

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G50420

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC012561	0.0	AC012561.2 Arabidopsis thaliana chromosome I BAC F11F12 genomic sequence, complete sequence.
GenBank	AY056154	0.0	AY056154.1 Arabidopsis thaliana putative scarecrow 3 protein (At1g50420) mRNA, complete cds.
GenBank	AY091260	0.0	AY091260.1 Arabidopsis thaliana putative scarecrow 3 protein (At1g50420) mRNA, complete cds.
GenBank	CP002684	0.0	CP002684.1 Arabidopsis thaliana chromosome 1 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_175459.1	0.0	scarecrow-like 3
Swissprot	Q9LPR8	0.0	SCL3_ARATH; Scarecrow-like protein 3
TrEMBL	A0A178WJ79	0.0	A0A178WJ79_ARATH; SCL3
STRING	AT1G50420.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4098	27	59
Representative plant	OGRP2564	14	33

Link Out ? help Back to Top
Phytozome	AT1G50420.1
Entrez Gene	841464
iHOP	AT1G50420
wikigenes	AT1G50420

Publications ? help Back to Top
Pysh LD,Wysocka-Diller JW,Camilleri C,Bouchez D,Benfey PN The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. Plant J., 1999. 18(1): p. 111-9 [PMID:10341448] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Ogawa M, et al. Gibberellin biosynthesis and response during Arabidopsis seed germination. Plant Cell, 2003. 15(7): p. 1591-604 [PMID:12837949] Dal Bosco C, et al. Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana. J. Biol. Chem., 2004. 279(2): p. 1060-9 [PMID:14576160] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Bolle C The role of GRAS proteins in plant signal transduction and development. Planta, 2004. 218(5): p. 683-92 [PMID:14760535] Goda H, et al. Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis. Plant Physiol., 2004. 134(4): p. 1555-73 [PMID:15047898] Tian C,Wan P,Sun S,Li J,Chen M Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol. Biol., 2004. 54(4): p. 519-32 [PMID:15316287] Gao MJ,Parkin I,Lydiate D,Hannoufa A An auxin-responsive SCARECROW-like transcriptional activator interacts with histone deacetylase. Plant Mol. Biol., 2004. 55(3): p. 417-31 [PMID:15604690] Curtis IS,Hanada A,Yamaguchi S,Kamiya Y Modification of plant architecture through the expression of GA 2-oxidase under the control of an estrogen inducible promoter in Arabidopsis thaliana L. Planta, 2005. 222(6): p. 957-67 [PMID:16270204] Levesque MP, et al. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol., 2006. 4(5): p. e143 [PMID:16640459] Cho YH,Yoo SD,Sheen J Regulatory functions of nuclear hexokinase1 complex in glucose signaling. Cell, 2006. 127(3): p. 579-89 [PMID:17081979] Zentella R, et al. Global analysis of della direct targets in early gibberellin signaling in Arabidopsis. Plant Cell, 2007. 19(10): p. 3037-57 [PMID:17933900] Lee MH, et al. Large-scale analysis of the GRAS gene family in Arabidopsis thaliana. Plant Mol. Biol., 2008. 67(6): p. 659-70 [PMID:18500650] Rieu I, et al. Genetic analysis reveals that C19-GA 2-oxidation is a major gibberellin inactivation pathway in Arabidopsis. Plant Cell, 2008. 20(9): p. 2420-36 [PMID:18805991] Heo JO, et al. Funneling of gibberellin signaling by the GRAS transcription regulator scarecrow-like 3 in the Arabidopsis root. Proc. Natl. Acad. Sci. U.S.A., 2011. 108(5): p. 2166-71 [PMID:21245304] Zhang ZL, et al. Scarecrow-like 3 promotes gibberellin signaling by antagonizing master growth repressor DELLA in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2011. 108(5): p. 2160-5 [PMID:21245327] Josse EM, et al. A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling. Plant Cell, 2011. 23(4): p. 1337-51 [PMID:21478445] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] Efroni I, et al. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Dev. Cell, 2013. 24(4): p. 438-45 [PMID:23449474] Archacki R, et al. BRAHMA ATPase of the SWI/SNF chromatin remodeling complex acts as a positive regulator of gibberellin-mediated responses in arabidopsis. PLoS ONE, 2013. 8(3): p. e58588 [PMID:23536800] Yoshida H, et al. DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(21): p. 7861-6 [PMID:24821766] 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] Yoshida H,Ueguchi-Tanaka M DELLA and SCL3 balance gibberellin feedback regulation by utilizing INDETERMINATE DOMAIN proteins as transcriptional scaffolds. Plant Signal Behav, 2014. 9(9): p. e29726 [PMID:25763707] Gong X, et al. SEUSS Integrates Gibberellin Signaling with Transcriptional Inputs from the SHR-SCR-SCL3 Module to Regulate Middle Cortex Formation in the Arabidopsis Root. Plant Physiol., 2016. 170(3): p. 1675-83 [PMID:26818732] Lee SA, et al. Interplay between ABA and GA Modulates the Timing of Asymmetric Cell Divisions in the Arabidopsis Root Ground Tissue. Mol Plant, 2016. 9(6): p. 870-84 [PMID:26970019] Choi JW,Lim J Control of Asymmetric Cell Divisions during Root Ground Tissue Maturation. Mol. Cells, 2016. 39(7): p. 524-9 [PMID:27306644]