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

AT4G00150.1

Common Name

ATHAM3, F6N15.20, HAM3, LOM3, SCL6, SCL6-IV

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: 558aa MW: 61167.8 Da PI: 5.656

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT4G00150.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	330.9	2.5e-101	206	554	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlsel.aspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlta 98 +e+L+++Ae+++s d+ laq +Larl+++ +sp g+p++R+a+yf+eAL++ l++ +++ ++++ + ++aa+k fse+sP+l+f+++t AT4G00150.1 206 TEQLVKAAEVIES-DTCLAQGILARLNQQlSSPVGKPLERAAFYFKEALNNLLHN---------VSQTLNPYSLIFKIAAYKSFSEISPVLQFANFTS 293 689****8887.9********998********************9.........55566667789******************* PP GRAS 99 NqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegpp.slRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledl.eleeL 194 Nqa+le+++g +r+HiiDfdi++G+QW++L+q+L R++ +p sl+iT+++sp+++++ el t+++L++fA+e++++++++vl +l+ l +++ AT4G00150.1 294 NQALLESFHGFHRLHIIDFDIGYGGQWASLMQELVLRDNAAPlSLKITVFASPANHDQLELGFTQDNLKHFASEINISLDIQVL---SLDLLgSISWP 388 **********************************99998************************************8...55555223333 PP GRAS 195 rvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgr 292 + +++Ea+aVn++ + ++ l + vL++vk+lsP+++v++++ +++++ +F ++++++l+ ++alf+sl+a ++ ++++k+Er+l+++ AT4G00150.1 389 NSSEKEAVAVNISAASFSHL----------PLVLRFVKHLSPTIIVCSDRGCERTDLPFSQQLAHSLHSHTALFESLDAV-NANLDAMQKIERFLIQP 475 5667******988887..........67*****************************************887.56779******** PP GRAS 293 eivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 ei+++v + + ++ +++W++++ ++GF+pv+ s+++++qa++l+++++++g++ve++++sl+l+W++ +Lv vSaWr AT4G00150.1 476 EIEKLVLDRSRP---IERPMMTWQAMFLQMGFSPVTHSNFTESQAECLVQRTPVRGFHVEKKHNSLLLCWQRTELVGVSAWR 554 ****9998...55677***********************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	41.544	179	534	IPR005202	Transcription factor GRAS
Pfam	PF03514	8.6E-99	206	554	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:0007623	Biological Process	circadian rhythm
GO:0048768	Biological Process	root hair cell tip growth
GO:0051301	Biological Process	cell division
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein 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:0000014	anatomy	rosette leaf
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009001	anatomy	fruit
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:0009049	anatomy	inflorescence
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: 558 aa Download sequence Send to blast
MPLPFEEFQG KGISCFSSFS SSFPQPPSSP LLSHRKARGG EEEEEEVPAA EPTSVLDSLI 60 SPTSSSTVSS SHGGNSAVGG GGDATTDEQC GAIGLGDWEE QVPHDHEQSI LGLIMGDSTD 120 PSLELNSILQ TSPTFHDSDY SSPGFGVVDT GFGLDHHSVP PSHVSGLLIN QSQTHYTQNP 180 AAIFYGHHHH TPPPAKRLNP GPVGITEQLV KAAEVIESDT CLAQGILARL NQQLSSPVGK 240 PLERAAFYFK EALNNLLHNV SQTLNPYSLI FKIAAYKSFS EISPVLQFAN FTSNQALLES 300 FHGFHRLHII DFDIGYGGQW ASLMQELVLR DNAAPLSLKI TVFASPANHD QLELGFTQDN 360 LKHFASEINI SLDIQVLSLD LLGSISWPNS SEKEAVAVNI SAASFSHLPL VLRFVKHLSP 420 TIIVCSDRGC ERTDLPFSQQ LAHSLHSHTA LFESLDAVNA NLDAMQKIER FLIQPEIEKL 480 VLDRSRPIER PMMTWQAMFL QMGFSPVTHS NFTESQAECL VQRTPVRGFH VEKKHNSLLL 540 CWQRTELVGV SAWRCRSS

Sequence ? help Back to Top

Protein Sequence Length: 558 aa Download sequence Send to blast

MPLPFEEFQG KGISCFSSFS SSFPQPPSSP LLSHRKARGG EEEEEEVPAA EPTSVLDSLI  60
SPTSSSTVSS SHGGNSAVGG GGDATTDEQC GAIGLGDWEE QVPHDHEQSI LGLIMGDSTD  120
PSLELNSILQ TSPTFHDSDY SSPGFGVVDT GFGLDHHSVP PSHVSGLLIN QSQTHYTQNP  180
AAIFYGHHHH TPPPAKRLNP GPVGITEQLV KAAEVIESDT CLAQGILARL NQQLSSPVGK  240
PLERAAFYFK EALNNLLHNV SQTLNPYSLI FKIAAYKSFS EISPVLQFAN FTSNQALLES  300
FHGFHRLHII DFDIGYGGQW ASLMQELVLR DNAAPLSLKI TVFASPANHD QLELGFTQDN  360
LKHFASEINI SLDIQVLSLD LLGSISWPNS SEKEAVAVNI SAASFSHLPL VLRFVKHLSP  420
TIIVCSDRGC ERTDLPFSQQ LAHSLHSHTA LFESLDAVNA NLDAMQKIER FLIQPEIEKL  480
VLDRSRPIER PMMTWQAMFL QMGFSPVTHS NFTESQAECL VQRTPVRGFH VEKKHNSLLL  540
CWQRTELVGV SAWRCRSS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5hyz_A	6e-32	205	554	4	375	GRAS family transcription factor containing protein, expressed
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.3732	0.0	leaf\| root\| seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	42566178	0.0
Genevisible	255698_at	0.0
Expression Atlas	AT4G00150	-
AtGenExpress	AT4G00150	-
ATTED-II	AT4G00150	-

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

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in plant development. {ECO:0000250}.

Function -- GeneRIF ? help Back to Top
AtHAM1, AtHAM2, and AtHAM3 are expressed in apical meristems and in differentiating and mature tissues of both shoot and root. [PMID: 21173022]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT4G00150.1

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

Interaction ? help Back to Top
Source	Intact With
IntAct	Search O81316

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G00150

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF462831	0.0	AF462831.1 Arabidopsis thaliana AT4g00150/F6N15_20 mRNA, complete cds.
GenBank	AK117298	0.0	AK117298.1 Arabidopsis thaliana mRNA, clone: RAFL16-86-D11.
GenBank	AL161471	0.0	AL161471.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 1.
GenBank	AY133537	0.0	AY133537.1 Arabidopsis thaliana At4g00150/F6N15_20 mRNA, complete cds.
GenBank	CP002687	0.0	CP002687.1 Arabidopsis thaliana chromosome 4 sequence.
GenBank	F6N15	0.0	AF069299.1 Arabidopsis thaliana BAC F6N15.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_191926.1	0.0	GRAS family transcription factor
Swissprot	O81316	0.0	SCL6_ARATH; Scarecrow-like protein 6
TrEMBL	A0A178V088	0.0	A0A178V088_ARATH; SCL6-IV
STRING	AT4G00150.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM8574	27	39
Representative plant	OGRP1750	12	42

Link Out ? help Back to Top
Phytozome	AT4G00150.1
Entrez Gene	828208
iHOP	AT4G00150
wikigenes	AT4G00150

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] Llave C,Kasschau KD,Rector MA,Carrington JC Endogenous and silencing-associated small RNAs in plants. Plant Cell, 2002. 14(7): p. 1605-19 [PMID:12119378] Llave C,Xie Z,Kasschau KD,Carrington JC Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 2002. 297(5589): p. 2053-6 [PMID:12242443] Kasschau KD, et al. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev. Cell, 2003. 4(2): p. 205-17 [PMID:12586064] 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] Chapman EJ,Prokhnevsky AI,Gopinath K,Dolja VV,Carrington JC Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev., 2004. 18(10): p. 1179-86 [PMID:15131083] Sunkar R,Zhu JK Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 2004. 16(8): p. 2001-19 [PMID:15258262] Yoo BC, et al. A systemic small RNA signaling system in plants. Plant Cell, 2004. 16(8): p. 1979-2000 [PMID:15258266] Souret FF,Kastenmayer JP,Green PJ AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol. Cell, 2004. 15(2): p. 173-83 [PMID:15260969] Bonnet E,Wuyts J,Rouz Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc. Natl. Acad. Sci. U.S.A., 2004. 101(31): p. 11511-6 [PMID:15272084] 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] Axtell MJ,Bartel DP Antiquity of microRNAs and their targets in land plants. Plant Cell, 2005. 17(6): p. 1658-73 [PMID:15849273] Xie Z, et al. Expression of Arabidopsis MIRNA genes. Plant Physiol., 2005. 138(4): p. 2145-54 [PMID:16040653] Nakayama N, et al. Gene trap lines define domains of gene regulation in Arabidopsis petals and stamens. Plant Cell, 2005. 17(9): p. 2486-506 [PMID:16055634] Jones L,Keining T,Eamens A,Vaistij FE Virus-induced gene silencing of argonaute genes in Nicotiana benthamiana demonstrates that extensive systemic silencing requires Argonaute1-like and Argonaute4-like genes. Plant Physiol., 2006. 141(2): p. 598-606 [PMID:16632593] Huang G, et al. A root-knot nematode secretory peptide functions as a ligand for a plant transcription factor. Mol. Plant Microbe Interact., 2006. 19(5): p. 463-70 [PMID:16673933] Wagner R,Pfannschmidt T Eukaryotic transcription factors in plastids--Bioinformatic assessment and implications for the evolution of gene expression machineries in plants. Gene, 2006. 381: p. 62-70 [PMID:16934950] Lewsey M,Robertson FC,Canto T,Palukaitis P,Carr JP Selective targeting of miRNA-regulated plant development by a viral counter-silencing protein. Plant J., 2007. 50(2): p. 240-52 [PMID:17444907] Ehrenreich IM,Purugganan MD Sequence variation of MicroRNAs and their binding sites in Arabidopsis. Plant Physiol., 2008. 146(4): p. 1974-82 [PMID:18305205] 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] Wang L,Mai YX,Zhang YC,Luo Q,Yang HQ MicroRNA171c-targeted SCL6-II, SCL6-III, and SCL6-IV genes regulate shoot branching in Arabidopsis. Mol Plant, 2010. 3(5): p. 794-806 [PMID:20720155] Hanada K, et al. Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana. Mol. Biol. Evol., 2011. 28(1): p. 377-82 [PMID:20736450] Schulze S,Sch LOST MERISTEMS genes regulate cell differentiation of central zone descendants in Arabidopsis shoot meristems. Plant J., 2010. 64(4): p. 668-78 [PMID:21070418] Engstrom EM, et al. Arabidopsis homologs of the petunia hairy meristem gene are required for maintenance of shoot and root indeterminacy. Plant Physiol., 2011. 155(2): p. 735-50 [PMID:21173022] Li G, et al. Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat. Cell Biol., 2011. 13(5): p. 616-22 [PMID:21499259] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] Bari A,Orazova S,Ivashchenko A miR156- and miR171-binding sites in the protein-coding sequences of several plant genes. Biomed Res Int, 2013. 2013: p. 307145 [PMID:23936788] Xue XY, et al. Interaction between two timing microRNAs controls trichome distribution in Arabidopsis. PLoS Genet., 2014. 10(4): p. e1004266 [PMID:24699192] Zhou Y, et al. Control of plant stem cell function by conserved interacting transcriptional regulators. Nature, 2015. 517(7534): p. 377-80 [PMID:25363783]