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

AT3G60630.1

Common Name

ATHAM2, HAM2, LOM2, SCL22, T4C21.40

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: 623aa MW: 68089.9 Da PI: 4.5267

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G60630.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	337.5	2.3e-103	244	622	2	374
GRAS 2 velLlecAeavss....gdlelaqalLarlselaspdgd........pmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsev 87 +++L+++A +++ ++ laq +Larl+++ +++ d p++R+a+y+teAL++ l++ ++ pps ++++n + ++aa+++fse+ AT3G60630.1 244 IDQLFSAAAELTTnggdNNPVLAQGILARLNHNLNNNNDdtnnnpkpPFHRAASYITEALHSLLQD-----SSLSPPSLSPPQNLIFRIAAYRAFSET 336 567888887777656434555**********55555447999999***************.....555599999999*********** PP GRAS 88 sPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLa.sRp..egppslRiTgvgspesg.skeeleetgerLakfAeelgvpfefnvl 181 sP+l+f ++taNq+Ile++eg +r+Hi+Dfdi++G+QW++L+q+La +R+ +++psl+iT+++sp+++ ++ el+ t+e+L++fA e+gv+fe+++l AT3G60630.1 337 SPFLQFVNFTANQTILESFEGFDRIHIVDFDIGYGGQWASLIQELAgKRNrsSSAPSLKITAFASPSTVsDEFELRFTEENLRSFAGETGVSFEIELL 434 ******************************************85556699*********9999*********************** PP GRAS 182 vakrledleleeLrvkp...gEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadh.nsesFlerflealeyysalfdsleakl 275 ++ l + +++ L++ + +Ea+aVnl ++ + + + +L+++k++sP+vvv++++ +d+ n+++F +++++al+yy++l++sl+++ AT3G60630.1 435 NMEILLNPTYWPLSLFRsseKEAIAVNLPISSMVSG--------YLPLILRFLKQISPNVVVCSDRSCDRnNDAPFPNGVINALQYYTSLLESLDSGN 524 99999999999998877777******766665........6677******************99******************8887 PP GRAS 276 preseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveee...sgslvlgWkdrpLvsv 370 +++e+++++Er++++++i+++++++ ++ +e+ Wr+ ++++GF+pv+ls++a++qa++ll++ +++g+++e++ s slvl+W++++Lv+v AT3G60630.1 525 LNNAEAATSIERFCVQPSIQKLLTNRYRW----MERSPPWRSLFGQCGFTPVTLSQTAETQAEYLLQRNPMRGFHLEKRqssSPSLVLCWQRKELVTV 618 7999*********************....9***************************************66555899********* PP GRAS 371 SaWr 374 SaW+ AT3G60630.1 619 SAWK 622 *8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	43.513	221	599	IPR005202	Transcription factor GRAS
Pfam	PF03514	8.1E-101	244	622	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: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: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:0000017	anatomy	vascular leaf primordium
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: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:0020148	anatomy	shoot apical meristem
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: 623 aa Download sequence Send to blast
MPLPFEQFQG KGVLGFLDSS SSPGYKIWAN PEKLHGRVEE DLCFVVNNGG FSEPTSVLDS 60 VRSPSPFVSS STTTLSSSHG GPSGGGAAAA TFSGADGKCD QMGFEDLDGV LSGGSPGQEQ 120 SIFRLIMAGD VVDPGSEFVG FDIGSGSDPV IDNPNPLFGY GFPFQNAPEE EKFQISINPN 180 PGFFSDPPSS PPAKRLNSGQ PGSQHLQWVF PFSDPGHESH DPFLTPPKIA GEDQNDQDQS 240 AVIIDQLFSA AAELTTNGGD NNPVLAQGIL ARLNHNLNNN NDDTNNNPKP PFHRAASYIT 300 EALHSLLQDS SLSPPSLSPP QNLIFRIAAY RAFSETSPFL QFVNFTANQT ILESFEGFDR 360 IHIVDFDIGY GGQWASLIQE LAGKRNRSSS APSLKITAFA SPSTVSDEFE LRFTEENLRS 420 FAGETGVSFE IELLNMEILL NPTYWPLSLF RSSEKEAIAV NLPISSMVSG YLPLILRFLK 480 QISPNVVVCS DRSCDRNNDA PFPNGVINAL QYYTSLLESL DSGNLNNAEA ATSIERFCVQ 540 PSIQKLLTNR YRWMERSPPW RSLFGQCGFT PVTLSQTAET QAEYLLQRNP MRGFHLEKRQ 600 SSSPSLVLCW QRKELVTVSA WKC

Sequence ? help Back to Top

Protein Sequence Length: 623 aa Download sequence Send to blast

MPLPFEQFQG KGVLGFLDSS SSPGYKIWAN PEKLHGRVEE DLCFVVNNGG FSEPTSVLDS  60
VRSPSPFVSS STTTLSSSHG GPSGGGAAAA TFSGADGKCD QMGFEDLDGV LSGGSPGQEQ  120
SIFRLIMAGD VVDPGSEFVG FDIGSGSDPV IDNPNPLFGY GFPFQNAPEE EKFQISINPN  180
PGFFSDPPSS PPAKRLNSGQ PGSQHLQWVF PFSDPGHESH DPFLTPPKIA GEDQNDQDQS  240
AVIIDQLFSA AAELTTNGGD NNPVLAQGIL ARLNHNLNNN NDDTNNNPKP PFHRAASYIT  300
EALHSLLQDS SLSPPSLSPP QNLIFRIAAY RAFSETSPFL QFVNFTANQT ILESFEGFDR  360
IHIVDFDIGY GGQWASLIQE LAGKRNRSSS APSLKITAFA SPSTVSDEFE LRFTEENLRS  420
FAGETGVSFE IELLNMEILL NPTYWPLSLF RSSEKEAIAV NLPISSMVSG YLPLILRFLK  480
QISPNVVVCS DRSCDRNNDA PFPNGVINAL QYYTSLLESL DSGNLNNAEA ATSIERFCVQ  540
PSIQKLLTNR YRWMERSPPW RSLFGQCGFT PVTLSQTAET QAEYLLQRNP MRGFHLEKRQ  600
SSSPSLVLCW QRKELVTVSA WKC

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5hyz_A	8e-35	240	622	1	375	GRAS family transcription factor containing protein, expressed
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.27084	0.0	floral meristem\| flower\| leaf

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	42566093	0.0
Genevisible	251376_at	0.0
Expression Atlas	AT3G60630	-
AtGenExpress	AT3G60630	-
ATTED-II	AT3G60630	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in seedlings, roots, leaves and flowers. {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
findings show that LOM1(AT2G45160) and LOM2 (AT3G60630) promote cell differentiation at the periphery of shoot meristems and help to maintain their polar organization [PMID: 21070418] 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	AT3G60630.1

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

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q9M000

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G60630

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AL162295	0.0	AL162295.1 Arabidopsis thaliana DNA chromosome 3, BAC clone T4C21.
GenBank	AY064062	0.0	AY064062.1 Arabidopsis thaliana putative scarecrow protein (At3g60630) mRNA, complete cds.
GenBank	AY096372	0.0	AY096372.1 Arabidopsis thaliana putative scarecrow protein (At3g60630) mRNA, complete cds.
GenBank	CP002686	0.0	CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_191622.1	0.0	GRAS family transcription factor
Swissprot	Q9M000	0.0	SCL22_ARATH; Scarecrow-like protein 22
TrEMBL	A0A178VED8	0.0	A0A178VED8_ARATH; LOM2
STRING	AT3G60630.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM15066	16	19
Representative plant	OGRP1750	12	42

Link Out ? help Back to Top
Phytozome	AT3G60630.1
Entrez Gene	825234
iHOP	AT3G60630
wikigenes	AT3G60630

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Reinhart BJ,Weinstein EG,Rhoades MW,Bartel B,Bartel DP MicroRNAs in plants. Genes Dev., 2002. 16(13): p. 1616-26 [PMID:12101121] 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] Boutet S, et al. Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr. Biol., 2003. 13(10): p. 843-8 [PMID:12747833] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Han MH,Goud S,Song L,Fedoroff N The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl. Acad. Sci. U.S.A., 2004. 101(4): p. 1093-8 [PMID:14722360] Bolle C The role of GRAS proteins in plant signal transduction and development. Planta, 2004. 218(5): p. 683-92 [PMID:14760535] Vazquez F,Gasciolli V,Cr The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol., 2004. 14(4): p. 346-51 [PMID:14972688] Vaucheret H,Vazquez F,Cr The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev., 2004. 18(10): p. 1187-97 [PMID:15131082] 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] 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] Vazquez F, et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell, 2004. 16(1): p. 69-79 [PMID:15469823] Hilson P, et al. Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res., 2004. 14(10B): p. 2176-89 [PMID:15489341] 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] Gustafson AM, et al. ASRP: the Arabidopsis Small RNA Project Database. Nucleic Acids Res., 2005. 33(Database issue): p. D637-40 [PMID:15608278] Axtell MJ,Bartel DP Antiquity of microRNAs and their targets in land plants. Plant Cell, 2005. 17(6): p. 1658-73 [PMID:15849273] Nawy T, et al. Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell, 2005. 17(7): p. 1908-25 [PMID:15937229] Kutter C,Schöb H,Stadler M,Meins F,Si-Ammour A MicroRNA-mediated regulation of stomatal development in Arabidopsis. Plant Cell, 2007. 19(8): p. 2417-29 [PMID:17704216] Ehrenreich IM,Purugganan MD Sequence variation of MicroRNAs and their binding sites in Arabidopsis. Plant Physiol., 2008. 146(4): p. 1974-82 [PMID:18305205] Bassel GW, et al. Elucidating the germination transcriptional program using small molecules. Plant Physiol., 2008. 147(1): p. 143-55 [PMID:18359847] 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] 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] 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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Xue XY, et al. Interaction between two timing microRNAs controls trichome distribution in Arabidopsis. PLoS Genet., 2014. 10(4): p. e1004266 [PMID:24699192] Ma Z, et al. Arabidopsis miR171-targeted scarecrow-like proteins bind to GT cis-elements and mediate gibberellin-regulated chlorophyll biosynthesis under light conditions. PLoS Genet., 2014. 10(8): p. e1004519 [PMID:25101599] Zhou Y, et al. Control of plant stem cell function by conserved interacting transcriptional regulators. Nature, 2015. 517(7534): p. 377-80 [PMID:25363783]