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

AT4G36710.1

Common Name

AtHAM4, C7A10.650, HAM4, SCL15

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: 486aa MW: 54148.3 Da PI: 4.9698

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT4G36710.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	334	2.8e-102	123	485	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlsel.aspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlta 98 +e L++++++v+s++l+laq +L+rl+++ +sp+g+p+qR+a+yf+eAL + l++ ++ p + +s+++ ++++ a k +s +sPi+ fsh+ta AT4G36710.1 123 IEDLIRVVDCVESDELQLAQVVLSRLNQRlRSPAGRPLQRAAFYFKEALGSFLTG-----SNRNPIRLSSWSEIVQRIRAIKEYSGISPIPLFSHFTA 215 678***********************99*********************.....888899999999********************** PP GRAS 99 NqaIleavege...ervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledlelee 193 NqaIl++++++ vH++Df+i+ G+Q+++L++++++++ + lR+T+v+++e + e++ ++e+L++fA+e++++f+++++++k++e+l++++ AT4G36710.1 216 NQAILDSLSSQsssPFVHVVDFEIGFGGQYASLMREITEKSVSGGFLRVTAVVAEE--CAVETRLVKENLTQFAAEMKIRFQIEFVLMKTFEMLSFKA 311 ****99977789**********************************66..9*********************************** PP GRAS 194 LrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqe..adh.nsesFlerflealeyysalfdsleaklpreseerikvEre 288 +r+ +gE ++V ++ +++r l s ++++++ ++++sPkvvv+v++e ++ +s+sF ++f++ale+y+++++sl+a +p+ + ++ vE++ AT4G36710.1 312 IRFVEGERTVVLISPAIFRRL-------SGITDFVNNLRRVSPKVVVFVDSEgwTEIaGSGSFRREFVSALEFYTMVLESLDAAAPPGDLVKKIVEAF 402 ****************9.......44677***************76677899********************************** PP GRAS 289 llgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 +l+++i+ +v ++ ++ rh+ ++Wre++ +aG++p++ls++a qa++ll+k +++g++v +++g+lvl+W++r+Lv++SaWr AT4G36710.1 403 VLRPKISAAVETAADR---RHTGEMTWREAFCAAGMRPIQLSQFADFQAECLLEKAQVRGFHVAKRQGELVLCWHGRALVATSAWR 485 ********9999...9***************************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	41.844	96	465	IPR005202	Transcription factor GRAS
Pfam	PF03514	9.7E-100	123	485	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:0030154	Biological Process	cell differentiation
GO:0048831	Biological Process	regulation of shoot system development
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: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: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: 486 aa Download sequence Send to blast
MKIPASSPQD TTNNNNNTNS TDSNHLSMDE HVMRSMDWDS IMKELELDDD SAPNSLKTGF 60 TTTTTDSTIL PLYAVDSNLP GFPDQIQPSD FESSSDVYPG QNQTTGYGFN SLDSVDNGGF 120 DFIEDLIRVV DCVESDELQL AQVVLSRLNQ RLRSPAGRPL QRAAFYFKEA LGSFLTGSNR 180 NPIRLSSWSE IVQRIRAIKE YSGISPIPLF SHFTANQAIL DSLSSQSSSP FVHVVDFEIG 240 FGGQYASLMR EITEKSVSGG FLRVTAVVAE ECAVETRLVK ENLTQFAAEM KIRFQIEFVL 300 MKTFEMLSFK AIRFVEGERT VVLISPAIFR RLSGITDFVN NLRRVSPKVV VFVDSEGWTE 360 IAGSGSFRRE FVSALEFYTM VLESLDAAAP PGDLVKKIVE AFVLRPKISA AVETAADRRH 420 TGEMTWREAF CAAGMRPIQL SQFADFQAEC LLEKAQVRGF HVAKRQGELV LCWHGRALVA 480 TSAWRF

Sequence ? help Back to Top

Protein Sequence Length: 486 aa Download sequence Send to blast

MKIPASSPQD TTNNNNNTNS TDSNHLSMDE HVMRSMDWDS IMKELELDDD SAPNSLKTGF  60
TTTTTDSTIL PLYAVDSNLP GFPDQIQPSD FESSSDVYPG QNQTTGYGFN SLDSVDNGGF  120
DFIEDLIRVV DCVESDELQL AQVVLSRLNQ RLRSPAGRPL QRAAFYFKEA LGSFLTGSNR  180
NPIRLSSWSE IVQRIRAIKE YSGISPIPLF SHFTANQAIL DSLSSQSSSP FVHVVDFEIG  240
FGGQYASLMR EITEKSVSGG FLRVTAVVAE ECAVETRLVK ENLTQFAAEM KIRFQIEFVL  300
MKTFEMLSFK AIRFVEGERT VVLISPAIFR RLSGITDFVN NLRRVSPKVV VFVDSEGWTE  360
IAGSGSFRRE FVSALEFYTM VLESLDAAAP PGDLVKKIVE AFVLRPKISA AVETAADRRH  420
TGEMTWREAF CAAGMRPIQL SQFADFQAEC LLEKAQVRGF HVAKRQGELV LCWHGRALVA  480
TSAWRF

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	9e-27	128	484	25	378	Protein SCARECROW
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.31304	0.0	flower\| leaf

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	240256196	0.0
Genevisible	246230_at	0.0
Expression Atlas	AT4G36710	-
AtGenExpress	AT4G36710	-
ATTED-II	AT4G36710	-

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
acts as an HDA19-associated regulator to repress embryonic traits in seedlings [PMID: 26129778]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT4G36710.1

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

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT1G46480

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G36710

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK118497	0.0	AK118497.1 Arabidopsis thaliana At4g36710 mRNA for ap2 SCARECROW-like protein, complete cds, clone: RAFL19-73-D11.
GenBank	CP002687	0.0	CP002687.1 Arabidopsis thaliana chromosome 4 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_195389.4	0.0	GRAS family transcription factor
Swissprot	O23210	0.0	SCL15_ARATH; Scarecrow-like protein 15
TrEMBL	A0A178UVI6	0.0	A0A178UVI6_ARATH; HAM4
STRING	AT4G36710.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4291	28	57
Representative plant	OGRP10323	6	10

Link Out ? help Back to Top
Phytozome	AT4G36710.1
Entrez Gene	829824
iHOP	AT4G36710
wikigenes	AT4G36710

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] Seki M, et al. Functional annotation of a full-length Arabidopsis cDNA collection. Science, 2002. 296(5565): p. 141-5 [PMID:11910074] Jiao Y, et al. A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol., 2003. 133(4): p. 1480-93 [PMID:14605227] Bolle C The role of GRAS proteins in plant signal transduction and development. Planta, 2004. 218(5): p. 683-92 [PMID:14760535] Hu W,Wang Y,Bowers C,Ma H Isolation, sequence analysis, and expression studies of florally expressed cDNAs in Arabidopsis. Plant Mol. Biol., 2003. 53(4): p. 545-63 [PMID:15010618] Yoo BC, et al. A systemic small RNA signaling system in plants. Plant Cell, 2004. 16(8): p. 1979-2000 [PMID:15258266] 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] Ohashi-Ito K,Kubo M,Demura T,Fukuda H Class III homeodomain leucine-zipper proteins regulate xylem cell differentiation. Plant Cell Physiol., 2005. 46(10): p. 1646-56 [PMID:16081527] Pineau C, et al. hca: an Arabidopsis mutant exhibiting unusual cambial activity and altered vascular patterning. Plant J., 2005. 44(2): p. 271-89 [PMID:16212606] Truman W,de Zabala MT,Grant M Type III effectors orchestrate a complex interplay between transcriptional networks to modify basal defence responses during pathogenesis and resistance. Plant J., 2006. 46(1): p. 14-33 [PMID:16553893] 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] 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] Klopffleisch K, et al. Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Mol. Syst. Biol., 2011. 7: p. 532 [PMID:21952135] 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] Zhou Y, et al. Control of plant stem cell function by conserved interacting transcriptional regulators. Nature, 2015. 517(7534): p. 377-80 [PMID:25363783] Gao MJ, et al. SCARECROW-LIKE15 interacts with HISTONE DEACETYLASE19 and is essential for repressing the seed maturation programme. Nat Commun, 2015. 6: p. 7243 [PMID:26129778]