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

AMDW01037147.1_FGP001

Organism

Oryza longistaminata

Taxonomic ID

4528

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza

Family

GRAS

Protein Properties

Length: 158aa MW: 17285.7 Da PI: 6.7986

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AMDW01037147.1_FGP001	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	176.9	1.5e-54	13	153	76	227
GRAS 76 eelaalklfsevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetge 163 +++aa+++f+ +sP++kfsh+taNqaI ea+e+eervHiiD+di+qGlQWp L++ LasRp+gpp++R+Tg+g+ s e+le+tg+ AMDW01037147.1_FGP001 13 RVAAAFQVFNGISPFVKFSHFTANQAIQEAFEREERVHIIDLDIMQGLQWPGLFHILASRPGGPPRVRLTGLGA----SMEALEATGK 96 567899******************************************************************....****** PP GRAS 164 rLakfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdev 227 rL++fA++lg+pfef + va++ +l++e+L v ++Ea+aV++ h+l+d ++s ++ + AMDW01037147.1_FGP001 97 RLSDFADTLGLPFEFCP-VADKAGNLDPEKLGVTRREAVAVHWLR--HSLYDVTGSDSN----T 153 *************.7**********************98..888877777766....4 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	31.89	1	158	IPR005202	Transcription factor GRAS
Pfam	PF03514	5.1E-52	13	153	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 158 aa Download sequence Send to blast
PSPSPAGARV HGRVAAAFQV FNGISPFVKF SHFTANQAIQ EAFEREERVH IIDLDIMQGL 60 QWPGLFHILA SRPGGPPRVR LTGLGASMEA LEATGKRLSD FADTLGLPFE FCPVADKAGN 120 LDPEKLGVTR REAVAVHWLR HSLYDVTGSD SNTLWLIQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	6e-89	13	158	94	239	Protein SCARECROW
5b3h_A	6e-89	13	158	93	238	Protein SCARECROW
5b3h_D	6e-89	13	158	93	238	Protein SCARECROW
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Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in asmmetric cell division in the cortex/endodermis progenitor cell and in the process of stomata and ligule formation in leaves. {ECO:0000250}.
UniProt	Probable transcription factor involved in asmmetric cell division in the cortex/endodermis progenitor cell and in the process of stomata and ligule formation in leaves. {ECO:0000269\|PubMed:12974810}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AMDW01037147.1_FGP001

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK243131	0.0	AK243131.1 Oryza sativa Japonica Group cDNA, clone: J100030A12, full insert sequence.
GenBank	AP014968	0.0	AP014968.1 Oryza sativa Japonica Group DNA, chromosome 12, cultivar: Nipponbare, complete sequence.
GenBank	BX000506	0.0	BX000506.4 Oryza sativa chromosome 12, . BAC OJ1311_G04 of library Monsanto from chromosome 12 of cultivar Nipponbare of ssp. japonica of Oryza sativa (rice), complete sequence.
GenBank	CP012620	0.0	CP012620.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 12 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015620600.1	1e-109	protein SCARECROW 2
Swissprot	A2ZHL0	1e-110	SCR2_ORYSI; Protein SCARECROW 2
Swissprot	Q2QYF3	1e-110	SCR2_ORYSJ; Protein SCARECROW 2
TrEMBL	I1R3J7	1e-110	I1R3J7_ORYGL; Uncharacterized protein
STRING	ORGLA12G0010300.1	1e-111	(Oryza glaberrima)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP1371	38	122

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G54220.1	2e-86	GRAS family protein

Publications ? help Back to Top
Kamiya N, et al. Rice globular embryo 4 (gle4) mutant is defective in radial pattern formation during embryogenesis. Plant Cell Physiol., 2003. 44(9): p. 875-83 [PMID:14519768] Lim J, et al. Conservation and diversification of SCARECROW in maize. Plant Mol. Biol., 2005. 59(4): p. 619-30 [PMID:16244911] Kaur P, et al. Genes controlling plant growth habit in Leymus (Triticeae): maize barren stalk1 (ba1), rice lax panicle, and wheat tiller inhibition (tin3) genes as possible candidates. Funct. Integr. Genomics, 2008. 8(4): p. 375-86 [PMID:18543009] Sazuka T, et al. A rice tryptophan deficient dwarf mutant, tdd1, contains a reduced level of indole acetic acid and develops abnormal flowers and organless embryos. Plant J., 2009. 60(2): p. 227-41 [PMID:19682283] Fan T, et al. Rice osa-miR171c Mediates Phase Change from Vegetative to Reproductive Development and Shoot Apical Meristem Maintenance by Repressing Four OsHAM Transcription Factors. PLoS ONE, 2015. 10(5): p. e0125833 [PMID:26023934] Yi J, et al. OsMPK6 plays a critical role in cell differentiation during early embryogenesis in Oryza sativa. J. Exp. Bot., 2016. 67(8): p. 2425-37 [PMID:26912801] Li S, et al. Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa. Plant Cell, 2016. 28(5): p. 1025-34 [PMID:27081181]