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

LOC_Os07g01820.4

Organism

Oryza sativa subsp. japonica

Taxonomic ID

39947

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; Oryza sativa

Family

MIKC_MADS

Protein Properties

Length: 241aa MW: 26734.4 Da PI: 8.2146

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os07g01820.4	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	98.1	3.5e-31	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krienk+nrqvtfskRrng+lKKA+E+SvLCdaeva i+fs++gklyey++ LOC_Os07g01820.4 9 KRIENKINRQVTFSKRRNGLLKKAHEISVLCDAEVAAIVFSPKGKLYEYAT 59 79***********************************************86 PP
2	K-box	105.1	8.4e-35	78	172	4	98
K-box 4 ssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrk 96 + s+e++ + ++++e++kLk++ie++q+ ++hl+GedLesL+lkeLqqLeqqLe+slk+i s+K++l+le+i+elqkke++lqeenkaL+k LOC_Os07g01820.4 78 KALISAESESEGNWCHEYRKLKAKIETIQKCHKHLMGEDLESLNLKELQQLEQQLESSLKHIISRKSHLMLESISELQKKERSLQEENKALQK 170 556667888899********************************************************************************9 PP K-box 97 kl 98 + LOC_Os07g01820.4 171 EC 172 86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	2.4E-42	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	32.674	1	61	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	6.54E-35	2	89	IPR002100	Transcription factor, MADS-box
CDD	cd00265	5.66E-41	2	76	No hit	No description
PRINTS	PR00404	1.5E-31	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.4E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.5E-31	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.5E-31	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	2.1E-29	84	172	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	16.598	88	178	IPR002487	Transcription factor, K-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 241 aa Download sequence Send to blast
MGRGKVQLKR IENKINRQVT FSKRRNGLLK KAHEISVLCD AEVAAIVFSP KGKLYEYATD 60 SRMDKILERY ERYSYAEKAL ISAESESEGN WCHEYRKLKA KIETIQKCHK HLMGEDLESL 120 NLKELQQLEQ QLESSLKHII SRKSHLMLES ISELQKKERS LQEENKALQK ECAHAAGGEA 180 EECEGPAASR AVGPNPGPGP GPSPTPSPDK LLLLLHAEGS AGTSSTTKYL LPAGDDGREK 240 *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6byy_A	6e-23	1	74	1	73	MEF2 CHIMERA
6byy_B	6e-23	1	74	1	73	MEF2 CHIMERA
6byy_C	6e-23	1	74	1	73	MEF2 CHIMERA
6byy_D	6e-23	1	74	1	73	MEF2 CHIMERA
6bz1_A	6e-23	1	74	1	73	MEF2 CHIMERA
6bz1_B	6e-23	1	74	1	73	MEF2 CHIMERA
6bz1_C	6e-23	1	74	1	73	MEF2 CHIMERA
6bz1_D	6e-23	1	74	1	73	MEF2 CHIMERA
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Os.12750	0.0	flower\| panicle

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	32982706	0.0

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in the floral meristem at very early stage of the spikelet (rice flower) development. Expressed in lemmas, paleas and lodicules from early to late stage of flower development. {ECO:0000269\|PubMed:10945340}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	LOC_Os07g01820.4

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

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os07g01820

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB003325	0.0	AB003325.1 Oryza sativa Japonica Group mRNA for MADS box-like protein, complete cds, clone:E31864.
GenBank	AY551920	0.0	AY551920.1 Oryza sativa (japonica cultivar-group) MADS-box protein RMADS215 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015645261.1	1e-175	MADS-box transcription factor 15 isoform X3
Swissprot	Q6Q9I2	1e-120	MAD15_ORYSJ; MADS-box transcription factor 15
TrEMBL	D3U2H5	1e-117	D3U2H5_ORYSA; MADS-box transcription factor 15
STRING	OS07T0108900-02	1e-118	(Oryza sativa)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G69120.1	9e-71	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	LOC_Os07g01820.4

Publications ? help Back to Top
Cai Q, et al. [PAEs in composts of municipal sludge and rice straw]. Ying Yong Sheng Tai Xue Bao, 2003. 14(11): p. 1993-6 [PMID:14997664] Wang K, et al. DEP and AFO regulate reproductive habit in rice. PLoS Genet., 2010. 6(1): p. e1000818 [PMID:20107517] Kobayashi K, et al. Inflorescence meristem identity in rice is specified by overlapping functions of three AP1/FUL-like MADS box genes and PAP2, a SEPALLATA MADS box gene. Plant Cell, 2012. 24(5): p. 1848-59 [PMID:22570445] Ramanujam R,Yishi X,Liu H,Naqvi NI Structure-function analysis of Rgs1 in Magnaporthe oryzae: role of DEP domains in subcellular targeting. PLoS ONE, 2012. 7(7): p. e41084 [PMID:22927898] Ang TN,Ngoh GC,Chua AS,Lee MG Elucidation of the effect of ionic liquid pretreatment on rice husk via structural analyses. Biotechnol Biofuels, 2012. 5(1): p. 67 [PMID:22958710] Zhang G,Huang K,Jiang X,Huang D,Yang Y Acetylation of rice straw for thermoplastic applications. Carbohydr Polym, 2013. 96(1): p. 218-26 [PMID:23688473] Wei X, et al. Fine mapping of BH1, a gene controlling lemma and palea development in rice. Plant Cell Rep., 2013. 32(9): p. 1455-63 [PMID:23689259] Hu S, et al. A point mutation in the zinc finger motif of RID1/EHD2/OsID1 protein leads to outstanding yield-related traits in japonica rice variety Wuyunjing 7. Rice (N Y), 2013. 6(1): p. 24 [PMID:24280027] Ji Y, et al. A comprehensive assessment of human exposure to phthalates from environmental media and food in Tianjin, China. J. Hazard. Mater., 2014. 279: p. 133-40 [PMID:25051237] Huang Y, et al. Phthalates in Commercial Chinese Rice Wines: Concentrations and the Cumulative Risk Assessment to Adult Males in Shanghai. Biomed. Environ. Sci., 2014. 27(10): p. 819-23 [PMID:25341819] Tamaki S, et al. FT-like proteins induce transposon silencing in the shoot apex during floral induction in rice. Proc. Natl. Acad. Sci. U.S.A., 2015. 112(8): p. E901-10 [PMID:25675495] Wu F, et al. The ABCs of flower development: mutational analysis of AP1/FUL-like genes in rice provides evidence for a homeotic (A)-function in grasses. Plant J., 2017. 89(2): p. 310-324 [PMID:27689766]