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_Os08g41950.1

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: 311aa MW: 36121.7 Da PI: 10.1175

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os08g41950.1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	99.3	1.5e-31	35	85	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krienk+nrqvtf+kRrng+lKKA+ELSvLCdaeva+iifs++gklye++s LOC_Os08g41950.1 35 KRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSNRGKLYEFCS 85 79***********************************************96 PP
2	K-box	16.9	2.6e-07	110	140	8	38
K-box 8 sleeakaeslqqelakLkkeienLqreqRhl 38 + e+++ + +++e+ kLk+++enLqr+qR++ LOC_Os08g41950.1 110 NRESEQLKASRNEYLKLKARVENLQRTQRQY 140 467888999********************97 PP
3	K-box	74.5	2.9e-25	165	237	28	100
K-box 28 ienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkklee 100 +e+L R+llGedL+sL +keL++Le+qL++slk++R++++++l++q+ elq+ke++++e+n++Lr+klee LOC_Os08g41950.1 165 TEKLCMYERNLLGEDLDSLGIKELESLEKQLDSSLKHVRTTRTKHLVDQLTELQRKEQMVSEANRCLRRKLEE 237 57889999**************************************************************987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	33.389	27	87	IPR002100	Transcription factor, MADS-box
SMART	SM00432	1.3E-41	27	86	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	9.03E-34	28	115	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.20E-43	28	103	No hit	No description
PRINTS	PR00404	1.5E-32	29	49	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	29	83	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	3.3E-26	36	83	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.5E-32	49	64	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.5E-32	64	85	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS51297	12.822	116	241	IPR002487	Transcription factor, K-box
Pfam	PF01486	3.4E-19	165	235	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:0009908	Biological Process	flower development
GO:0030154	Biological Process	cell differentiation
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 311 aa Download sequence Send to blast
MAEKKKKKKK KKPQSLLVLT SWRSIGMGRG RVELKRIENK INRQVTFAKR RNGLLKKAYE 60 LSVLCDAEVA LIIFSNRGKL YEFCSTQSMT KTLEKYQKCS YAGPETAVQN RESEQLKASR 120 NEYLKLKARV ENLQRTQRQY YKSKHRLCLV RSKVWNLVKI RDDVTEKLCM YERNLLGEDL 180 DSLGIKELES LEKQLDSSLK HVRTTRTKHL VDQLTELQRK EQMVSEANRC LRRKLEESNH 240 VRGQQVWEQG CNLIGYERQP EVQQPLHGGN GFFHPLDAAG EPTLQIGYPA EHHEAMNSAC 300 MNTYMPPWLP *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ox0_A	4e-22	101	237	1	103	Developmental protein SEPALLATA 3
4ox0_B	4e-22	101	237	1	103	Developmental protein SEPALLATA 3
4ox0_C	4e-22	101	237	1	103	Developmental protein SEPALLATA 3
4ox0_D	4e-22	101	237	1	103	Developmental protein SEPALLATA 3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	2	12	EKKKKKKKKKP
2	3	11	KKKKKKKKK
3	5	11	KKKKKKK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Os.2236	0.0	flower\| panicle\| seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	45385963	0.0

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed at early stage of flower development in the spikelet (rice flower) primordia and later in stamen and pistil primordia. Expressed during ovule development in the inner and outer integuments. {ECO:0000269\|PubMed:12395189, ECO:0000269\|PubMed:9065695}.
Uniprot	TISSUE SPECIFICITY: Expressed in lodicules, stamens and carpels. {ECO:0000269\|PubMed:12395189, ECO:0000269\|PubMed:9065695, ECO:0000269\|PubMed:9339904}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor.
UniProt	Probable transcription factor. May be involved in the control of flowering time. {ECO:0000269\|PubMed:9339904, ECO:0000269\|Ref.10}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	LOC_Os08g41950.1

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

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os08g41950

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY551921	0.0	AY551921.1 Oryza sativa (japonica cultivar-group) MADS-box protein RMADS216 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015648762.1	1e-179	MADS-box transcription factor 7
Swissprot	P0C5B0	1e-180	MADS7_ORYSI; MADS-box transcription factor 7
Swissprot	Q0J466	1e-180	MADS7_ORYSJ; MADS-box transcription factor 7
TrEMBL	A0A0E0IF02	0.0	A0A0E0IF02_ORYNI; Uncharacterized protein
STRING	ONIVA08G24560.1	0.0	(Oryza nivara)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP3483	34	69
Representative plant	OGRP16	17	761

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G24260.1	9e-85	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	LOC_Os08g41950.1

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Shitsukawa N, et al. Genetic and epigenetic alteration among three homoeologous genes of a class E MADS box gene in hexaploid wheat. Plant Cell, 2007. 19(6): p. 1723-37 [PMID:17586655] Bai X,Wang Q,Chu C Excision of a selective marker in transgenic rice using a novel Cre/loxP system controlled by a floral specific promoter. Transgenic Res., 2008. 17(6): p. 1035-43 [PMID:18437520] Qu L, et al. Expression pattern and functional analysis of a MADS-box gene M79 from rice. Sci. China, C, Life Sci., 2001. 44(2): p. 161-9 [PMID:18726433] Cui R, et al. Functional conservation and diversification of class E floral homeotic genes in rice (Oryza sativa). Plant J., 2010. 61(5): p. 767-81 [PMID:20003164] Li H, et al. The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice. Cell Res., 2010. 20(3): p. 299-313 [PMID:20038961] Seok HY, et al. Rice ternary MADS protein complexes containing class B MADS heterodimer. Biochem. Biophys. Res. Commun., 2010. 401(4): p. 598-604 [PMID:20888318] Tang X, et al. Global gene profiling of laser-captured pollen mother cells indicates molecular pathways and gene subfamilies involved in rice meiosis. Plant Physiol., 2010. 154(4): p. 1855-70 [PMID:20959420] Wang SS,Wang CS,Tseng TH,Hou YL,Chen KY High-resolution genetic mapping and candidate gene identification of the SLP1 locus that controls glume development in rice. Theor. Appl. Genet., 2011. 122(8): p. 1489-96 [PMID:21327937] Li H, et al. Rice MADS6 interacts with the floral homeotic genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in specifying floral organ identities and meristem fate. Plant Cell, 2011. 23(7): p. 2536-52 [PMID:21784949] Yoshida H Is the lodicule a petal: molecular evidence? Plant Sci., 2012. 184: p. 121-8 [PMID:22284716] Duan Y, et al. Characterization of Osmads6-5, a null allele, reveals that OsMADS6 is a critical regulator for early flower development in rice (Oryza sativa L.). Plant Mol. Biol., 2012. 80(4-5): p. 429-42 [PMID:22933119] Wong CE,Singh MB,Bhalla PL Novel members of the AGAMOUS LIKE 6 subfamily of MIKCC-type MADS-box genes in soybean. BMC Plant Biol., 2013. 13: p. 105 [PMID:23870482] Hu Z,Ding X,Hu S,Sun Y,Xia L Tissue-specifically regulated site-specific excision of selectable marker genes in bivalent insecticidal, genetically-modified rice. Biotechnol. Lett., 2013. 35(12): p. 2177-83 [PMID:23974493] Bai X, et al. Regulatory role of FZP in the determination of panicle branching and spikelet formation in rice. Sci Rep, 2016. 6: p. 19022 [PMID:26744119] Dreni L,Zhang D Flower development: the evolutionary history and functions of the AGL6 subfamily MADS-box genes. J. Exp. Bot., 2016. 67(6): p. 1625-38 [PMID:26956504]