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_Os08g41950.2

Common Name

AGL6, LOC4346134, M79, MADS45, MADS7, Os08g0531700, P0702E04.10

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: 250aa MW: 28713.7 Da PI: 8.9742

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os08g41950.2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	99.8	1.1e-31	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krienk+nrqvtf+kRrng+lKKA+ELSvLCdaeva+iifs++gklye++s LOC_Os08g41950.2 9 KRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSNRGKLYEFCS 59 79***********************************************96 PP
2	K-box	97.4	2.1e-32	84	176	8	100
K-box 8 sleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkklee 100 + e+++ + +++e+ kLk+++enLqr+qR+llGedL+sL +keL++Le+qL++slk++R++++++l++q+ elq+ke++++e+n++Lr+klee LOC_Os08g41950.2 84 NRESEQLKASRNEYLKLKARVENLQRTQRNLLGEDLDSLGIKELESLEKQLDSSLKHVRTTRTKHLVDQLTELQRKEQMVSEANRCLRRKLEE 176 467888999*********************************************************************************987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	33.389	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	1.3E-41	1	60	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.30E-44	2	77	No hit	No description
SuperFamily	SSF55455	5.76E-34	2	89	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	9.2E-33	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	2.3E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	9.2E-33	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	9.2E-33	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	1.1E-24	86	174	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	14.804	90	180	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

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009030	anatomy	carpel
PO:0007130	developmental stage	sporophyte reproductive stage
PO:0007606	developmental stage	gynoecium development stage

Sequence ? help Back to Top
Protein Sequence Length: 250 aa Download sequence Send to blast
MGRGRVELKR IENKINRQVT FAKRRNGLLK KAYELSVLCD AEVALIIFSN RGKLYEFCST 60 QSMTKTLEKY QKCSYAGPET AVQNRESEQL KASRNEYLKL KARVENLQRT QRNLLGEDLD 120 SLGIKELESL EKQLDSSLKH VRTTRTKHLV DQLTELQRKE QMVSEANRCL RRKLEESNHV 180 RGQQVWEQGC NLIGYERQPE VQQPLHGGNG FFHPLDAAGE PTLQIGYPAE HHEAMNSACM 240 NTYMPPWLP*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ox0_A	3e-29	75	176	1	103	Developmental protein SEPALLATA 3
4ox0_B	3e-29	75	176	1	103	Developmental protein SEPALLATA 3
4ox0_C	3e-29	75	176	1	103	Developmental protein SEPALLATA 3
4ox0_D	3e-29	75	176	1	103	Developmental protein SEPALLATA 3
Search in ModeBase

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 Atlas	Q0J466	-

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_Os08g41950.2

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

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q0J466

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK100263	0.0	AK100263.1 Oryza sativa Japonica Group cDNA clone:J023063L04, full insert sequence.
GenBank	FJ750934	0.0	FJ750934.1 Oryza sativa clone KCS054B01 MADS-box transcription factor 7 mRNA, complete cds.
GenBank	OSU31994	0.0	U31994.1 Oryza sativa MADS box protein OsMADS45 mRNA, complete cds.
GenBank	OSU78891	0.0	U78891.2 Oryza sativa MADS box protein (MADS7) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015648762.1	0.0	MADS-box transcription factor 7
Swissprot	P0C5B0	0.0	MADS7_ORYSI; MADS-box transcription factor 7
Swissprot	Q0J466	0.0	MADS7_ORYSJ; MADS-box transcription factor 7
TrEMBL	D3U2G6	0.0	D3U2G6_ORYSA; MADS-box transcription factor 7
TrEMBL	I1QLJ9	0.0	I1QLJ9_ORYGL; Uncharacterized protein
STRING	OS08T0531700-01	0.0	(Oryza sativa)
STRING	ORGLA08G0230000.1	0.0	(Oryza glaberrima)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G24260.1	1e-92	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	LOC_Os08g41950.2
Entrez Gene	4346134

Publications ? help Back to Top
Moon YH, et al. Determination of the motif responsible for interaction between the rice APETALA1/AGAMOUS-LIKE9 family proteins using a yeast two-hybrid system. Plant Physiol., 1999. 120(4): p. 1193-204 [PMID:10444103] Favaro R, et al. Ovule-specific MADS-box proteins have conserved protein-protein interactions in monocot and dicot plants. Mol. Genet. Genomics, 2002. 268(2): p. 152-9 [PMID:12395189] Cooper B, et al. A network of rice genes associated with stress response and seed development. Proc. Natl. Acad. Sci. U.S.A., 2003. 100(8): p. 4945-50 [PMID:12684538] 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] Fornara F, et al. Functional characterization of OsMADS18, a member of the AP1/SQUA subfamily of MADS box genes. Plant Physiol., 2004. 135(4): p. 2207-19 [PMID:15299121] 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] Greco R, et al. MADS box genes expressed in developing inflorescences of rice and sorghum. Mol. Gen. Genet., 1997. 253(5): p. 615-23 [PMID:9065695] Kang HG,Jang S,Chung JE,Cho YG,An G Characterization of two rice MADS box genes that control flowering time. Mol. Cells, 1997. 7(4): p. 559-66 [PMID:9339904]