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_Os12g10540.3

Common Name

LOC4351753, MADS13, MAF1, Os12g0207000, OsJ_35557

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: 271aa MW: 30268.5 Da PI: 9.5082

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os12g10540.3	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	96.5	1.2e-30	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien++ rqvtf+kRrng+lKKA+ELSvLCdaeva+i+fss+g+lyeys+ LOC_Os12g10540.3 9 KRIENTTSRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYSN 59 79***********************************************95 PP
2	K-box	100.6	2.1e-33	86	176	10	100
K-box 10 eeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkklee 100 e + ++++qqe+akL+ +i++Lq++++hl+G+++++LslkeL+qLe++Lek+++kiR++Knell ++i+++ k+e elq++n++Lr+k++e LOC_Os12g10540.3 86 EVNAQQYYQQESAKLRHQIQMLQNTNKHLVGDNVSNLSLKELKQLESRLEKGISKIRARKNELLASEINYMAKREIELQNDNMDLRTKIAE 176 567789**********************************************************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	3.4E-41	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	33.557	1	61	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.34E-41	2	75	No hit	No description
SuperFamily	SSF55455	5.36E-32	2	76	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.6E-32	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.8E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.6E-32	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.6E-32	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	6.6E-25	87	174	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	15.141	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:0010622	Biological Process	specification of ovule identity
GO:0048283	Biological Process	indeterminate inflorescence morphogenesis
GO:0048481	Biological Process	plant ovule development
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:0009072	anatomy	plant ovary
PO:0007042	developmental stage	whole plant fruit formation stage

Sequence ? help Back to Top
Protein Sequence Length: 271 aa Download sequence Send to blast
MGRGRIEIKR IENTTSRQVT FCKRRNGLLK KAYELSVLCD AEVALIVFSS RGRLYEYSNN 60 NNVKATIDRY KKAHACGSTS GAPLIEVNAQ QYYQQESAKL RHQIQMLQNT NKHLVGDNVS 120 NLSLKELKQL ESRLEKGISK IRARKNELLA SEINYMAKRE IELQNDNMDL RTKIAEEEQQ 180 LQQVTVARSA AMELQAAAAA QQQQQNPFAV AAAQLDMKCF FPLNLFEAAA QVQAVAAQRQ 240 QIIPTELNLG YHHHLAIPGA AAADAPPPHF *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1tqe_P	1e-18	1	61	1	61	Myocyte-specific enhancer factor 2B
1tqe_Q	1e-18	1	61	1	61	Myocyte-specific enhancer factor 2B
1tqe_R	1e-18	1	61	1	61	Myocyte-specific enhancer factor 2B
1tqe_S	1e-18	1	61	1	61	Myocyte-specific enhancer factor 2B
6c9l_A	1e-18	1	61	1	61	Myocyte-specific enhancer factor 2B
6c9l_B	1e-18	1	61	1	61	Myocyte-specific enhancer factor 2B
6c9l_C	1e-18	1	61	1	61	Myocyte-specific enhancer factor 2B
6c9l_D	1e-18	1	61	1	61	Myocyte-specific enhancer factor 2B
6c9l_E	1e-18	1	61	1	61	Myocyte-specific enhancer factor 2B
6c9l_F	1e-18	1	61	1	61	Myocyte-specific enhancer factor 2B
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Os.2345	0.0	flower\| panicle\| seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	32980449	0.0
Expression Atlas	Q2QW53	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed during ovule development. First detected in the ovule primordia and later in the inner and outer integuments, nucellus tissue and the inner layer of the carpel wall. {ECO:0000269\|PubMed:10528264}.

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

Cis-element ? help Back to Top
Source	Link
PlantRegMap	LOC_Os12g10540.3

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

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q2QW53

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os12g10540

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK070425	0.0	AK070425.1 Oryza sativa Japonica Group cDNA clone:J023050A03, full insert sequence.
GenBank	AY332475	0.0	AY332475.1 Oryza sativa (japonica cultivar-group) MADS protein (MAF1) mRNA, complete cds.
GenBank	FJ750941	0.0	FJ750941.1 Oryza sativa clone KCS112D08 MADS-box transcription factor 13 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015618486.1	0.0	MADS-box transcription factor 13 isoform X2
Refseq	XP_015618487.1	0.0	MADS-box transcription factor 13 isoform X2
Swissprot	Q2QW53	0.0	MAD13_ORYSJ; MADS-box transcription factor 13
TrEMBL	A0A0E0RF26	0.0	A0A0E0RF26_ORYRU; Uncharacterized protein
TrEMBL	D3U2H3	0.0	D3U2H3_ORYSA; MADS-box transcription factor 13
STRING	ORUFI12G06810.1	0.0	(Oryza rufipogon)
STRING	OS12T0207000-01	0.0	(Oryza sativa)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G18960.1	2e-82	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	LOC_Os12g10540.3
Entrez Gene	4351753

Publications ? help Back to Top
Lopez-Dee ZP, et al. OsMADS13, a novel rice MADS-box gene expressed during ovule development. Dev. Genet., 1999. 25(3): p. 237-44 [PMID:10528264] Gindullis F,Rose A,Patel S,Meier I Four signature motifs define the first class of structurally related large coiled-coil proteins in plants. BMC Genomics, 2002. 3: p. 9 [PMID:11972898] 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] Yamaki S,Satoh H,Nagato Y Gypsy embryo specifies ovule curvature by regulating ovule/integument development in rice. Planta, 2005. 222(3): p. 408-17 [PMID:16001259] Rice Chromosomes 11 and 12 Sequencing Consortia The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol., 2005. 3: p. 20 [PMID:16188032] Dreni L, et al. The D-lineage MADS-box gene OsMADS13 controls ovule identity in rice. Plant J., 2007. 52(4): p. 690-9 [PMID:17877710] Yamaki S,Nagato Y,Kurata N,Nonomura K Ovule is a lateral organ finally differentiated from the terminating floral meristem in rice. Dev. Biol., 2011. 351(1): p. 208-16 [PMID:21146515] Li H,Liang W,Yin C,Zhu L,Zhang D Genetic interaction of OsMADS3, DROOPING LEAF, and OsMADS13 in specifying rice floral organ identities and meristem determinacy. Plant Physiol., 2011. 156(1): p. 263-74 [PMID:21444646] 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]