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_Os05g34940.1

Common Name

MADS4, OJ1212_B02.5, Os05g0423400

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: 216aa MW: 24908.5 Da PI: 9.0978

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os05g34940.1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	85.8	2.6e-27	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien++nrqvtfskRr+gilKKA E+ vLCdaev v+ifss gkl +y++ LOC_Os05g34940.1 9 KRIENSTNRQVTFSKRRAGILKKAREIGVLCDAEVGVVIFSSAGKLSDYCT 59 79***********************************************96 PP
2	K-box	67.7	3.9e-23	76	172	1	97
K-box 1 yqkssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenka 93 yq++sgk l+++k++sl+ e++++kke++n+q e+Rh++GedL+sL+ keL +e++L+++ + R+k +++++++ ++ ++ e+e++ + LOC_Os05g34940.1 76 YQTNSGKILWDEKHKSLSAEIDRVKKENDNMQIELRHMKGEDLNSLQPKELIAIEEALNNGQANLRDKMMDHWRMHKRNEKMLEDEHKMLAFR 168 89999999************************************************************9988888888888888887777666 PP K-box 94 Lrkk 97 +++ LOC_Os05g34940.1 169 VHQQ 172 6665 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	3.5E-39	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	31.469	1	61	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.09E-30	2	100	IPR002100	Transcription factor, MADS-box
CDD	cd00265	2.34E-40	2	85	No hit	No description
PRINTS	PR00404	9.6E-28	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	2.8E-23	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	9.6E-28	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	9.6E-28	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	6.0E-16	87	169	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	12.69	89	175	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:0010097	Biological Process	specification of stamen identity
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: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: 216 aa Download sequence Send to blast
MGRGKIEIKR IENSTNRQVT FSKRRAGILK KAREIGVLCD AEVGVVIFSS AGKLSDYCTP 60 KTTSVFPPLS RILEKYQTNS GKILWDEKHK SLSAEIDRVK KENDNMQIEL RHMKGEDLNS 120 LQPKELIAIE EALNNGQANL RDKMMDHWRM HKRNEKMLED EHKMLAFRVH QQEVELSGGI 180 RELELGYHHD DRDFAASMPF TFRVQPSHPN LQQEK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6bz1_A	4e-17	1	86	1	86	MEF2 CHIMERA
6bz1_B	4e-17	1	86	1	86	MEF2 CHIMERA
6bz1_C	4e-17	1	86	1	86	MEF2 CHIMERA
6bz1_D	4e-17	1	86	1	86	MEF2 CHIMERA
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Os.2214	0.0	panicle

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	32985442	0.0
Expression Atlas	Q40703	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Highly expressed in lodicules, at intermediate levels in stamens, and weakly in carpels. Expressed in pollen. {ECO:0000269\|PubMed:10394955, ECO:0000269\|PubMed:12905025, ECO:0000269\|Ref.1}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in the development of floral organs. B-class protein required for normal development of lodicules and stamens (whorls 2 and 3). May function as a heterodimer with MADS16. {ECO:0000269\|PubMed:9869408}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	LOC_Os05g34940.1

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

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os05g34940

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK100233	0.0	AK100233.1 Oryza sativa Japonica Group cDNA clone:J023051B10, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015640709.1	1e-154	MADS-box transcription factor 4 isoform X2
Swissprot	Q40703	1e-162	MADS4_ORYSJ; MADS-box transcription factor 4
TrEMBL	B8AYK1	1e-152	B8AYK1_ORYSI; Uncharacterized protein
TrEMBL	B9FPP6	1e-152	B9FPP6_ORYSJ; Uncharacterized protein
STRING	OS05T0423400-01	1e-160	(Oryza sativa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP3434	38	77
Representative plant	OGRP5302	12	22

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G20240.1	8e-72	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	LOC_Os05g34940.1

Publications ? help Back to Top
Moon YH,Jung JY,Kang HG,An G Identification of a rice APETALA3 homologue by yeast two-hybrid screening. Plant Mol. Biol., 1999. 40(1): p. 167-77 [PMID:10394955] Ronai Z, et al. Transcription factor binding study by capillary zone electrophoretic mobility shift assay. Electrophoresis, 2003. 24(1-2): p. 96-100 [PMID:12652578] 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] Lee S, et al. Alteration of floral organ identity in rice through ectopic expression of OsMADS16. Planta, 2003. 217(6): p. 904-11 [PMID:12905025] Kang HG,An G Morphological alterations by ectopic expression of the rice OsMADS4 gene in tobacco plants. Plant Cell Rep., 2005. 24(2): p. 120-6 [PMID:15703945] Cheng CH, et al. A fine physical map of the rice chromosome 5. Mol. Genet. Genomics, 2005. 274(4): p. 337-45 [PMID:16261349] Chen C, et al. Adapting rice anther culture to gene transformation and RNA interference. Sci. China, C, Life Sci., 2006. 49(5): p. 414-28 [PMID:17172048] Yoshida H, et al. superwoman1-cleistogamy, a hopeful allele for gene containment in GM rice. Plant Biotechnol. J., 2007. 5(6): p. 835-46 [PMID:17764519] Yao SG,Ohmori S,Kimizu M,Yoshida H Unequal genetic redundancy of rice PISTILLATA orthologs, OsMADS2 and OsMADS4, in lodicule and stamen development. Plant Cell Physiol., 2008. 49(5): p. 853-7 [PMID:18378529] 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] Wang H, et al. OsMADS32 interacts with PI-like proteins and regulates rice flower development. J Integr Plant Biol, 2015. 57(5): p. 504-13 [PMID:25081486] Kang HG,Jeon JS,Lee S,An G Identification of class B and class C floral organ identity genes from rice plants. Plant Mol. Biol., 1998. 38(6): p. 1021-9 [PMID:9869408]