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_Os03g54170.1

Common Name

LOC4334141, MADS34, OJ1112_G08.14, Os03g0753100, OSJNBa0032E21.03, OSJNBa0047E24.1

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: 240aa MW: 26880.5 Da PI: 7.5519

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os03g54170.1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	87.9	5.5e-28	10	59	2	51
---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 rienk+ rqvtf+kRrng+lKKA+ELS+LCdaeva+++fs+ g+ly +ss LOC_Os03g54170.1 10 RIENKISRQVTFAKRRNGLLKKAYELSILCDAEVALVLFSHAGRLYQFSS 59 9***********************************************96 PP
2	K-box	92.3	8.1e-31	79	174	5	100
K-box 5 sgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkk 97 + + ++ ++++ +qe+ +Lk+ +e Lq++qR+llGedL +L +eL+qLe+q+ + lk+iRs+K+++ll+++ +l++ke++lq++n+ L++k LOC_Os03g54170.1 79 DAAAPTSDEMQNNYQEYVNLKAHVEILQQSQRNLLGEDLAPLATNELEQLESQVVRTLKQIRSRKTQVLLDELCDLKRKEQMLQDANRVLKRK 171 444567889************************************************************************************ PP K-box 98 lee 100 l+e LOC_Os03g54170.1 172 LDE 174 986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	31.02	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	2.9E-36	1	60	IPR002100	Transcription factor, MADS-box
CDD	cd00265	2.16E-41	2	79	No hit	No description
SuperFamily	SSF55455	7.33E-31	2	83	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.6E-29	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.1E-25	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.6E-29	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.6E-29	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	9.2E-27	85	172	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	14.723	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

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009047	anatomy	stem
PO:0007010	developmental stage	whole plant fruit ripening stage
PO:0007130	developmental stage	sporophyte reproductive stage

Sequence ? help Back to Top
Protein Sequence Length: 240 aa Download sequence Send to blast
MGRGKVVLQR IENKISRQVT FAKRRNGLLK KAYELSILCD AEVALVLFSH AGRLYQFSSS 60 SNMLKTLERY QRYIYASQDA AAPTSDEMQN NYQEYVNLKA HVEILQQSQR NLLGEDLAPL 120 ATNELEQLES QVVRTLKQIR SRKTQVLLDE LCDLKRKEQM LQDANRVLKR KLDEIDVEAA 180 PPQPPWNGNC SNGHGGGGGV FSSEPPQPEH FFQALGLHAV DVNQPPAPPP GGYPPEWMA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ox0_A	2e-21	93	172	22	101	Developmental protein SEPALLATA 3
4ox0_B	2e-21	93	172	22	101	Developmental protein SEPALLATA 3
4ox0_C	2e-21	93	172	22	101	Developmental protein SEPALLATA 3
4ox0_D	2e-21	93	172	22	101	Developmental protein SEPALLATA 3
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Os.49761	0.0	flower\| panicle

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	32985436	0.0
Expression Atlas	Q6Q9H6	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Highly expressed in leaves and at low levels in roots and spikelets (rice flower). {ECO:0000269\|Ref.7}.

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

Function -- GeneRIF ? help Back to Top
controls different aspects of inflorescence structure, branching and meristem activity synergistically with LAX PANICLE1 (LAX1) and FLORAL ORGAN NUMBER4 (FON4) [PMID: 28843032]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	LOC_Os03g54170.1

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

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os03g54170

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB003324	0.0	AB003324.1 Oryza sativa Japonica Group mRNA for MADS box-like protein, complete cds, clone:E31254.
GenBank	AY551917	0.0	AY551917.1 Oryza sativa (japonica cultivar-group) MADS-box protein RMADS212 mRNA, complete cds.
GenBank	AY551922	0.0	AY551922.1 Oryza sativa (japonica cultivar-group) MADS-box protein RMADS217 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015631035.1	1e-178	MADS-box transcription factor 34
Swissprot	Q6Q9H6	1e-180	MAD34_ORYSJ; MADS-box transcription factor 34
TrEMBL	A0A0E0GTX1	1e-177	A0A0E0GTX1_ORYNI; Uncharacterized protein
TrEMBL	A0A0E0P1F8	1e-177	A0A0E0P1F8_ORYRU; Uncharacterized protein
STRING	ORUFI03G35940.1	1e-178	(Oryza rufipogon)
STRING	OS03T0753100-01	1e-178	(Oryza sativa)
STRING	ONIVA03G35990.1	1e-178	(Oryza nivara)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP13618	26	30
Representative plant	OGRP16	17	761

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G15800.1	3e-75	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	LOC_Os03g54170.1
Entrez Gene	4334141

Publications ? help Back to Top
Shinozuka Y, et al. Isolation and characterization of rice MADS box gene homologues and their RFLP mapping. DNA Res., 1999. 6(2): p. 123-9 [PMID:10382970] Kobayashi K,Maekawa M,Miyao A,Hirochika H,Kyozuka J PANICLE PHYTOMER2 (PAP2), encoding a SEPALLATA subfamily MADS-box protein, positively controls spikelet meristem identity in rice. Plant Cell Physiol., 2010. 51(1): p. 47-57 [PMID:19933267] Gao X, et al. The SEPALLATA-like gene OsMADS34 is required for rice inflorescence and spikelet development. Plant Physiol., 2010. 153(2): p. 728-40 [PMID:20395452] Khanday I,Yadav SR,Vijayraghavan U Rice LHS1/OsMADS1 controls floret meristem specification by coordinated regulation of transcription factors and hormone signaling pathways. Plant Physiol., 2013. 161(4): p. 1970-83 [PMID:23449645] Lin X, et al. The pleiotropic SEPALLATA-like gene OsMADS34 reveals that the 'empty glumes' of rice (Oryza sativa) spikelets are in fact rudimentary lemmas. New Phytol., 2014. 202(2): p. 689-702 [PMID:24372518] Conrad LJ, et al. The polycomb group gene EMF2B is essential for maintenance of floral meristem determinacy in rice. Plant J., 2014. 80(5): p. 883-94 [PMID:25279942] Liu M,Li H,Su Y,Li W,Shi C G1/ELE Functions in the Development of Rice Lemmas in Addition to Determining Identities of Empty Glumes. Front Plant Sci, 2016. 7: p. 1006 [PMID:27462334] Meng Q, et al. Regulatory network and genetic interactions established by OsMADS34 in rice inflorescence and spikelet morphogenesis. J Integr Plant Biol, 2017. 59(9): p. 693-707 [PMID:28843032]