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_Os03g03100.1

Common Name

OJ1126B12.10

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

M-type_MADS

Protein Properties

Length: 117aa MW: 13279.6 Da PI: 11.1997

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os03g03100.1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	96.7	9.6e-31	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRrng+lKKA+ELSvLCdaeva+i+fs++gklye++s LOC_Os03g03100.1 9 KRIENPTSRQVTFSKRRNGLLKKAFELSVLCDAEVALIVFSPRGKLYEFAS 59 79***********************************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	9.8E-41	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	31.595	1	61	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.26E-29	3	66	IPR002100	Transcription factor, MADS-box
CDD	cd00265	8.38E-37	3	59	No hit	No description
PRINTS	PR00404	1.3E-31	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	6.0E-28	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.3E-31	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.3E-31	38	59	IPR002100	Transcription factor, MADS-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:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 117 aa Download sequence Send to blast
MVRGKTQMKR IENPTSRQVT FSKRRNGLLK KAFELSVLCD AEVALIVFSP RGKLYEFASA 60 RKIRPEKTAK TIFPRVAIEL PSKQSHYFHK EISCETGKVR NSENIGNLVL AFRRAI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3mu6_A	4e-18	3	60	2	59	Myocyte-specific enhancer factor 2A
3mu6_B	4e-18	3	60	2	59	Myocyte-specific enhancer factor 2A
3mu6_C	4e-18	3	60	2	59	Myocyte-specific enhancer factor 2A
3mu6_D	4e-18	3	60	2	59	Myocyte-specific enhancer factor 2A
5f28_A	4e-18	1	60	1	60	MEF2C
5f28_B	4e-18	1	60	1	60	MEF2C
5f28_C	4e-18	1	60	1	60	MEF2C
5f28_D	4e-18	1	60	1	60	MEF2C
6byy_A	5e-18	1	60	1	60	MEF2 CHIMERA
6byy_B	5e-18	1	60	1	60	MEF2 CHIMERA
6byy_C	5e-18	1	60	1	60	MEF2 CHIMERA
6byy_D	5e-18	1	60	1	60	MEF2 CHIMERA
6bz1_A	5e-18	1	60	1	60	MEF2 CHIMERA
6bz1_B	5e-18	1	60	1	60	MEF2 CHIMERA
6bz1_C	5e-18	1	60	1	60	MEF2 CHIMERA
6bz1_D	5e-18	1	60	1	60	MEF2 CHIMERA
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	45385951	0.0
Expression Atlas	Q8H8H1	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Low expression in the young panicle continues to decline as the organ mature. {ECO:0000269\|PubMed:15144377, ECO:0000269\|PubMed:17166135}.
Uniprot	TISSUE SPECIFICITY: Expressed in mature leaves and at low levels in roots and young panicles. {ECO:0000269\|PubMed:15144377, ECO:0000269\|PubMed:17166135}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor active in flowering time control. May control internode elongation and promote floral transition phase. May act upstream of the floral regulators MADS1, MADS14, MADS15 and MADS18 in the floral induction pathway. {ECO:0000269\|PubMed:15144377, ECO:0000269\|PubMed:17166135}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	LOC_Os03g03100.1

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

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os03g03100

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY551915	0.0	AY551915.1 Oryza sativa (japonica cultivar-group) MADS-box protein RMADS210 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006649298.1	4e-35	PREDICTED: MADS-box transcription factor 50-like
Refseq	XP_007134936.1	3e-35	hypothetical protein PHAVU_010G088100g
Refseq	XP_007134937.1	3e-35	hypothetical protein PHAVU_010G088100g
Refseq	XP_015630979.1	4e-35	MADS-box transcription factor 50
Refseq	XP_015691000.1	4e-35	PREDICTED: MADS-box transcription factor 50-like
Refseq	XP_015691001.1	4e-35	PREDICTED: MADS-box transcription factor 50-like
Refseq	XP_025880188.1	4e-35	MADS-box transcription factor 50
Swissprot	Q9XJ60	3e-36	MAD50_ORYSJ; MADS-box transcription factor 50
TrEMBL	A0A0D3FD59	4e-79	A0A0D3FD59_9ORYZ; Uncharacterized protein
TrEMBL	Q8H8H1	4e-79	Q8H8H1_ORYSJ; Agamous-like MADS box protein AGL14, putative, expressed
STRING	OBART03G01800.1	6e-80	(Oryza barthii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP129	38	398
Representative plant	OGRP16	17	761

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G45660.1	4e-36	AGAMOUS-like 20

Link Out ? help Back to Top
Phytozome	LOC_Os03g03100.1

Publications ? help Back to Top
Thomson MJ,Edwards JD,Septiningsih EM,Harrington SE,McCouch SR Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL. Genetics, 2006. 172(4): p. 2501-14 [PMID:16452146] Park SJ, et al. Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod. Plant J., 2008. 56(6): p. 1018-29 [PMID:18774969] Lee S,Jeong DH,An G A possible working mechanism for rice SVP-group MADS-box proteins as negative regulators of brassinosteroid responses. Plant Signal Behav, 2008. 3(7): p. 471-4 [PMID:19704489] Maas LF,McClung A,McCouch S Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice. Theor. Appl. Genet., 2010. 120(5): p. 895-908 [PMID:19949767] Sun C, et al. The histone methyltransferase SDG724 mediates H3K36me2/3 deposition at MADS50 and RFT1 and promotes flowering in rice. Plant Cell, 2012. 24(8): p. 3235-47 [PMID:22892321] Choi SC, et al. Trithorax group protein Oryza sativa Trithorax1 controls flowering time in rice via interaction with early heading date3. Plant Physiol., 2014. 164(3): p. 1326-37 [PMID:24420930] Núñez-López L,Aguirre-Cruz A,Barrera-Figueroa BE,Peña-Castro JM Improvement of enzymatic saccharification yield in Arabidopsis thaliana by ectopic expression of the rice SUB1A-1 transcription factor. PeerJ, 2015. 3: p. e817 [PMID:25780769] Jin J, et al. MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice. Plant Physiol., 2015. 168(4): p. 1275-85 [PMID:25855537] Liu X, et al. Brassinosteroid (BR) biosynthetic gene lhdd10 controls late heading and plant height in rice (Oryza sativa L.). Plant Cell Rep., 2016. 35(2): p. 357-68 [PMID:26518431] Hwang YH, et al. Functional conservation of rice OsNF-YB/YC and Arabidopsis AtNF-YB/YC proteins in the regulation of flowering time. Plant Cell Rep., 2016. 35(4): p. 857-65 [PMID:26754793] Shibaya T, et al. Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice. Plant Cell Physiol., 2016. 57(9): p. 1828-38 [PMID:27318280] Alter P, et al. Flowering Time-Regulated Genes in Maize Include the Transcription Factor ZmMADS1. Plant Physiol., 2016. 172(1): p. 389-404 [PMID:27457125]