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

Seita.9G561000.1.p

Common Name

SETIT_038257mg

Organism

Setaria italica

Taxonomic ID

4555

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria

Family

M-type_MADS

Protein Properties

Length: 62aa MW: 6973.2 Da PI: 11.3251

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Seita.9G561000.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	97.7	4.7e-31	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRrng+lKKA+ELSvLCdaeva+++fs++gklye+++ Seita.9G561000.1.p 9 KRIENPTSRQVTFSKRRNGLLKKAFELSVLCDAEVALVVFSPRGKLYEFAN 59 79***********************************************85 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	31.048	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	3.7E-39	1	60	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	2.88E-29	3	59	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	9.4E-32	3	23	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.39E-37	3	59	No hit	No description
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.1E-28	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	9.4E-32	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	9.4E-32	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: 62 aa Download sequence Send to blast
MVRGKTQMKR IENPTSRQVT FSKRRNGLLK KAFELSVLCD AEVALVVFSP RGKLYEFANG 60 R*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3mu6_A	3e-18	3	59	2	58	Myocyte-specific enhancer factor 2A
3mu6_B	3e-18	3	59	2	58	Myocyte-specific enhancer factor 2A
3mu6_C	3e-18	3	59	2	58	Myocyte-specific enhancer factor 2A
3mu6_D	3e-18	3	59	2	58	Myocyte-specific enhancer factor 2A
5f28_A	6e-18	1	58	1	58	MEF2C
5f28_B	6e-18	1	58	1	58	MEF2C
5f28_C	6e-18	1	58	1	58	MEF2C
5f28_D	6e-18	1	58	1	58	MEF2C
6byy_A	5e-18	1	59	1	59	MEF2 CHIMERA
6byy_B	5e-18	1	59	1	59	MEF2 CHIMERA
6byy_C	5e-18	1	59	1	59	MEF2 CHIMERA
6byy_D	5e-18	1	59	1	59	MEF2 CHIMERA
6bz1_A	6e-18	1	59	1	59	MEF2 CHIMERA
6bz1_B	6e-18	1	59	1	59	MEF2 CHIMERA
6bz1_C	6e-18	1	59	1	59	MEF2 CHIMERA
6bz1_D	6e-18	1	59	1	59	MEF2 CHIMERA
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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	Seita.9G561000.1.p

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC098695	5e-87	AC098695.2 Oryza sativa Japonica Group chromosome 3 clone OJ1126B12, complete sequence.
GenBank	AC210475	5e-87	AC210475.1 Oryza glaberrima clone OG_BBa0054O06, complete sequence.
GenBank	AC213915	5e-87	AC213915.1 Oryza minuta clone OM__Ba0240A18, complete sequence.
GenBank	AC215814	5e-87	AC215814.1 Oryza minuta clone OM__Ba0123B04, complete sequence.
GenBank	AP014959	5e-87	AP014959.1 Oryza sativa Japonica Group DNA, chromosome 3, cultivar: Nipponbare, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_022678747.1	1e-36	MADS-box transcription factor 50 isoform X1
Refseq	XP_022678748.1	1e-36	MADS-box transcription factor 50 isoform X1
Swissprot	Q9XJ60	1e-35	MAD50_ORYSJ; MADS-box transcription factor 50
TrEMBL	A0A368SWI3	9e-37	A0A368SWI3_SETIT; Uncharacterized protein
TrEMBL	K4AHA0	1e-36	K4AHA0_SETIT; Uncharacterized protein
STRING	Si038257m	2e-37	(Setaria italica)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP129	38	398

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G45660.1	7e-36	AGAMOUS-like 20

Link Out ? help Back to Top
Phytozome	Seita.9G561000.1.p

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]