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

Tp57577_TGAC_v2_mRNA2039

Organism

Trifolium pratense

Taxonomic ID

57577

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium

Family

M-type_MADS

Protein Properties

Length: 102aa MW: 12293.2 Da PI: 10.5228

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp57577_TGAC_v2_mRNA2039	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	101.1	4.1e-32	36	86	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krienk+nrqvtf+kRrng+lKKA+ELSvLCdaeva+iifs++gklye+ss Tp57577_TGAC_v2_mRNA2039 36 KRIENKINRQVTFAKRRNGVLKKAYELSVLCDAEVALIIFSNRGKLYEFSS 86 79***********************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	33.529	28	88	IPR002100	Transcription factor, MADS-box
SMART	SM00432	1.5E-40	28	87	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	4.19E-30	29	90	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.89E-38	29	88	No hit	No description
PRINTS	PR00404	4.1E-33	30	50	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	30	84	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	4.0E-26	37	84	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.1E-33	50	65	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.1E-33	65	86	IPR002100	Transcription factor, MADS-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 102 aa Download sequence Send to blast
LFYPFWYPKQ RDYLRKHSHF SSLNQTKMGR GRVELKRIEN KINRQVTFAK RRNGVLKKAY 60 ELSVLCDAEV ALIIFSNRGK LYEFSSTSRY LFTHHFLFEY Y*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6byy_A	3e-20	28	88	1	61	MEF2 CHIMERA
6byy_B	3e-20	28	88	1	61	MEF2 CHIMERA
6byy_C	3e-20	28	88	1	61	MEF2 CHIMERA
6byy_D	3e-20	28	88	1	61	MEF2 CHIMERA
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Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor.
UniProt	Probable transcription factor active in inflorescence development and floral organogenesis. Functions with SEPALLATA1/AGL2 and SEPALLATA2/AGL4 to ensure proper development of petals, stamens and carpels and to prevent the indeterminate growth of the flower meristem. Interacts with APETALA1, AGAMOUS or APETALA3/PISTILLATA to form complexes, that could be involved in genes regulation during floral meristem development (PubMed:10821278, PubMed:11206550). Binds specifically to the CArG box DNA sequence 5'-CC (A/T)6 GG-3' (PubMed:16080001). {ECO:0000269\|PubMed:10821278, ECO:0000269\|PubMed:11206550, ECO:0000269\|PubMed:16080001}.
UniProt	Probable transcription factor. {ECO:0000269\|PubMed:9869431}.
UniProt	Probable transcription factor. Functions with SEPALLATA2/AGL4 and SEPALLATA3/AGL9 to ensure proper development of petals, stamens and carpels, and to prevent the indeterminate growth of the flower meristem. Forms a heterodimer via the K-box domain with AGAMOUS, that could be involved in genes regulation during floral meristem development.
UniProt	Probable transcription factor involved in flower development. {ECO:0000250\|UniProtKB:Q0HA25}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Tp57577_TGAC_v2_mRNA2039

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	AF129875	6e-51	AF129875.1 Capsicum annuum MADS box transcription factor MADS1 (MADS1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_016546327.1	3e-36	PREDICTED: agamous-like MADS-box protein AGL9 homolog
Swissprot	O22456	3e-35	SEP3_ARATH; Developmental protein SEPALLATA 3
Swissprot	O65874	3e-35	MTF1_PEA; MADS-box transcription factor 1
Swissprot	P29382	3e-35	SEP1_ARATH; Developmental protein SEPALLATA 1
Swissprot	Q03489	2e-35	AGL9_PETHY; Agamous-like MADS-box protein AGL9 homolog
Swissprot	Q8LLR0	2e-35	MADS4_VITVI; Agamous-like MADS-box protein MADS4
TrEMBL	A0A4D6KVL5	8e-37	A0A4D6KVL5_VIGUN; MADS-box transcription factor
STRING	cassava4.1_030388m	3e-36	(Manihot esculenta)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF119	33	360

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G24260.3	9e-38	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	Tp57577_TGAC_v2_mRNA2039

Publications ? help Back to Top
Immink RG,Gadella TW,Ferrario S,Busscher M,Angenent GC Analysis of MADS box protein-protein interactions in living plant cells. Proc. Natl. Acad. Sci. U.S.A., 2002. 99(4): p. 2416-21 [PMID:11854533] Immink RG, et al. Analysis of the petunia MADS-box transcription factor family. Mol. Genet. Genomics, 2003. 268(5): p. 598-606 [PMID:12589434] Angenent GC,Busscher M,Franken J,Mol JN,van Tunen AJ Differential expression of two MADS box genes in wild-type and mutant petunia flowers. Plant Cell, 1992. 4(8): p. 983-93 [PMID:1356537] Tonaco IA,Borst JW,de Vries SC,Angenent GC,Immink RG In vivo imaging of MADS-box transcription factor interactions. J. Exp. Bot., 2006. 57(1): p. 33-42 [PMID:16291798] Jaillon O, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 2007. 449(7161): p. 463-7 [PMID:17721507] Díaz-Riquelme J,Lijavetzky D,Martínez-Zapater JM,Carmona MJ Genome-wide analysis of MIKCC-type MADS box genes in grapevine. Plant Physiol., 2009. 149(1): p. 354-69 [PMID:18997115] Maejima K, et al. Recognition of floral homeotic MADS domain transcription factors by a phytoplasmal effector, phyllogen, induces phyllody. Plant J., 2014. 78(4): p. 541-54 [PMID:24597566] MacLean AM, et al. Phytoplasma effector SAP54 hijacks plant reproduction by degrading MADS-box proteins and promotes insect colonization in a RAD23-dependent manner. PLoS Biol., 2014. 12(4): p. e1001835 [PMID:24714165] Iglesias FM, et al. The arabidopsis DNA polymerase δ has a role in the deposition of transcriptionally active epigenetic marks, development and flowering. PLoS Genet., 2015. 11(2): p. e1004975 [PMID:25693187] He Q,Fu AY,Zhang GC,Li TJ,Zhang JH Arabidopsis thaliana SEPALLATA3 protein prokaryotic expression and purification. Cell. Mol. Biol. (Noisy-le-grand), 2015. 61(2): p. 60-3 [PMID:26025404] Maejima K, et al. Degradation of class E MADS-domain transcription factors in Arabidopsis by a phytoplasmal effector, phyllogen. Plant Signal Behav, 2015. 10(8): p. e1042635 [PMID:26179462] Muiño JM, et al. Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor. Mol. Biol. Evol., 2016. 33(1): p. 185-200 [PMID:26429922] Shi Q,Zhou J,Wang P,Lin X,Xu Y Protein expression and characterization of SEP3 from Arabidopsis thaliana. Genet. Mol. Res., 2015. 14(4): p. 12529-36 [PMID:26505403] He Q,Fu AY,Zhang GC,Li TJ,Zhang JH Cloning, Prokaryotic Expression and Purification of CpfS1 Gene from Arabidopsis Thaliana. Cell. Mol. Biol. (Noisy-le-grand), 2015. 61(8): p. 123-7 [PMID:26718440] Grimplet J,Martínez-Zapater JM,Carmona MJ Structural and functional annotation of the MADS-box transcription factor family in grapevine. BMC Genomics, 2016. 17: p. 80 [PMID:26818751] Soza VL,Snelson CD,Hewett Hazelton KD,Di Stilio VS Partial redundancy and functional specialization of E-class SEPALLATA genes in an early-diverging eudicot. Dev. Biol., 2016. 419(1): p. 143-155 [PMID:27502434] Conn VM, et al. A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Nat Plants, 2017. 3: p. 17053 [PMID:28418376] Käppel S,Melzer R,Rümpler F,Gafert C,Theißen G The floral homeotic protein SEPALLATA3 recognizes target DNA sequences by shape readout involving a conserved arginine residue in the MADS-domain. Plant J., 2018. 95(2): p. 341-357 [PMID:29744943] Buchner P,Boutin JP A MADS box transcription factor of the AP1/AGL9 subfamily is also expressed in the seed coat of pea (Pisum sativum) during development. Plant Mol. Biol., 1998. 38(6): p. 1253-5 [PMID:9869431]