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

Pavir.4NG331800.2.p

Organism

Panicum virgatum

Taxonomic ID

38727

Taxonomic Lineage

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

Family

MIKC_MADS

Protein Properties

Length: 193aa MW: 22439.8 Da PI: 9.9919

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.4NG331800.2.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	90.9	6.3e-29	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien +nrqvt+skRr+gi+KKA EL vLCda+va+i+fsstgk +e++s Pavir.4NG331800.2.p 9 KRIENATNRQVTYSKRRTGIMKKARELTVLCDAQVAIIMFSSTGKYHEFCS 59 79***********************************************96 PP
2	K-box	86.1	6.9e-29	71	159	1	89
K-box 1 yqkssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqe 89 yq++ g+sl+ +++e++q+ l+ Lk+ ++nL++e+R+++GedL+sL++ eL+ Leq+++++lk++R +K++++ +q+e+ +kk +++ Pavir.4NG331800.2.p 71 YQQAIGTSLWVEQYENMQRTLSHLKDINRNLRTEIRQRMGEDLDSLEFDELRGLEQNVDTALKEVRHRKYHVISTQTETYKKKVIRIKT 159 67888999***************************************************************************988775 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	2.6E-42	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	32.59	1	61	IPR002100	Transcription factor, MADS-box
CDD	cd00265	2.17E-41	2	80	No hit	No description
SuperFamily	SSF55455	1.31E-36	2	95	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.6E-28	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	2.2E-24	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.6E-28	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.6E-28	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	2.3E-20	82	156	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	13.328	84	172	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:0010093	Biological Process	specification of floral organ identity
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

Sequence ? help Back to Top
Protein Sequence Length: 193 aa Download sequence Send to blast
MGRGKIEIKR IENATNRQVT YSKRRTGIMK KARELTVLCD AQVAIIMFSS TGKYHEFCSP 60 GTDIKTIFDR YQQAIGTSLW VEQYENMQRT LSHLKDINRN LRTEIRQRMG EDLDSLEFDE 120 LRGLEQNVDT ALKEVRHRKY HVISTQTETY KKKVIRIKTS IFQYHHVIPH TLLCIDLLVH 180 FPSQLGNASL KS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	2e-17	1	73	1	71	MEF2C
5f28_B	2e-17	1	73	1	71	MEF2C
5f28_C	2e-17	1	73	1	71	MEF2C
5f28_D	2e-17	1	73	1	71	MEF2C
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in lodicules, stamens and carpels. {ECO:0000269\|PubMed:10394955, ECO:0000269\|PubMed:12506001, ECO:0000269\|PubMed:12905025, ECO:0000269\|PubMed:14558657}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in the development of floral organs. Required for normal development of lodicules and stamens (whorls 2 and 3). May function as a heterodimer with MADS4. {ECO:0000269\|PubMed:12506001, ECO:0000269\|PubMed:12905025, ECO:0000269\|PubMed:14558657}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00077	ChIP-seq	Transfer from AT3G54340	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.4NG331800.2.p

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT018998	0.0	BT018998.1 Zea mays clone Contig486.F mRNA sequence.
GenBank	BT039988	0.0	BT039988.1 Zea mays full-length cDNA clone ZM_BFc0056L03 mRNA, complete cds.
GenBank	EU965657	0.0	EU965657.1 Zea mays clone 287776 MADS-box transcription factor 16 mRNA, complete cds.
GenBank	EU966237	0.0	EU966237.1 Zea mays clone 292756 MADS-box transcription factor 16 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004966424.1	1e-109	MADS-box transcription factor 16
Refseq	XP_025812646.1	1e-109	MADS-box transcription factor 16
Swissprot	Q944S9	1e-107	MAD16_ORYSJ; MADS-box transcription factor 16
TrEMBL	A0A2S3HGN1	1e-108	A0A2S3HGN1_9POAL; Uncharacterized protein
TrEMBL	A0A2T7DU70	1e-108	A0A2T7DU70_9POAL; Uncharacterized protein
TrEMBL	K3XZ63	1e-107	K3XZ63_SETIT; Uncharacterized protein
STRING	Pavir.Db00185.1.p	1e-109	(Panicum virgatum)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G54340.1	2e-57	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	Pavir.4NG331800.2.p

Publications ? help Back to Top
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] Chen ZX, et al. Morphogenesis and molecular basis on naked seed rice, a novel homeotic mutation of OsMADS1 regulating transcript level of AP3 homologue in rice. Planta, 2006. 223(5): p. 882-90 [PMID:16254725] Zhang Q, et al. Morphological, anatomical and genetic analysis for a rice mutant with abnormal hull. J Genet Genomics, 2007. 34(6): p. 519-26 [PMID:17601611] 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] Xiao H, et al. STAMENLESS 1, encoding a single C2H2 zinc finger protein, regulates floral organ identity in rice. Plant J., 2009. 59(5): p. 789-801 [PMID:19453444] 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] Li H, et al. Rice MADS6 interacts with the floral homeotic genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in specifying floral organ identities and meristem fate. Plant Cell, 2011. 23(7): p. 2536-52 [PMID:21784949] Sato H,Yoshida K,Mitsuda N,Ohme-Takagi M,Takamizo T Male-sterile and cleistogamous phenotypes in tall fescue induced by chimeric repressors of SUPERWOMAN1 and OsMADS58. Plant Sci., 2012. 183: p. 183-9 [PMID:22195592] Ohmori S,Tabuchi H,Yatou O,Yoshida H Agronomic traits and gene containment capability of cleistogamous rice lines with the superwoman1-cleistogamy mutation. Breed. Sci., 2012. 62(2): p. 124-32 [PMID:23136523] Yun D, et al. OsMADS16 genetically interacts with OsMADS3 and OsMADS58 in specifying floral patterning in rice. Mol Plant, 2013. 6(3): p. 743-56 [PMID:23300256] Lombardo F, et al. The superwoman1-cleistogamy2 mutant is a novel resource for gene containment in rice. Plant Biotechnol. J., 2017. 15(1): p. 97-106 [PMID:27336225]