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.6NG327900.2.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

M-type_MADS

Protein Properties

Length: 135aa MW: 15375.7 Da PI: 10.3984

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.6NG327900.2.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	87.8	5.8e-28	39	88	2	51
---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 rie+ + rqv fskRr g++KKA+ELSvLCda+va+i+fs+ g+lye++s Pavir.6NG327900.2.p 39 RIEDRTSRQVRFSKRRSGLFKKAYELSVLCDAQVALIVFSPAGRLYEFAS 88 8***********************************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	30.305	30	90	IPR002100	Transcription factor, MADS-box
SMART	SM00432	6.8E-35	30	89	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.5E-29	32	52	IPR002100	Transcription factor, MADS-box
CDD	cd00265	3.30E-34	32	94	No hit	No description
SuperFamily	SSF55455	7.19E-28	32	102	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	5.3E-27	39	86	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.5E-29	52	67	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.5E-29	67	88	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: 135 aa Download sequence Send to blast
MEEREEATTA RRAELQLLQQ LDKEEIKGKR KRGRVELRRI EDRTSRQVRF SKRRSGLFKK 60 AYELSVLCDA QVALIVFSPA GRLYEFASSG SRGMEANAEE MSMTEIRNLE ETVTDALAAI 120 RNKLRMKVVG LPQT*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1n6j_A	4e-18	32	89	2	59	Myocyte-specific enhancer factor 2B
1n6j_B	4e-18	32	89	2	59	Myocyte-specific enhancer factor 2B
1tqe_P	3e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
1tqe_Q	3e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
1tqe_R	3e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
1tqe_S	3e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_A	3e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_B	3e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_C	3e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_D	3e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_E	3e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_F	3e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.18053	1e-34	leaf\| stem

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Widely expressed. {ECO:0000269\|PubMed:10382970}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in the regulation of flowering time under short day (SD) conditions. Functions as promoter of flowering under SD conditions, upstream of EHD1, HD3A and MADS14, but downstream of GIGANTEA (GI). May transmit a SD promotion signal from GI to EHD1. Functions independently of MADS50 to control flowering time. {ECO:0000269\|PubMed:17951465}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.6NG327900.2.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	AP005529	2e-66	AP005529.3 Oryza sativa Japonica Group genomic DNA, chromosome 8, PAC clone:P0702E04.
GenBank	AP014964	2e-66	AP014964.1 Oryza sativa Japonica Group DNA, chromosome 8, cultivar: Nipponbare, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025820080.1	2e-57	MADS-box transcription factor 51-like isoform X1
Refseq	XP_025820081.1	2e-57	MADS-box transcription factor 51-like isoform X1
Swissprot	Q9XJ61	2e-28	MAD51_ORYSJ; MADS-box transcription factor 51
TrEMBL	A0A3L6PT54	2e-68	A0A3L6PT54_PANMI; MADS-box transcription factor 56-like
STRING	Pavir.J26790.1.p	5e-58	(Panicum virgatum)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G11880.1	1e-25	AGAMOUS-like 14

Link Out ? help Back to Top
Phytozome	Pavir.6NG327900.2.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] Kim SL,Lee S,Kim HJ,Nam HG,An G OsMADS51 is a short-day flowering promoter that functions upstream of Ehd1, OsMADS14, and Hd3a. Plant Physiol., 2007. 145(4): p. 1484-94 [PMID:17951465]