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.8KG132000.1.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: 60aa MW: 6652.79 Da PI: 10.6864

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.8KG132000.1.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	79.2	2.8e-25	3	50	4	51
-SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 4 enksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 e+ rqv fskRr+g+lKKA+ELS LCdaeva+++fs+ g+lyey+s Pavir.8KG132000.1.p 3 EDRASRQVRFSKRRAGLLKKAFELSLLCDAEVALLVFSPAGRLYEYAS 50 78899*****************************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	4.2E-21	1	51	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	24.123	1	52	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	7.46E-22	2	52	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.2E-23	3	48	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.3E-17	14	29	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.3E-17	29	50	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: 60 aa Download sequence Send to blast
MAEDRASRQV RFSKRRAGLL KKAFELSLLC DAEVALLVFS PAGRLYEYAS ARFVRPPPP*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1tqe_P	1e-16	4	51	13	60	Myocyte-specific enhancer factor 2B
1tqe_Q	1e-16	4	51	13	60	Myocyte-specific enhancer factor 2B
1tqe_R	1e-16	4	51	13	60	Myocyte-specific enhancer factor 2B
1tqe_S	1e-16	4	51	13	60	Myocyte-specific enhancer factor 2B
6c9l_A	1e-16	4	51	13	60	Myocyte-specific enhancer factor 2B
6c9l_B	1e-16	4	51	13	60	Myocyte-specific enhancer factor 2B
6c9l_C	1e-16	4	51	13	60	Myocyte-specific enhancer factor 2B
6c9l_D	1e-16	4	51	13	60	Myocyte-specific enhancer factor 2B
6c9l_E	1e-16	4	51	13	60	Myocyte-specific enhancer factor 2B
6c9l_F	1e-16	4	51	13	60	Myocyte-specific enhancer factor 2B
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.575	2e-44	callus\| leaf\| root

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.8KG132000.1.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	KF184819	2e-62	KF184819.1 Saccharum hybrid cultivar R570 clone BAC 004J16 complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_024315790.1	2e-24	MADS-box transcription factor 51 isoform X1
Swissprot	Q9XJ61	2e-23	MAD51_ORYSJ; MADS-box transcription factor 51
TrEMBL	A0A1D6N2V4	1e-24	A0A1D6N2V4_MAIZE; MADS-box transcription factor 56
TrEMBL	A0A3L6FKB5	1e-24	A0A3L6FKB5_MAIZE; MADS-box transcription factor 51
TrEMBL	A0A3L6SPM4	2e-24	A0A3L6SPM4_PANMI; MADS-box transcription factor
STRING	Pavir.J08622.1.p	2e-27	(Panicum virgatum)

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	4e-21	AGAMOUS-like 20

Link Out ? help Back to Top
Phytozome	Pavir.8KG132000.1.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]