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.J642900.1.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: 93aa MW: 10731.3 Da PI: 10.9025

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.J642900.1.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	89.1	2.4e-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.J642900.1.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
CDD	cd00265	1.18E-32	32	92	No hit	No description
SuperFamily	SSF55455	3.14E-27	32	90	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.8E-29	32	52	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	2.2E-27	39	86	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.8E-29	52	67	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.8E-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: 93 aa Download sequence Send to blast
MEEREEATTA RRAELQLLQQ LDKEEIKGKR KRGRVELRRI EDRTSRQVRF SKRRSGLFKK 60 AYELSVLCDA QVALIVFSPA GRLYEFASSG SR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1n6j_A	1e-18	32	89	2	59	Myocyte-specific enhancer factor 2B
1n6j_B	1e-18	32	89	2	59	Myocyte-specific enhancer factor 2B
1tqe_P	1e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
1tqe_Q	1e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
1tqe_R	1e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
1tqe_S	1e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_A	1e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_B	1e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_C	1e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_D	1e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_E	1e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
6c9l_F	1e-18	32	89	3	60	Myocyte-specific enhancer factor 2B
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Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor.
UniProt	Probable transcription factor.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.J642900.1.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	AP005529	4e-67	AP005529.3 Oryza sativa Japonica Group genomic DNA, chromosome 8, PAC clone:P0702E04.
GenBank	AP014964	4e-67	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	1e-38	MADS-box transcription factor 51-like isoform X1
Refseq	XP_025820081.1	1e-38	MADS-box transcription factor 51-like isoform X1
Swissprot	A2Z9Q7	2e-27	MAD56_ORYSI; MADS-box transcription factor 56
Swissprot	P0C5B2	2e-27	MAD56_ORYSJ; MADS-box transcription factor 56
TrEMBL	A0A3L6PT54	2e-48	A0A3L6PT54_PANMI; MADS-box transcription factor 56-like
STRING	Pavir.J26790.1.p	6e-58	(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
AT4G11880.1	4e-26	AGAMOUS-like 14

Link Out ? help Back to Top
Phytozome	Pavir.J642900.1.p

Publications ? help Back to Top
Rice Chromosome 10 Sequencing Consortium In-depth view of structure, activity, and evolution of rice chromosome 10. Science, 2003. 300(5625): p. 1566-9 [PMID:12791992] 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] Bai Z, et al. The impact and origin of copy number variations in the Oryza species. BMC Genomics, 2016. 17: p. 261 [PMID:27025496] 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] Han Z,Zhang B,Zhao H,Ayaad M,Xing Y Genome-Wide Association Studies Reveal that Diverse Heading Date Genes Respond to Short and Long Day Lengths between Indica and Japonica Rice. Front Plant Sci, 2016. 7: p. 1270 [PMID:27621738]