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.5KG175400.1.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: 100aa MW: 11362.9 Da PI: 10.0536

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.5KG175400.1.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	99.2	1.7e-31	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien++ rqvtf+kRrng+lKKA+ELSvLCdaeva+i+fss+g+lyeys+ Pavir.5KG175400.1.p 9 KRIENNTSRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYSN 59 79***********************************************95 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	32.828	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	1.5E-39	1	60	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.29E-37	2	64	No hit	No description
SuperFamily	SSF55455	3.14E-30	2	79	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.9E-32	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	2.3E-27	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.9E-32	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.9E-32	38	59	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: 100 aa Download sequence Send to blast
MGRARIEIKR IENNTSRQVT FCKRRNGLLK KAYELSVLCD AEVALIVFSS RGRLYEYSNN 60 RSQGRPWICC YQQRSSNTRS DKPSVAIGGN DYQASCQLH*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1tqe_P	4e-20	1	60	1	60	Myocyte-specific enhancer factor 2B
1tqe_Q	4e-20	1	60	1	60	Myocyte-specific enhancer factor 2B
1tqe_R	4e-20	1	60	1	60	Myocyte-specific enhancer factor 2B
1tqe_S	4e-20	1	60	1	60	Myocyte-specific enhancer factor 2B
5f28_A	5e-20	1	58	1	58	MEF2C
5f28_B	5e-20	1	58	1	58	MEF2C
5f28_C	5e-20	1	58	1	58	MEF2C
5f28_D	5e-20	1	58	1	58	MEF2C
6c9l_A	4e-20	1	60	1	60	Myocyte-specific enhancer factor 2B
6c9l_B	4e-20	1	60	1	60	Myocyte-specific enhancer factor 2B
6c9l_C	4e-20	1	60	1	60	Myocyte-specific enhancer factor 2B
6c9l_D	4e-20	1	60	1	60	Myocyte-specific enhancer factor 2B
6c9l_E	4e-20	1	60	1	60	Myocyte-specific enhancer factor 2B
6c9l_F	4e-20	1	60	1	60	Myocyte-specific enhancer factor 2B
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in developing seeds. {ECO:0000269\|PubMed:14701936}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.5KG175400.1.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	X81199	5e-67	X81199.1 Zea mays ZMM1 gene.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025817347.1	1e-35	MADS-box transcription factor 21-like
Swissprot	Q8RU31	4e-35	MAD21_ORYSJ; MADS-box transcription factor 21
TrEMBL	A0A1E5WD87	6e-35	A0A1E5WD87_9POAL; MADS-box transcription factor 21
STRING	Pavir.Ea01147.1.p	5e-68	(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
AT4G09960.2	1e-35	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	Pavir.5KG175400.1.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] Dreni L, et al. The D-lineage MADS-box gene OsMADS13 controls ovule identity in rice. Plant J., 2007. 52(4): p. 690-9 [PMID:17877710]