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.5KG053700.1.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

C3H

Protein Properties

Length: 382aa MW: 40386.1 Da PI: 7.1971

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.5KG053700.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	26.7	9.8e-09	122	142	5	26
--SGGGGTS--TTTTT-SS-SS CS zf-CCCH 5 lCrffartGtCkyGdrCkFaHg 26 C++f++ G Ck+Gd C FaHg Pavir.5KG053700.1.p 122 ACPDFRK-GGCKRGDACEFAHG 142 7****.***********9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00356	2.3E-5	117	143	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.159	118	144	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	5.5E-6	121	144	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	7.2E-7	122	142	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	12	152	175	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	6.258	152	176	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 382 aa Download sequence Send to blast
MMMMGEGVSV PPWSHHLPVS GVDVGGGTTG GDEMTPYLLS ALHQYLPCND AGAGADDDEA 60 AAAAAMAAGV DGYGSDEFRM YEFKVRRCAR ARSHDWTECP FAHPGEKARR RDPRKYHYSG 120 TACPDFRKGG CKRGDACEFA HGVFECWLHP ARYRTQPCKD GTACRRRVCF FAHTPDQLRV 180 LPAQQSSPRG AAAAASPLAE SYDGSPLRRQ AFESYLTKSI MSSSPTSTLM SPPKSPPSES 240 PPLSPDGAAA AFRRGSWPGV GSPVNEVLAS LRQLRLSKAN SSPAGGWSGY PSSAVAYGSP 300 TATGLYSLPS TPTTMGGYMA NLEPLDVSFG GGDEEPVQRV ESGRALRAKV FERLSREGAV 360 SGDATAAIGG PDVGWVSDLI N*

Sequence ? help Back to Top

Protein Sequence Length: 382 aa Download sequence Send to blast

MMMMGEGVSV PPWSHHLPVS GVDVGGGTTG GDEMTPYLLS ALHQYLPCND AGAGADDDEA  60
AAAAAMAAGV DGYGSDEFRM YEFKVRRCAR ARSHDWTECP FAHPGEKARR RDPRKYHYSG  120
TACPDFRKGG CKRGDACEFA HGVFECWLHP ARYRTQPCKD GTACRRRVCF FAHTPDQLRV  180
LPAQQSSPRG AAAAASPLAE SYDGSPLRRQ AFESYLTKSI MSSSPTSTLM SPPKSPPSES  240
PPLSPDGAAA AFRRGSWPGV GSPVNEVLAS LRQLRLSKAN SSPAGGWSGY PSSAVAYGSP  300
TATGLYSLPS TPTTMGGYMA NLEPLDVSFG GGDEEPVQRV ESGRALRAKV FERLSREGAV  360
SGDATAAIGG PDVGWVSDLI N*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.7586	0.0	callus\| root\| stem

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in leaf and panicles, but is down-regulated during natural leaf senescence, panicle development and pollination. {ECO:0000269\|PubMed:16778011}.

Functional Description ? help Back to Top
Source	Description
UniProt	Involved in leaf senescence delay. May repress jasmonic acid (JA) signaling role in promoting leaf senescence. May regulate panicle development and pollination/fertilization process. {ECO:0000269\|PubMed:16778011}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.5KG053700.1.p

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025817903.1	0.0	zinc finger CCCH domain-containing protein 2-like
Swissprot	Q9FU27	0.0	C3H2_ORYSJ; Zinc finger CCCH domain-containing protein 2
TrEMBL	A0A2S3HYP5	0.0	A0A2S3HYP5_9POAL; Uncharacterized protein
STRING	Pavir.Eb00253.1.p	0.0	(Panicum virgatum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP1578	34	93

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G19810.1	2e-87	C3H family protein

Link Out ? help Back to Top
Phytozome	Pavir.5KG053700.1.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] Mebel AM,Kislov VV,Hayashi M Prediction of product branching ratios in the C(3P)+C2H2-->l-C3H+H/c-C3H+H/C3+H2 reaction using ab initio coupled clusters calculations extrapolated to the complete basis set combined with Rice-Ramsperger-Kassel-Marcus and radiationless transition theories. J Chem Phys, 2007. 126(20): p. 204310 [PMID:17552765] Miyazawa T,Shibata A,Nakagawa K,Tsuzuki T Anti-angiogenic function of tocotrienol. Asia Pac J Clin Nutr, 2008. 17 Suppl 1: p. 253-6 [PMID:18296349]