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.5NG509100.1.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: 308aa MW: 33006.7 Da PI: 8.5842

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.5NG509100.1.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	25.3	2.7e-08	1	18	10	27
GGTS--TTTTT-SS-SSS CS zf-CCCH 10 artGtCkyGdrCkFaHgp 27 ++tG+Ck+G++CkF+H++ Pavir.5NG509100.1.p 1 MKTGHCKFGGTCKFHHPE 18 89**************96 PP
2	zf-CCCH	39.6	8.9e-13	146	172	1	27
--S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 1 yktelCrffartGtCkyGdrCkFaHgp 27 +++++C ++++tG CkyG+ Ck++H++ Pavir.5NG509100.1.p 146 PGQPECEHYMKTGACKYGAACKYHHPQ 172 5789*********************97 PP
3	zf-CCCH	33.7	6.4e-11	194	218	3	27
S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 3 telCrffartGtCkyGdrCkFaHgp 27 +C ++a+ G+Ck+G++CkF H++ Pavir.5NG509100.1.p 194 SQPCTYYAQHGFCKFGPTCKFDHPM 218 679********************95 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	10.887	1	19	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	44	1	18	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	8.3E-6	1	18	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	14.53	145	173	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.3E-6	145	172	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.5E-10	147	172	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.22E-5	149	172	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	4.6E-4	151	170	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.178	191	219	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.5E-6	191	218	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.31E-6	193	222	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.3E-8	193	218	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	3.8E-5	195	216	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: 308 aa Download sequence Send to blast
MKTGHCKFGG TCKFHHPELG ILSETPTMYP PVQPSPVSSP HPYPHLANWQ MGRLPVVPGS 60 FLPGSYPPMM LPPTLMPMQG WNPYISPMNQ VAPAGGQQTI QPGPPYGLSH QGPTSAVTYG 120 SHYAQLYSSA GTSSSNIQEY ALPERPGQPE CEHYMKTGAC KYGAACKYHH PQYFSGPKSN 180 CALSPLGLPL RPGSQPCTYY AQHGFCKFGP TCKFDHPMGT LNYSPSVSSL TDVPVTPYPL 240 TFPVTPMAPY LSSSDLRPQY TLTKEHSANP PAVPGTTYGP VGTISKVYAP HTLIRPLNAT 300 AAGMQAS*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.749	1e-135	callus\| root\| stem

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.5NG509100.1.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_025815660.1	0.0	uncharacterized protein LOC112892755
Swissprot	Q5NAV3	1e-158	C3H5_ORYSJ; Zinc finger CCCH domain-containing protein 5
TrEMBL	A0A3L6R430	0.0	A0A3L6R430_PANMI; Zinc finger CCCH domain-containing protein 5-like
STRING	Pavir.Eb00943.1.p	0.0	(Panicum virgatum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP2761	38	89

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G47850.3	2e-48	C3H family protein

Link Out ? help Back to Top
Phytozome	Pavir.5NG509100.1.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]