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

XP_009143827.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica

Family

C3H

Protein Properties

Length: 624aa MW: 68246.1 Da PI: 7.2695

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009143827.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	21.8	3.3e-07	152	172	5	26
--SGGGGTS--TTTTT-SS-SS CS zf-CCCH 5 lCrffartGtCkyGdrCkFaHg 26 +C+ffa+ G C G++C+F H+ XP_009143827.1 152 PCKFFAQ-GRCTKGNSCRFLHV 172 7****.***********6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF90229	1.88E-6	147	171	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.0043	147	173	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.76	147	174	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	3.4E-5	152	173	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.2E-4	152	172	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010220	Biological Process	positive regulation of vernalization response
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 624 aa Download sequence Send to blast
MSDSDMDIDD DEVQVNVQHT IAGESRLLAR PIEASNSQND VKKHLDEQLK IINGNLQPNL 60 SGNSGNNLFL EGEKGIILPS LRLPAPGQSY PLVNGPGQSK IINGYVQPNL SGSSGKKLML 120 EGEKDTVLSR FPAPVQSLPP ANGPEQKRPA YPCKFFAQGR CTKGNSCRFL HVNENMNRTS 180 QQQVVNNMAG TSGIQSIEER RPLESKEGIR FPMLSTNGVT SLVNPPAGQR VFPFTNEMRF 240 MPPLENMGRG SLQKCGAVFT ENRPVFGNST SSFPLRSSFV QEYGSFITSN RQTDMGSSGP 300 AWTGSVFSSA PLNQYASPFG NFENRNDING SESLPMEQAL SVPSVQDAEV DTTSDTKEVS 360 SNDWEPSEPF RPSFTIPPYI LPSSDALYDP FTDIENPEDR SPKAQSSTKG KDAQKKPGQQ 420 KDGDSASNDK NSSCSQNQFQ ETVVRKNLEA HGVVEGVATS VVDQNDASAT TPSKEISSSA 480 AVENRVVLKR SKPAGHESWH RSDGSSHQKK LKTDDMDGEV RSDAGTKVMR QFRTAVVETI 540 KDMLKPLWRE GRLSKDVHNM IVKRATEKIV SAAVQLHQVP TNSESVEKYL SMSSTRIVKL 600 VEGYVEKYGK PQSKPSGIIK SKAS

Sequence ? help Back to Top

Protein Sequence Length: 624 aa Download sequence Send to blast

MSDSDMDIDD DEVQVNVQHT IAGESRLLAR PIEASNSQND VKKHLDEQLK IINGNLQPNL  60
SGNSGNNLFL EGEKGIILPS LRLPAPGQSY PLVNGPGQSK IINGYVQPNL SGSSGKKLML  120
EGEKDTVLSR FPAPVQSLPP ANGPEQKRPA YPCKFFAQGR CTKGNSCRFL HVNENMNRTS  180
QQQVVNNMAG TSGIQSIEER RPLESKEGIR FPMLSTNGVT SLVNPPAGQR VFPFTNEMRF  240
MPPLENMGRG SLQKCGAVFT ENRPVFGNST SSFPLRSSFV QEYGSFITSN RQTDMGSSGP  300
AWTGSVFSSA PLNQYASPFG NFENRNDING SESLPMEQAL SVPSVQDAEV DTTSDTKEVS  360
SNDWEPSEPF RPSFTIPPYI LPSSDALYDP FTDIENPEDR SPKAQSSTKG KDAQKKPGQQ  420
KDGDSASNDK NSSCSQNQFQ ETVVRKNLEA HGVVEGVATS VVDQNDASAT TPSKEISSSA  480
AVENRVVLKR SKPAGHESWH RSDGSSHQKK LKTDDMDGEV RSDAGTKVMR QFRTAVVETI  540
KDMLKPLWRE GRLSKDVHNM IVKRATEKIV SAAVQLHQVP TNSESVEKYL SMSSTRIVKL  600
VEGYVEKYGK PQSKPSGIIK SKAS

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bra.18218	0.0	leaf

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in root and shoot apices and vasculature. {ECO:0000269\|PubMed:16291783}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional activator involved in the FRIGIDA-mediated vernalization pathway, but not in the autonomous flowering pathway. Acts cooperatively with FRI (FRIGIDA) or FRL1 (FRIGIDA-LIKE 1) to promote FLC (FLOWERING LOCUS C) expression. Required for the stabilization of the FRI-C complex. {ECO:0000269\|PubMed:16291783, ECO:0000269\|PubMed:21282526}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009143827.1

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_009143827.1	0.0	PREDICTED: protein FRIGIDA-ESSENTIAL 1
Swissprot	Q84VG7	0.0	FES1_ARATH; Protein FRIGIDA-ESSENTIAL 1
TrEMBL	M4CMN0	0.0	M4CMN0_BRARP; Uncharacterized protein
STRING	Bra005468.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM13468	15	21

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33835.1	0.0	C3H family protein

Publications ? help Back to Top
Ding L,Kim SY,Michaels SD FLOWERING LOCUS C EXPRESSOR family proteins regulate FLOWERING LOCUS C expression in both winter-annual and rapid-cycling Arabidopsis. Plant Physiol., 2013. 163(1): p. 243-52 [PMID:23899645]