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

GSBRNA2T00038832001

Common Name

GSBRNA2T00038832001

Organism

Brassica napus

Taxonomic ID

3708

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: 690aa MW: 75439.6 Da PI: 8.2095

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00038832001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	21.7	3.7e-07	152	172	5	26
--SGGGGTS--TTTTT-SS-SS CS zf-CCCH 5 lCrffartGtCkyGdrCkFaHg 26 +C+ffa+ G C G++C+F H+ GSBRNA2T00038832001 152 PCKFFAQ-GRCTKGNSCRFLHV 172 7****.***********6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00356	0.0043	147	173	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	2.04E-6	147	171	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.76	147	174	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	3.8E-5	152	173	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.3E-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: 690 aa Download sequence Send to blast
MSDSDMDIDD DEVQVQVQPT AAGESRLLAR PIEASNSQND VKKHSDEQLK IINGNLQPNL 60 SGNSGKNPIL EGEKGTILPS LRFPAPGQSF PLVNGPEQSK IINGYLQPNL SGSSGKKLML 120 EGEKDTVLSR FPAPMQTLPP ANGPEQKRPA YPCKFFAQGR CTKGNSCRFL HVNENMNRTS 180 QQQVVNNMAG TSGIQSIEER RPLESKEGVR FSMLSTNGVT SLVNPPAGQR VFPFTNEMRF 240 MPSLENMGRG SLQKCGAVFT ENRPVFGNST SSFPLRSSFV QEHGSFITSN RQTDMGSSGP 300 AWTGSVFSSA PLNQYASPFG NFENRNDINE SGSLPMEQAL SVPSVQDAEV DTTSDKKEVS 360 SNDWEPSEPF RPSFTIPPYI LPSSDALYDP FMDIENPEGR SPKAQSSTKG KDAQKKSGQQ 420 KDGDSASNDK NSSCSQNQFQ ETVVRKKLET HGLVEGVATS VVDQNDASAT TPSKEISSSA 480 AVENRAVLKR SKPAGHGSWH RSDGSSHQKK LKTDEMDGEV RSDAGTKVMR QFRTAVVETI 540 KDMLKPLWRE GRLSKDVHNM IVKRATEKIV SAAVQLHQVP TNNESVEKYL SMSSTRIVKL 600 VEGYVEKFGK PQSKPSGLAP IFLHLHSYPF TNNGRRLELE LCRGILCLFG IASEAGEGGN 660 RKKRNSVEGT LSNILTMFLC LRTIQIVSD*

Sequence ? help Back to Top

Protein Sequence Length: 690 aa Download sequence Send to blast

MSDSDMDIDD DEVQVQVQPT AAGESRLLAR PIEASNSQND VKKHSDEQLK IINGNLQPNL  60
SGNSGKNPIL EGEKGTILPS LRFPAPGQSF PLVNGPEQSK IINGYLQPNL SGSSGKKLML  120
EGEKDTVLSR FPAPMQTLPP ANGPEQKRPA YPCKFFAQGR CTKGNSCRFL HVNENMNRTS  180
QQQVVNNMAG TSGIQSIEER RPLESKEGVR FSMLSTNGVT SLVNPPAGQR VFPFTNEMRF  240
MPSLENMGRG SLQKCGAVFT ENRPVFGNST SSFPLRSSFV QEHGSFITSN RQTDMGSSGP  300
AWTGSVFSSA PLNQYASPFG NFENRNDINE SGSLPMEQAL SVPSVQDAEV DTTSDKKEVS  360
SNDWEPSEPF RPSFTIPPYI LPSSDALYDP FMDIENPEGR SPKAQSSTKG KDAQKKSGQQ  420
KDGDSASNDK NSSCSQNQFQ ETVVRKKLET HGLVEGVATS VVDQNDASAT TPSKEISSSA  480
AVENRAVLKR SKPAGHGSWH RSDGSSHQKK LKTDEMDGEV RSDAGTKVMR QFRTAVVETI  540
KDMLKPLWRE GRLSKDVHNM IVKRATEKIV SAAVQLHQVP TNNESVEKYL SMSSTRIVKL  600
VEGYVEKFGK PQSKPSGLAP IFLHLHSYPF TNNGRRLELE LCRGILCLFG IASEAGEGGN  660
RKKRNSVEGT LSNILTMFLC LRTIQIVSD*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bna.10643	8e-71	microspore-derived embryo

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	GSBRNA2T00038832001

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_013748521.1	0.0	protein FRIGIDA-ESSENTIAL 1-like isoform X1
Swissprot	Q84VG7	0.0	FES1_ARATH; Protein FRIGIDA-ESSENTIAL 1
TrEMBL	A0A078GS05	0.0	A0A078GS05_BRANA; BnaCnng05170D protein
STRING	Bo4g042370.1	0.0	(Brassica oleracea)

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] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293]