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

GSBRNA2T00137434001

Common Name

GSBRNA2T00137434001, LOC106439533

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

Protein Properties

Length: 330aa MW: 38058.1 Da PI: 9.4459

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00137434001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	53.6	4.1e-17	5	96	1	96
EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS B3 1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 ff +l+ s++ +++rl++p kf+++++ + s+ + l+ ++g +W+v l+ + +++++++GW+eFv+ ++ g ++F+++g+s f GSBRNA2T00137434001 5 FFHKLIFSSTIQEKRLRVPDKFVSRFKDE--LSVAVALTVPDGHVWRVGLRKADNNNKIWFQDGWQEFVDRYSIRIGYLLIFRYEGNSAF-- 92 899999***************999755..99*************88888888**************************9999.. PP EEEE CS B3 93 vvkv 96 v + GSBRNA2T00137434001 93 SVCI 96 5544 PP
2	B3	54.4	2.3e-17	232	324	1	98
EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 f vl ps+ + ++++lp fae++ +g++ + +++ ++ ++W v++ k gr +++GW eF +n+L egD++vF+l ++++ GSBRNA2T00137434001 232 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKV---QLGEKQWPVRC--LYKAGRAKFSQGWYEFTVENNLGEGDVCVFELLRTRD 315 677899******************84442.43344...4677***..666666779*******************999 PP E..EEEEE- CS B3 90 felvvkvfr 98 f l+v+++r GSBRNA2T00137434001 316 FVLKVTAYR 324 *99998877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	3.9E-21	3	98	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	2.55E-21	3	107	IPR015300	DNA-binding pseudobarrel domain
Pfam	PF02362	1.4E-14	5	96	IPR003340	B3 DNA binding domain
CDD	cd10017	1.21E-20	5	98	No hit	No description
PROSITE profile	PS50863	14.367	5	100	IPR003340	B3 DNA binding domain
SMART	SM01019	7.6E-16	5	100	IPR003340	B3 DNA binding domain
Gene3D	G3DSA:2.40.330.10	6.3E-23	224	324	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	4.32E-22	225	326	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.76E-20	230	324	No hit	No description
PROSITE profile	PS50863	12.534	232	326	IPR003340	B3 DNA binding domain
Pfam	PF02362	9.7E-16	232	324	IPR003340	B3 DNA binding domain
SMART	SM01019	3.5E-21	232	326	IPR003340	B3 DNA binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 330 aa Download sequence Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVSRF KDELSVAVAL TVPDGHVWRV GLRKADNNNK 60 IWFQDGWQEF VDRYSIRIGY LLIFRYEGNS AFSVCIYNLP QSEINYHSTG LMDSASHNNH 120 FKRPRLFEDL EDEDAETLHT TASAIQSFFT GPVKPEEATP TQTSKVPKKR GRKKKNADHP 180 EEVNSSAPRD DDPESRSKFY ESASARKRTV NAEERERAVN AAKTFEPTNP FFRVVLRPSY 240 LYRGCIMYLP SGFAEKYLSG ISGFIKVQLG EKQWPVRCLY KAGRAKFSQG WYEFTVENNL 300 GEGDVCVFEL LRTRDFVLKV TAYRVNEYV*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4i1k_A	3e-90	198	329	15	146	B3 domain-containing transcription factor VRN1
4i1k_B	3e-90	198	329	15	146	B3 domain-containing transcription factor VRN1
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots and at lower levels in aerial parts. {ECO:0000269\|PubMed:12114624}.

Functional Description ? help Back to Top
Source	Description
UniProt	Involved in the regulation of vernalization. Acts as transcriptional repressor of FLC, a major target of the vernalization pathway. Binds DNA in vitro in a non-sequence-specific manner. {ECO:0000269\|PubMed:12114624}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00137434001

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	AY517929	0.0	AY517929.1 Brassica rapa cultivar Kwonsim reduced vernalization response 1 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001288881.1	0.0	B3 domain-containing transcription factor VRN1-like
Refseq	XP_013736461.1	0.0	B3 domain-containing transcription factor VRN1
Swissprot	Q8L3W1	0.0	VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBL	Q6R2U8	0.0	Q6R2U8_BRACM; Reduced vernalization response 1
STRING	Bo3g071890.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1124	28	103

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G18990.1	0.0	B3 family protein

Link Out ? help Back to Top
Entrez Gene	106439533

Publications ? help Back to Top
Mantegazza O, et al. Analysis of the arabidopsis REM gene family predicts functions during flower development. Ann. Bot., 2014. 114(7): p. 1507-15 [PMID:25002525] 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] Kumar A,Singh A,Panigrahy M,Sahoo PK,Panigrahi KCS Carbon nanoparticles influence photomorphogenesis and flowering time in Arabidopsis thaliana. Plant Cell Rep., 2018. 37(6): p. 901-912 [PMID:29541883]