PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Crotonoideae; Jatropheae; Jatropha

Family

Protein Properties

Length: 391aa MW: 45199.3 Da PI: 8.1952

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Jcr4S04166.20	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	35.6	1.7e-11	5	86	11	98
HHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE- CS B3 11 lksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfr 98 k+ + ++p +f++++g++ s +l + g +W v l k ++++++ +GW+eF + ++ g f+vF+++g+ f +v++f+ Jcr4S04166.20 5 EKLYLQRIPDNFVRKFGND--LSAFGRLSVPGGPVWPVGL--IKADDKFWFHEGWQEFMERYSIRIGYFLVFRYEGHAVF--TVHIFN 86 5556668*******877..77788999*******..9*****************************998888..888885 PP
2	B3	58.8	9.9e-19	290	380	4	98
E-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE- CS B3 4 vltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfr 98 vl ps+ + ++++lp fae+h +g++ ++l+ ++g++W v++ yr+++ l++GW eF +n+L egD++vF+l ++++ l+v+vfr Jcr4S04166.20 290 VLRPSYLYRGCIMYLPSCFAEKHlQGVSG---FIKLQFSDGKQWPVRCLYRGGR--AKLSQGWYEFSLENNLGEGDVCVFELLRSRDIVLKVTVFR 380 78899****************977744...59999999****665555..66*********************999999999999997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50863	11.533	1	88	IPR003340	B3 DNA binding domain
SMART	SM01019	1.3E-6	4	88	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.4E-8	9	86	IPR003340	B3 DNA binding domain
SuperFamily	SSF101936	1.63E-17	9	87	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	4.2E-17	10	88	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.32E-12	11	86	No hit	No description
Gene3D	G3DSA:2.40.330.10	7.4E-24	280	380	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	4.05E-24	281	380	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.87E-21	285	380	No hit	No description
SMART	SM01019	7.5E-18	287	382	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.479	287	382	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.1E-16	290	380	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:0009909	Biological Process	regulation of flower development
GO:0010048	Biological Process	vernalization response
GO:0005654	Cellular Component	nucleoplasm
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 391 aa Download sequence Send to blast
MEYNEKLYLQ RIPDNFVRKF GNDLSAFGRL SVPGGPVWPV GLIKADDKFW FHEGWQEFME 60 RYSIRIGYFL VFRYEGHAVF TVHIFNLSAS EINYQSNALS GRRYLVFEEM EDDDFIEHLS 120 SSSPCLIPNS LKSKVFDERL DQMTIKKSCN PPALQNLFHE SKLNYINWSG EGNLHLSKGA 180 SISHMVDQDT RDVGVQFNAI EGKNCIEDVK FYSPDGVGEM QKPKKQGRKK RKLDPNEQHP 240 SSQQEDEADV RFRFYESASA RKRTVTAEER ERAINAAKTF EPVNPFCRVV LRPSYLYRGC 300 IMYLPSCFAE KHLQGVSGFI KLQFSDGKQW PVRCLYRGGR AKLSQGWYEF SLENNLGEGD 360 VCVFELLRSR DIVLKVTVFR VLENAGRMNR P

Sequence ? help Back to Top

Protein Sequence Length: 391 aa Download sequence Send to blast

MEYNEKLYLQ RIPDNFVRKF GNDLSAFGRL SVPGGPVWPV GLIKADDKFW FHEGWQEFME  60
RYSIRIGYFL VFRYEGHAVF TVHIFNLSAS EINYQSNALS GRRYLVFEEM EDDDFIEHLS  120
SSSPCLIPNS LKSKVFDERL DQMTIKKSCN PPALQNLFHE SKLNYINWSG EGNLHLSKGA  180
SISHMVDQDT RDVGVQFNAI EGKNCIEDVK FYSPDGVGEM QKPKKQGRKK RKLDPNEQHP  240
SSQQEDEADV RFRFYESASA RKRTVTAEER ERAINAAKTF EPVNPFCRVV LRPSYLYRGC  300
IMYLPSCFAE KHLQGVSGFI KLQFSDGKQW PVRCLYRGGR AKLSQGWYEF SLENNLGEGD  360
VCVFELLRSR DIVLKVTVFR VLENAGRMNR P

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4i1k_A	3e-75	253	383	15	144	B3 domain-containing transcription factor VRN1
4i1k_B	3e-75	253	383	15	144	B3 domain-containing transcription factor VRN1
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	222	231	PKKQGRKKRK

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}.

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_012069205.1	0.0	B3 domain-containing transcription factor VRN1 isoform X1
Swissprot	Q8L3W1	1e-122	VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBL	A0A067LCQ1	0.0	A0A067LCQ1_JATCU; Uncharacterized protein
STRING	cassava4.1_006855m	0.0	(Manihot esculenta)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF2147	34	85

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G18990.1	2e-79	B3 family protein

Link Out ? help Back to Top
Entrez Gene	105631633

Publications ? help Back to Top
Zhang L, et al. Global analysis of gene expression profiles in physic nut (Jatropha curcas L.) seedlings exposed to salt stress. PLoS ONE, 2014. 9(5): p. e97878 [PMID:24837971] 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] 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]