PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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

Family

Protein Properties

Length: 339aa MW: 38959.2 Da PI: 9.5176

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KFK39227.1	genome	MPIPBR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	54.8	1.7e-17	5	95	1	97
EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97 ff +l+ s++ +++rl++p kf+++++ + s+ + l+ ++g +W+v l rk +++++ +GW+eFv+ ++ g ++F+++g+s f v +f KFK39227.1 5 FFHKLIFSSTIQEKRLRVPDKFVSKFKDE--LSVAVALTVPDGHVWRVGL--RKAENKIWFHDGWQEFVDRYSIRIGYLLIFRYEGNSAF--SVYIF 95 899999***************999755..99*************..********************************9999..88777 PP
2	B3	55.1	1.4e-17	244	337	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE- CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfr 98 f vl ps+ + ++++lp fae++ +g++ + ++++ + ++W v++ k gr +++GW eF +n+L egD++vF+l ++++f l+v++fr KFK39227.1 244 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKVQ---LAEKQWPVRC--LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFR 336 677899******************84442.444555...567***..666666779********************99*****9998 PP S CS B3 99 k 99 KFK39227.1 337 V 337 5 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	2.0E-22	3	97	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.63E-21	3	97	IPR015300	DNA-binding pseudobarrel domain
PROSITE profile	PS50863	14.579	5	98	IPR003340	B3 DNA binding domain
SMART	SM01019	5.0E-17	5	98	IPR003340	B3 DNA binding domain
CDD	cd10017	5.33E-19	5	96	No hit	No description
Pfam	PF02362	8.6E-15	5	96	IPR003340	B3 DNA binding domain
Gene3D	G3DSA:2.40.330.10	5.3E-23	236	336	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	5.3E-22	237	338	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.95E-20	242	336	No hit	No description
SMART	SM01019	8.1E-22	244	338	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.619	244	338	IPR003340	B3 DNA binding domain
Pfam	PF02362	5.1E-16	244	337	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: 339 aa Download sequence Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVSKF KDELSVAVAL TVPDGHVWRV GLRKAENKIW 60 FHDGWQEFVD RYSIRIGYLL IFRYEGNSAF SVYIFNLSHS EINYHSTGLM DSAHNHFKRA 120 RLFEDLEDED AEVIYPSSVY PSTLPDSTAP ANKGYAGTAI QSLFTGPVKD EEATPTPKVP 180 KKRGRKKKNA DPEEINSSAP RDDDPENRSK FYESASARKR TVTAVERDRA INASKTFEPT 240 NPFFRVVLRP SYLYRGCIMY LPSGFAEKYL SGISGFIKVQ LAEKQWPVRC LYKAGRAKFS 300 QGWYEFTLEN NLGEGDVCVF ELLRTRDFVL KVTAFRVNE

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4i1k_A	4e-89	210	339	15	144	B3 domain-containing transcription factor VRN1
4i1k_B	4e-89	210	339	15	144	B3 domain-containing transcription factor VRN1
Search in ModeBase

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	KFK39227.1

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	AK353269	0.0	AK353269.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-34-E14.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006406545.1	0.0	B3 domain-containing transcription factor VRN1
Swissprot	Q8L3W1	0.0	VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBL	A0A087HAS5	0.0	A0A087HAS5_ARAAL; B3 domain-containing transcription factor vrn1-like
STRING	A0A087HAS5	0.0	(Arabis alpina)

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

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] 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]