PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

Protein Properties

Length: 346aa MW: 39598.2 Da PI: 9.5867

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.013G040000.2	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	50	5.3e-16	5	95	1	97
EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..E CS B3 1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelv 93 ff +l+ s +l+++ l++p +f++++ + s+ l+ ++g +W+v + +k ++++++++GW+eF + +++g ++vF+++g+s f Gorai.013G040000.2 5 FFHKLILSTTLQEKKLRIPDNFVKKFRDE--LSVAAALTVPDGHVWRVGI--KKVDNKVWFQEGWQEFLERYYIRVGYVLVFRYEGNSAF--S 91 788999999************999755..999************..********************************9999..8 PP EEEE CS B3 94 vkvf 97 v++f Gorai.013G040000.2 92 VSIF 95 8887 PP
2	B3	65.5	7.8e-21	243	333	4	98
E-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..E CS B3 4 vltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelv 93 vl ps+ + ++++lp fae+h +g++ + ++l+ ++gr+W+v++ y++++ +++GW eF +n+L egD++vF+l +++ef l+ Gorai.013G040000.2 243 VLRPSYLYRGCIMYLPSCFAEKHlSGVS-G--SIKLQLPDGRQWSVRCLYKGGK--AKFSQGWYEFTLENNLGEGDVCVFELLRSREFVLK 328 78899****************86663.3..59999*******555555..6699******************999** PP EEEE- CS B3 94 vkvfr 98 v+vfr Gorai.013G040000.2 329 VTVFR 333 *98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.2E-21	3	96	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	9.61E-21	3	96	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.18E-17	5	96	No hit	No description
Pfam	PF02362	7.2E-13	5	95	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.521	5	98	IPR003340	B3 DNA binding domain
SMART	SM01019	1.2E-12	6	98	IPR003340	B3 DNA binding domain
Gene3D	G3DSA:2.40.330.10	6.9E-25	232	333	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.57E-24	233	333	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.51E-23	238	333	No hit	No description
PROSITE profile	PS50863	13.958	240	335	IPR003340	B3 DNA binding domain
SMART	SM01019	7.1E-23	240	335	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.2E-18	243	333	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: 346 aa Download sequence Send to blast
MPRPFFHKLI LSTTLQEKKL RIPDNFVKKF RDELSVAAAL TVPDGHVWRV GIKKVDNKVW 60 FQEGWQEFLE RYYIRVGYVL VFRYEGNSAF SVSIFNLYNS EINYQTNALV GTQYNHGKQY 120 PFEQLEDDEC ISPALQNLFG GSKLNNCINW GGDANLQTSK GVNNQPIRGS GAMKPEPKKR 180 GRKRKFDPNV QDSSAGREDD VDMRFRCYES ASARKRTVTA EERERAINAA KAFEPTNPFC 240 RVVLRPSYLY RGCIMYLPSC FAEKHLSGVS GSIKLQLPDG RQWSVRCLYK GGKAKFSQGW 300 YEFTLENNLG EGDVCVFELL RSREFVLKVT VFRVMESGGL MHRSQ*

Sequence ? help Back to Top

Protein Sequence Length: 346 aa Download sequence Send to blast

MPRPFFHKLI LSTTLQEKKL RIPDNFVKKF RDELSVAAAL TVPDGHVWRV GIKKVDNKVW  60
FQEGWQEFLE RYYIRVGYVL VFRYEGNSAF SVSIFNLYNS EINYQTNALV GTQYNHGKQY  120
PFEQLEDDEC ISPALQNLFG GSKLNNCINW GGDANLQTSK GVNNQPIRGS GAMKPEPKKR  180
GRKRKFDPNV QDSSAGREDD VDMRFRCYES ASARKRTVTA EERERAINAA KAFEPTNPFC  240
RVVLRPSYLY RGCIMYLPSC FAEKHLSGVS GSIKLQLPDG RQWSVRCLYK GGKAKFSQGW  300
YEFTLENNLG EGDVCVFELL RSREFVLKVT VFRVMESGGL MHRSQ*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4i1k_A	6e-74	208	336	17	144	B3 domain-containing transcription factor VRN1
4i1k_B	6e-74	208	336	17	144	B3 domain-containing transcription factor VRN1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Gra.3149	0.0	flower\|seedling\| flowering

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}.

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	JX587993	1e-58	JX587993.1 Gossypium hirsutum clone NBRI_GE22287 microsatellite sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012462595.1	0.0	PREDICTED: B3 domain-containing transcription factor VRN1-like isoform X2
Refseq	XP_016745121.1	0.0	PREDICTED: B3 domain-containing transcription factor VRN1-like isoform X2
Swissprot	Q8L3W1	1e-156	VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBL	A0A0D2VAA8	0.0	A0A0D2VAA8_GOSRA; Uncharacterized protein
TrEMBL	A0A1U8P1N3	0.0	A0A1U8P1N3_GOSHI; B3 domain-containing transcription factor VRN1-like isoform X2
TrEMBL	A0A2P5RSY0	0.0	A0A2P5RSY0_GOSBA; Uncharacterized protein
STRING	Gorai.013G040000.1	0.0	(Gossypium raimondii)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G18990.1	1e-152	B3 family protein

Link Out ? help Back to Top
Phytozome	Gorai.013G040000.2
Entrez Gene	105782416

Publications ? help Back to Top
Paterson AH, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 2012. 492(7429): p. 423-7 [PMID:23257886] 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]