PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja

Family

Protein Properties

Length: 436aa MW: 49452.9 Da PI: 8.9669

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.20G008700.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	57.6	2.3e-18	8	96	4	98
E-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEE CS B3 4 vltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvk 95 +l+ + +l+s++l++p +f++++g + s+ tl+ ++g +W++ l +k ++r+++ +GW++Fv+ + +g f+vF+++g+s+f v+ Glyma.20G008700.1.p 8 KLVLPTTLQSRQLRIPDNFLRKYGTQ--LSTIATLTVPDGSVWRIGL--KKADNRILFVDGWQDFVQHYSIGVGYFLVFMYEGNSSF--IVH 93 555677888889*********966..9999***********..***********************************9..999 PP EE- CS B3 96 vfr 98 +f+ Glyma.20G008700.1.p 94 IFN 96 986 PP
2	B3	59.2	7.1e-19	301	392	4	99
E-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS B3 4 vltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 vl ps+ + ++++lp fae++ +g++ ++l+ ++gr+W+v++ yr+++ l++GW eF +n+L egD++vF+l +++e l Glyma.20G008700.1.p 301 VLRPSYLYRGCIMYLPSCFAEKNlNGVSG---FIKLQLSNGRQWSVRCLYRGGR--AKLSQGWFEFTVENNLGEGDVCVFELLRTKEVVL 385 78899****************876743...59999999****665555..66********************99999999 PP EEEEE-S CS B3 93 vvkvfrk 99 v+vfr Glyma.20G008700.1.p 386 QVTVFRV 392 99985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	5.49E-24	3	97	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	9.5E-23	3	97	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.76E-19	4	96	No hit	No description
PROSITE profile	PS50863	13.606	5	98	IPR003340	B3 DNA binding domain
SMART	SM01019	3.3E-16	6	98	IPR003340	B3 DNA binding domain
Pfam	PF02362	5.2E-16	8	96	IPR003340	B3 DNA binding domain
Gene3D	G3DSA:2.40.330.10	1.6E-24	290	391	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	2.16E-24	291	392	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.30E-22	296	391	No hit	No description
SMART	SM01019	3.7E-19	298	393	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	14.099	298	393	IPR003340	B3 DNA binding domain
Pfam	PF02362	8.7E-17	301	391	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: 436 aa Download sequence Send to blast
MPRPCFHKLV LPTTLQSRQL RIPDNFLRKY GTQLSTIATL TVPDGSVWRI GLKKADNRIL 60 FVDGWQDFVQ HYSIGVGYFL VFMYEGNSSF IVHIFNLSTS EVNYQSAIRN RNEGSCLANY 120 HHIFDEMEDV DSLDLSDLSP QYLTPGSLQN KGCVGSVDQL TPGKSHTPAL QNLFNGGSKL 180 NRINWGDGGS AFSSKNANSQ GNQSTRDIGV QFNANEFKRS TEELKLRYSN EETVNKTAKK 240 KRKSEPYGEE PSGENEEEAE MRYRFYESAS ARKRTVTAEE RERAINASKT FEPTNPFCRV 300 VLRPSYLYRG CIMYLPSCFA EKNLNGVSGF IKLQLSNGRQ WSVRCLYRGG RAKLSQGWFE 360 FTVENNLGEG DVCVFELLRT KEVVLQVTVF RVTEDAGLLN QPPMMQQQHI PNMSHTKLLN 420 PHLQHRVSTT KLIRN*

Sequence ? help Back to Top

Protein Sequence Length: 436 aa Download sequence Send to blast

MPRPCFHKLV LPTTLQSRQL RIPDNFLRKY GTQLSTIATL TVPDGSVWRI GLKKADNRIL  60
FVDGWQDFVQ HYSIGVGYFL VFMYEGNSSF IVHIFNLSTS EVNYQSAIRN RNEGSCLANY  120
HHIFDEMEDV DSLDLSDLSP QYLTPGSLQN KGCVGSVDQL TPGKSHTPAL QNLFNGGSKL  180
NRINWGDGGS AFSSKNANSQ GNQSTRDIGV QFNANEFKRS TEELKLRYSN EETVNKTAKK  240
KRKSEPYGEE PSGENEEEAE MRYRFYESAS ARKRTVTAEE RERAINASKT FEPTNPFCRV  300
VLRPSYLYRG CIMYLPSCFA EKNLNGVSGF IKLQLSNGRQ WSVRCLYRGG RAKLSQGWFE  360
FTVENNLGEG DVCVFELLRT KEVVLQVTVF RVTEDAGLLN QPPMMQQQHI PNMSHTKLLN  420
PHLQHRVSTT KLIRN*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4i1k_A	1e-72	264	394	15	144	B3 domain-containing transcription factor VRN1
4i1k_B	1e-72	264	394	15	144	B3 domain-containing transcription factor VRN1
Search in ModeBase

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	Glyma.20G008700.1.p

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	BT094686	0.0	BT094686.1 Soybean clone JCVI-FLGm-24P12 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_003555681.1	0.0	B3 domain-containing transcription factor VRN1 isoform X1
Refseq	XP_028222197.1	0.0	B3 domain-containing transcription factor VRN1-like isoform X1
Swissprot	Q8L3W1	1e-125	VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBL	A0A0B2NPL0	0.0	A0A0B2NPL0_GLYSO; B3 domain-containing transcription factor VRN1
TrEMBL	I1ND23	0.0	I1ND23_SOYBN; Uncharacterized protein
STRING	GLYMA20G01130.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF2147	34	85
Representative plant	OGRP2051	14	36

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G18990.1	1e-123	B3 family protein

Link Out ? help Back to Top
Phytozome	Glyma.20G008700.1.p
Entrez Gene	100789352

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]