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: 469aa MW: 53047.1 Da PI: 8.6766

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.07G163700.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	55.5	1.1e-17	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.07G163700.1.p 8 KLVLPTTLQSRQLRIPDNFLRKYGTQ--LSTIATLTVPDGSVWPIGL--KKADNRIWFVDGWQDFVQRYSIGVGYFLVFMYEGNSSF--IVH 93 445567778888*********966..9999***********..***********************************9..999 PP EE- CS B3 96 vfr 98 +f+ Glyma.07G163700.1.p 94 IFN 96 986 PP
2	B3	60.1	3.7e-19	334	425	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.07G163700.1.p 334 VLRPSYLYRGCIMYLPSTFAEKNlNGVSG---FIKLQLSNGRQWSVRCLYRGGR--AKLSQGWFEFTVENNLGEGDVCVFELLRMKEVVL 418 78899****************876743...59999999****665555..66*********************998899999 PP EEEEE-S CS B3 93 vvkvfrk 99 v+vfr Glyma.07G163700.1.p 419 QVTVFRV 425 9999985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	6.28E-24	3	97	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	8.9E-23	3	97	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.96E-19	4	96	No hit	No description
PROSITE profile	PS50863	13.352	5	98	IPR003340	B3 DNA binding domain
SMART	SM01019	1.5E-16	6	98	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.4E-15	10	96	IPR003340	B3 DNA binding domain
Gene3D	G3DSA:2.40.330.10	1.2E-24	323	424	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	2.55E-24	324	425	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.91E-21	329	424	No hit	No description
SMART	SM01019	3.5E-19	331	426	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	14.325	331	426	IPR003340	B3 DNA binding domain
Pfam	PF02362	9.0E-17	334	424	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: 469 aa Download sequence Send to blast
MPRPCFDKLV LPTTLQSRQL RIPDNFLRKY GTQLSTIATL TVPDGSVWPI GLKKADNRIW 60 FVDGWQDFVQ RYSIGVGYFL VFMYEGNSSF IVHIFNLSTS EVNYQSAMRN HNEGSCFANY 120 HHIFDEMEDV DSLGLSDLSP QYLTPGALQS KGFAGSVDQL TPGKSHTPAL QNLFNGGSKL 180 NRVNWGDGGS AFSLKDANSQ GNQSTRDIGV QFNAVEFKRS TEELKLRYSN SNEEAVNKTA 240 KKKRKSEPCK FLFLFKFSLS GNVKDDIFLL ITNTMCGTID GEEPSGENEE EAEMRYRFYE 300 SASARKRTVT AEERERAINA SKTFEPTNPF CRVVLRPSYL YRGCIMYLPS TFAEKNLNGV 360 SGFIKLQLSN GRQWSVRCLY RGGRAKLSQG WFEFTVENNL GEGDVCVFEL LRMKEVVLQV 420 TVFRVTEDAG LLNQLPMQQQ QQSPNISHTK LLNPHLQHRI STTKLIRN*

Sequence ? help Back to Top

Protein Sequence Length: 469 aa Download sequence Send to blast

MPRPCFDKLV LPTTLQSRQL RIPDNFLRKY GTQLSTIATL TVPDGSVWPI GLKKADNRIW  60
FVDGWQDFVQ RYSIGVGYFL VFMYEGNSSF IVHIFNLSTS EVNYQSAMRN HNEGSCFANY  120
HHIFDEMEDV DSLGLSDLSP QYLTPGALQS KGFAGSVDQL TPGKSHTPAL QNLFNGGSKL  180
NRVNWGDGGS AFSLKDANSQ GNQSTRDIGV QFNAVEFKRS TEELKLRYSN SNEEAVNKTA  240
KKKRKSEPCK FLFLFKFSLS GNVKDDIFLL ITNTMCGTID GEEPSGENEE EAEMRYRFYE  300
SASARKRTVT AEERERAINA SKTFEPTNPF CRVVLRPSYL YRGCIMYLPS TFAEKNLNGV  360
SGFIKLQLSN GRQWSVRCLY RGGRAKLSQG WFEFTVENNL GEGDVCVFEL LRMKEVVLQV  420
TVFRVTEDAG LLNQLPMQQQ QQSPNISHTK LLNPHLQHRI STTKLIRN*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4i1k_A	2e-71	297	427	15	144	B3 domain-containing transcription factor VRN1
4i1k_B	2e-71	297	427	15	144	B3 domain-containing transcription factor VRN1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Gma.18998	0.0	leaf\| root\| somatic embryo

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.07G163700.1.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_003529203.1	0.0	B3 domain-containing transcription factor VRN1
Refseq	XP_028240648.1	0.0	B3 domain-containing transcription factor VRN1-like
Swissprot	Q8L3W1	2e-71	VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBL	K7L245	0.0	K7L245_SOYBN; Uncharacterized protein
STRING	GLYMA07G21160.2	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
AT1G49480.1	4e-73	related to vernalization1 1

Link Out ? help Back to Top
Phytozome	Glyma.07G163700.1.p

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]