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: 439aa MW: 49911.8 Da PI: 9.4767

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KHN25328.1	genome	TCUHK	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	59.4	6.3e-19	6	96	1	97
EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97 f k l+ps v +++l+lp +f++++gg+ +tl ++g +W+v l +k +++y++ +GWkeFvk + g +vFk++g+s+f v++f KHN25328.1 6 FHKLLLPSTVQPNQQLRLPDNFMRKYGGE--LLPIVTLSVPDGSVWRVGL--KKADNKYWFLDGWKEFVKHYSISIGYLLVFKYEGKSSF--SVHIF 96 899*********************877..44599**********..*******************************99999..88887 PP
2	B3	56.5	5.1e-18	300	390	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+ ++gr+W v++ yr+++ l++GW eF +n+L egD++vF+l + +e l v+vfr KHN25328.1 300 VLRPSYLYRGCIMYLPSCFAEKHlNGVSG---FIKLQISNGRQWPVRCLYRGGR--AKLSQGWFEFSLENNLGEGDVCVFELLRMKEVVLQVTVFR 390 78899****************877743...59**********665555..66*********************998889989999998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	5.89E-23	2	97	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	4.5E-24	3	97	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.65E-23	4	97	No hit	No description
PROSITE profile	PS50863	14.466	6	99	IPR003340	B3 DNA binding domain
SMART	SM01019	7.4E-19	6	99	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.9E-16	6	96	IPR003340	B3 DNA binding domain
Gene3D	G3DSA:2.40.330.10	3.3E-24	289	390	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.96E-24	290	390	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.13E-22	295	390	No hit	No description
SMART	SM01019	4.6E-16	297	392	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.479	297	392	IPR003340	B3 DNA binding domain
Pfam	PF02362	9.4E-16	300	390	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: 439 aa Download sequence Send to blast
MPHPSFHKLL LPSTVQPNQQ LRLPDNFMRK YGGELLPIVT LSVPDGSVWR VGLKKADNKY 60 WFLDGWKEFV KHYSISIGYL LVFKYEGKSS FSVHIFNLAT SEINYQSATR SSNEGLHFTN 120 RLKLFEEMED EDSIEISDSS PSHLAPSSLQ NQALTGSVDK MMPGKSYTPP ALQNLFNGSK 180 LNSINWGEGG NAHSSRIANS LDNRLTRDIG LQFNAVEFKR STEELKLRAS MEERMKKTTR 240 KKRKSDGQDP SAEHEEEVEM RLRFYESASA RKRTVTAEER ERAINAAKAF EPPNPFCRVV 300 LRPSYLYRGC IMYLPSCFAE KHLNGVSGFI KLQISNGRQW PVRCLYRGGR AKLSQGWFEF 360 SLENNLGEGD VCVFELLRMK EVVLQVTVFR VIEDVGLLSP PLQQNQNMSS AKMLNTPLQQ 420 HLTSTKMVRN QQQGDLSGT

Sequence ? help Back to Top

Protein Sequence Length: 439 aa Download sequence Send to blast

MPHPSFHKLL LPSTVQPNQQ LRLPDNFMRK YGGELLPIVT LSVPDGSVWR VGLKKADNKY  60
WFLDGWKEFV KHYSISIGYL LVFKYEGKSS FSVHIFNLAT SEINYQSATR SSNEGLHFTN  120
RLKLFEEMED EDSIEISDSS PSHLAPSSLQ NQALTGSVDK MMPGKSYTPP ALQNLFNGSK  180
LNSINWGEGG NAHSSRIANS LDNRLTRDIG LQFNAVEFKR STEELKLRAS MEERMKKTTR  240
KKRKSDGQDP SAEHEEEVEM RLRFYESASA RKRTVTAEER ERAINAAKAF EPPNPFCRVV  300
LRPSYLYRGC IMYLPSCFAE KHLNGVSGFI KLQISNGRQW PVRCLYRGGR AKLSQGWFEF  360
SLENNLGEGD VCVFELLRMK EVVLQVTVFR VIEDVGLLSP PLQQNQNMSS AKMLNTPLQQ  420
HLTSTKMVRN QQQGDLSGT

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4i1k_A	1e-72	263	395	15	146	B3 domain-containing transcription factor VRN1
4i1k_B	1e-72	263	395	15	146	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	KHN25328.1

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	EU857413	0.0	EU857413.1 Glycine max reduced vernalization response 1 (VRN1) gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_028194626.1	0.0	B3 domain-containing transcription factor VRN1-like isoform X2
Swissprot	Q8L3W1	1e-132	VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBL	A0A445HKM5	0.0	A0A445HKM5_GLYSO; B3 domain-containing transcription factor VRN1 isoform B
STRING	GLYMA12G05250.1	0.0	(Glycine max)

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
AT1G49480.1	2e-74	related to vernalization1 1

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] Qi X, et al. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun, 2014. 5: p. 4340 [PMID:25004933] 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]