PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

XP_009595180.1

Organism

Nicotiana tomentosiformis

Taxonomic ID

4098

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana

Family

Protein Properties

Length: 852aa MW: 93814.7 Da PI: 6.5006

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009595180.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	59.9	4.4e-19	328	427	1	98
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 f+kvl+ sd+++ grlvlpk +ae++ +++ + ++++d +g++W++++++ +++s++yvl+ G + +L++gD+v+F++++ +++ XP_009595180.1 328 FEKVLSASDAGRIGRLVLPKACAEAYfpPINQSDGLPIRIQDIKGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQNMQLQAGDTVTFSRID-PGGK 420 99************************556666778***********99899999999.*******************887.7887 PP .EEEEE- CS B3 92 lvvkvfr 98 lv+++++ XP_009595180.1 421 LVMGFRK 427 8888776 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.6E-29	325	431	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	6.02E-21	325	428	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.29E-24	326	427	No hit	No description
PROSITE profile	PS50863	11.237	328	429	IPR003340	B3 DNA binding domain
SMART	SM01019	3.1E-22	328	428	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.1E-16	328	427	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	13.76	552	606	IPR011124	Zinc finger, CW-type
Pfam	PF07496	3.8E-10	557	603	IPR011124	Zinc finger, CW-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010030	Biological Process	positive regulation of seed germination
GO:0045892	Biological Process	negative regulation of transcription, DNA-templated
GO:2000034	Biological Process	regulation of seed maturation
GO:0005634	Cellular Component	nucleus
GO:0005739	Cellular Component	mitochondrion
GO:0003677	Molecular Function	DNA binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 852 aa Download sequence Send to blast
MGSMICMNEV CRKTTSSEWK KGWSLKSGGF ANLCYNCGSA FENLSFCETF HMGDSGWREC 60 KMCGKHLHCG CIASKYLFEY LDFGGVGCIS CARCLDDHSM RPMQVPADDF RDSAFGTNFI 120 QPLHVEKGVD KTNFDKGRLP TVNNIMEISE PGQPFQSQKD ENNVSLGKTK QEKVLPVGDV 180 STCFSNLNQQ SIASLFREQD NSKPNQGVKE MYDTTNQPSL DFSLSTPVGC SSSGLSFPDG 240 GVEGREHEKT PFQQGLRTRH ILLKPLKPSP SFGSDSNKEL PSQTRIARPP AEGRGGRNQL 300 LPRYWPRITD QELCQLSGDL NSAIVPLFEK VLSASDAGRI GRLVLPKACA EAYFPPINQS 360 DGLPIRIQDI KGKEWTFQFR FWPNNNSRMY VLEGVTPCIQ NMQLQAGDTV TFSRIDPGGK 420 LVMGFRKATN SVETQDPQSS HLPDGSGSAD TSFTGLTENL NNGGRTSADS VHRQVPVSEK 480 KKTTNIGSKN KRLLMHADDA MELRITWEES QELLRPPPTT QPTILVIEDC EFEAYDEPPV 540 FGKQTIFTSR PSGDQEQWAQ CDSCSKWRRL PMHVLLPPKW TCSDNIWDSN SFLYRCSCSA 600 PEEIKAKELE AFFRVSKGHK RQKIAGKNED CEPSGLNALA TVAVLGDSIS DLGEPLVGAT 660 TKHPRHRPGC TCIVCIQPPS GKGKHQPTCK CNACLSAERR FKTLMLRKKK KQSEREAEVA 720 QAKDQVPPKD GSETDGASGA ELMMQTSHSE NERNTNGDHM EKVGAGKGQL DLNCHPNRED 780 EMLIEAAAGI SMTSLINAAD LPLDMYQTQN GLATLDKCLL SLATAGSEGQ QPDNGCVRPA 840 DAQVQENNGD NG

Sequence ? help Back to Top

Protein Sequence Length: 852 aa Download sequence Send to blast

MGSMICMNEV CRKTTSSEWK KGWSLKSGGF ANLCYNCGSA FENLSFCETF HMGDSGWREC  60
KMCGKHLHCG CIASKYLFEY LDFGGVGCIS CARCLDDHSM RPMQVPADDF RDSAFGTNFI  120
QPLHVEKGVD KTNFDKGRLP TVNNIMEISE PGQPFQSQKD ENNVSLGKTK QEKVLPVGDV  180
STCFSNLNQQ SIASLFREQD NSKPNQGVKE MYDTTNQPSL DFSLSTPVGC SSSGLSFPDG  240
GVEGREHEKT PFQQGLRTRH ILLKPLKPSP SFGSDSNKEL PSQTRIARPP AEGRGGRNQL  300
LPRYWPRITD QELCQLSGDL NSAIVPLFEK VLSASDAGRI GRLVLPKACA EAYFPPINQS  360
DGLPIRIQDI KGKEWTFQFR FWPNNNSRMY VLEGVTPCIQ NMQLQAGDTV TFSRIDPGGK  420
LVMGFRKATN SVETQDPQSS HLPDGSGSAD TSFTGLTENL NNGGRTSADS VHRQVPVSEK  480
KKTTNIGSKN KRLLMHADDA MELRITWEES QELLRPPPTT QPTILVIEDC EFEAYDEPPV  540
FGKQTIFTSR PSGDQEQWAQ CDSCSKWRRL PMHVLLPPKW TCSDNIWDSN SFLYRCSCSA  600
PEEIKAKELE AFFRVSKGHK RQKIAGKNED CEPSGLNALA TVAVLGDSIS DLGEPLVGAT  660
TKHPRHRPGC TCIVCIQPPS GKGKHQPTCK CNACLSAERR FKTLMLRKKK KQSEREAEVA  720
QAKDQVPPKD GSETDGASGA ELMMQTSHSE NERNTNGDHM EKVGAGKGQL DLNCHPNRED  780
EMLIEAAAGI SMTSLINAAD LPLDMYQTQN GLATLDKCLL SLATAGSEGQ QPDNGCVRPA  840
DAQVQENNGD NG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	4e-69	306	435	2	131	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL2/HSL1. {ECO:0000269\|PubMed:15894743, ECO:0000269\|PubMed:17158584, ECO:0000269\|PubMed:17267611}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009595178.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like isoform X1
Swissprot	Q6Z3U3	0.0	Y7797_ORYSJ; B3 domain-containing protein Os07g0679700
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	A0A1J6I6X9	0.0	A0A1J6I6X9_NICAT; B3 domain-containing protein
STRING	XP_009595178.1	0.0	(Nicotiana tomentosiformis)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G30470.1	0.0	high-level expression of sugar-inducible gene 2

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Jia H,McCarty DR,Suzuki M Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression. Plant Physiol., 2013. 163(3): p. 1293-305 [PMID:24043445] Schneider A, et al. Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos. Plant J., 2016. 85(2): p. 305-19 [PMID:26678037] Chhun T, et al. HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth. Plant Cell Physiol., 2016. 57(8): p. 1689-706 [PMID:27335347] Qüesta JI,Song J,Geraldo N,An H,Dean C Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization. Science, 2016. 353(6298): p. 485-8 [PMID:27471304] Yuan W, et al. A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis. Nat. Genet., 2016. 48(12): p. 1527-1534 [PMID:27819666] Merini W, et al. The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development. Plant Physiol., 2017. 173(1): p. 627-641 [PMID:27837089] Li C,Cui Y A DNA element that remembers winter. Nat. Genet., 2016. 48(12): p. 1451-1452 [PMID:27898079] Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis. Plant Cell, 2018. 30(3): p. 600-619 [PMID:29475938] Sasnauskas G,Kauneckaite K,Siksnys V Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1. Nucleic Acids Res., 2018. 46(8): p. 4316-4324 [PMID:29660015] Wu B, et al. Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana. Biochem. Biophys. Res. Commun., 2018. 501(2): p. 415-422 [PMID:29733847]