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

Rsa1.0_01254.1_g00002.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

Protein Properties

Length: 751aa MW: 82179.5 Da PI: 8.0626

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_01254.1_g00002.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	61.6	1.3e-19	286	385	1	98
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvF 82 f+k+l+ sd+++ grlvlpk +ae++ +++ e++ l+++d +g +W++++++ +++s++yvl+ G v++ +L++gD+v+F Rsa1.0_01254.1_g00002.1 286 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVRGTEWTFQFRFwpNNNSRMYVLE-GVTACVQSMKLQAGDTVTF 370 99************************666678889***********99899999999.****************** PP EE-SSSEE..EEEEE- CS B3 83 kldgrsefelvvkvfr 98 ++++ +++l +++++ Rsa1.0_01254.1_g00002.1 371 SRVD-PGGKLIMGFRK 385 *766.77777777665 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.97E-21	284	385	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.13E-25	284	385	No hit	No description
Gene3D	G3DSA:2.40.330.10	4.2E-30	284	387	IPR015300	DNA-binding pseudobarrel domain
SMART	SM01019	2.7E-23	286	386	IPR003340	B3 DNA binding domain
Pfam	PF02362	6.3E-17	286	385	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.926	286	387	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	9	538	583	IPR011124	Zinc finger, CW-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 751 aa Download sequence Send to blast
MFQVNTGSKM CMNASCGSTS TVEWKRGWPL RSGALADLCF RCGSAYESSV FCETFHSDQS 60 GWRECYLCNK RLHCGCIASK LVVEFMDYGG VGCTTCTNCH QPNLSNRGEN PGLFSRLPMN 120 RQHTNGEIGM SVDGVIRSQA DLFSQPLVQG DDKREEEFMP HRGFGNLMKP DNATTNVKTH 180 ESSSSTPSSQ PSLETLPYSL SFANAASQSH TLQRSASSSI LQKPSKSVVL GTPPGTISKS 240 AQPRIGRPPV EGRGKSHLLP RYWPKYTDKE LQQISGNLNL KIVPLFEKTL SASDAGRIGR 300 LVLPKACAEA YFPPISQSEG IPLKIQDVRG TEWTFQFRFW PNNNSRMYVL EGVTACVQSM 360 KLQAGDTVTF SRVDPGGKLI MGFRKAAHTG DILGSGGLTN GASNEDTSSS GVTETPTSIN 420 ASSCPSQTPP EELKGLLPER LSSKKSEMNG GKSCDDDDPS RVKAKKRTRT VGAAKSKRML 480 WDSEESKEVR ITWEETQELI RPSPSEEPSI VLIEEHEFEE FDEPPVFGKR TIITSRPSGE 540 QERWASCDDC SKWRRLPLDA LLPAKCSCSA PEESVKELEN VLRVGKEYKK RRTGGSQTGR 600 TEEEPSGLDA LASAAALGEA ATTTRHPRHR VGCSCIVCIQ PPSGTGRHKP NCMCTVCSTV 660 KRRFKTQMMR RKKRQLEREE AAAAADQEKK KGEGKTGRID LNSDPSKREE VGAVREDESE 720 KRGVAQAGDV VGGTELEGEG EKIGEESKGA S

Sequence ? help Back to Top

Protein Sequence Length: 751 aa Download sequence Send to blast

MFQVNTGSKM CMNASCGSTS TVEWKRGWPL RSGALADLCF RCGSAYESSV FCETFHSDQS  60
GWRECYLCNK RLHCGCIASK LVVEFMDYGG VGCTTCTNCH QPNLSNRGEN PGLFSRLPMN  120
RQHTNGEIGM SVDGVIRSQA DLFSQPLVQG DDKREEEFMP HRGFGNLMKP DNATTNVKTH  180
ESSSSTPSSQ PSLETLPYSL SFANAASQSH TLQRSASSSI LQKPSKSVVL GTPPGTISKS  240
AQPRIGRPPV EGRGKSHLLP RYWPKYTDKE LQQISGNLNL KIVPLFEKTL SASDAGRIGR  300
LVLPKACAEA YFPPISQSEG IPLKIQDVRG TEWTFQFRFW PNNNSRMYVL EGVTACVQSM  360
KLQAGDTVTF SRVDPGGKLI MGFRKAAHTG DILGSGGLTN GASNEDTSSS GVTETPTSIN  420
ASSCPSQTPP EELKGLLPER LSSKKSEMNG GKSCDDDDPS RVKAKKRTRT VGAAKSKRML  480
WDSEESKEVR ITWEETQELI RPSPSEEPSI VLIEEHEFEE FDEPPVFGKR TIITSRPSGE  540
QERWASCDDC SKWRRLPLDA LLPAKCSCSA PEESVKELEN VLRVGKEYKK RRTGGSQTGR  600
TEEEPSGLDA LASAAALGEA ATTTRHPRHR VGCSCIVCIQ PPSGTGRHKP NCMCTVCSTV  660
KRRFKTQMMR RKKRQLEREE AAAAADQEKK KGEGKTGRID LNSDPSKREE VGAVREDESE  720
KRGVAQAGDV VGGTELEGEG EKIGEESKGA S

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	4e-80	264	394	2	132	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	660	672	KRRFKTQMMRRKK
2	660	673	KRRFKTQMMRRKKR

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_01254.1_g00002.1

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_018485193.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like
Refseq	XP_018485194.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	V4NXH2	0.0	V4NXH2_EUTSA; Uncharacterized protein
STRING	XP_006410148.1	0.0	(Eutrema salsugineum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6923	24	40

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
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]