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

RrC4353_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

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: 761aa MW: 83991.3 Da PI: 7.2329

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC4353_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	51.2	2.3e-16	289	381	8	98
-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE- CS B3 8 sdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfr 98 sd+++ grlvlpk +ae++ +++ e++ l+++d +g++W++++++ +++s++yvl+ G ++ L++gD+v+F++++ +++l +++++ RrC4353_p1 289 SDAGRIGRLVLPKACAEAYfpPISQSEGIPLQIQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTTCIQSMMLQAGDTVTFSRVD-PGGKLIMGFRK 381 899999*************666678889***********99899999999.*******************766.77777777665 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01019	1.9E-16	282	382	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	9.305	282	383	IPR003340	B3 DNA binding domain
Gene3D	G3DSA:2.40.330.10	1.9E-24	288	383	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.19E-19	288	381	No hit	No description
SuperFamily	SSF101936	4.84E-16	288	382	IPR015300	DNA-binding pseudobarrel domain
Pfam	PF02362	4.5E-14	289	381	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	9.715	524	573	IPR011124	Zinc finger, CW-type
Pfam	PF07496	9.3E-6	530	570	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: 761 aa Download sequence Send to blast
MNASCGSTST VEWKKGWPLR SGSLADLCFR CGSAYETSLF CETFHLEQSG WRECYLCNKR 60 LHCGCIASKL MVEFMDYGGV GCTSCTHSHQ LNLNKRGENP VVFSRLAIIN SQHTNGESGM 120 SIRSETDLFS QSQPLVHGDD KREEFMAHRG FNNFMKPENN TNNNNNNATT TTTTGYKLNG 180 GEMHEPSSTP PQPSFNMALA TLPYSPSFAT TPVDGNKLMA AAASQSHIAQ CSASKPPKLV 240 LGTPPGTSKS AQTRVGRPPV DGRGKGHLLP RYWPKYTDKE LQQISGNASD AGRIGRLVLP 300 KACAEAYFPP ISQSEGIPLQ IQDVRGKEWT FQFRFWPNNN SRMYVLEGVT TCIQSMMLQA 360 GDTVTFSRVD PGGKLIMGFR KAAYTTVDMQ RCGGLANEDT SSSGVTENPT SINASSCPSQ 420 TLEDFKSVPE HLSSPYGKKS EICDDLSRVK EKKRTRTIGA KNKRLLMRSE ESMELRLTWE 480 EAQELLRPSP SAKPTVVVIE EHEFEEFDEP PVFGKRTIVT SKPSGEQERW ASCDECTKRR 540 LPLDALLPAK WTCSDNVWDV SRCSCSAPEE SLKELENVLR AGKEYKKRRY QTAKTEEEPS 600 GLDALASAAV LGEGLGCGGH SEVATTTRHP RHRVGCSCIV CIQPPSGKGR HKPTCVCTVC 660 STVKRRFKTL MMRRKKRQLE RDEIAAATEA YEESNKEGTE QAESDENNGD KEGRIDLNSD 720 PYRNREGVEA EKEESERREC SGVADVLGLT ELGGEAAQAA T

Sequence ? help Back to Top

Protein Sequence Length: 761 aa Download sequence Send to blast

MNASCGSTST VEWKKGWPLR SGSLADLCFR CGSAYETSLF CETFHLEQSG WRECYLCNKR  60
LHCGCIASKL MVEFMDYGGV GCTSCTHSHQ LNLNKRGENP VVFSRLAIIN SQHTNGESGM  120
SIRSETDLFS QSQPLVHGDD KREEFMAHRG FNNFMKPENN TNNNNNNATT TTTTGYKLNG  180
GEMHEPSSTP PQPSFNMALA TLPYSPSFAT TPVDGNKLMA AAASQSHIAQ CSASKPPKLV  240
LGTPPGTSKS AQTRVGRPPV DGRGKGHLLP RYWPKYTDKE LQQISGNASD AGRIGRLVLP  300
KACAEAYFPP ISQSEGIPLQ IQDVRGKEWT FQFRFWPNNN SRMYVLEGVT TCIQSMMLQA  360
GDTVTFSRVD PGGKLIMGFR KAAYTTVDMQ RCGGLANEDT SSSGVTENPT SINASSCPSQ  420
TLEDFKSVPE HLSSPYGKKS EICDDLSRVK EKKRTRTIGA KNKRLLMRSE ESMELRLTWE  480
EAQELLRPSP SAKPTVVVIE EHEFEEFDEP PVFGKRTIVT SKPSGEQERW ASCDECTKRR  540
LPLDALLPAK WTCSDNVWDV SRCSCSAPEE SLKELENVLR AGKEYKKRRY QTAKTEEEPS  600
GLDALASAAV LGEGLGCGGH SEVATTTRHP RHRVGCSCIV CIQPPSGKGR HKPTCVCTVC  660
STVKRRFKTL MMRRKKRQLE RDEIAAATEA YEESNKEGTE QAESDENNGD KEGRIDLNSD  720
PYRNREGVEA EKEESERREC SGVADVLGLT ELGGEAAQAA T

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	1e-65	274	390	2	131	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	663	675	KRRFKTLMMRRKK
2	663	676	KRRFKTLMMRRKKR

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_018476649.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	M4E201	0.0	M4E201_BRARP; Uncharacterized protein
STRING	Bra022801.1-P	0.0	(Brassica rapa)

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]