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

RrC1328_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: 750aa MW: 82172.6 Da PI: 8.0681

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC1328_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	56.5	4.9e-18	282	373	1	98
EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97 f+k+l+ sd+++ grlvlpk +ae+ g++ l+++d +g++W++++++ +++s++yvl+ G ++ +L++gD+v+F++++ +++l ++++ RrC1328_p1 282 FEKTLSASDAGRIGRLVLPKACAESEGIP------LKVQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMRLQAGDTVTFSRVD-PGGKLIMGAR 372 99*******************877766......9**********99899999999.*******************766.8888888877 PP - CS B3 98 r 98 + RrC1328_p1 373 K 373 6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	3.2E-23	279	375	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	9.68E-17	279	369	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.57E-22	280	373	No hit	No description
PROSITE profile	PS50863	10.673	282	375	IPR003340	B3 DNA binding domain
Pfam	PF02362	5.5E-15	282	373	IPR003340	B3 DNA binding domain
SMART	SM01019	1.3E-18	282	375	IPR003340	B3 DNA binding domain

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

Sequence ? help Back to Top
Protein Sequence Length: 750 aa Download sequence Send to blast
MIKFLIVVYR SAYETSRFCE TFHLEQSGWR ECYLCNKVSF CLLINFLFSS AMLRLHCGCI 60 ASKLMVEFMD YGGVGCTSCT NCNSKRGENP GVFSRLPMNT QHTNGESGVR SEANLFSQPP 120 VPVDDKKEEF KPHLGFSNLM KPDNNVTNTT TTTTGYRHES SSSSPSPSQP SLNMALATLP 180 YSPSFATPVA DGGKKLMGGG GGASSQPHLF QCSASSILQK PSKILLGPPP PGTSKSAQAR 240 IGRPPVEGRG KGHLLPRYWP KYTDKELQQI SGNLNLNIVP LFEKTLSASD AGRIGRLVLP 300 KACAESEGIP LKVQDVRGKE WTFQFRFWPN NNSRMYVLEG VTPCIQSMRL QAGDTVTFSR 360 VDPGGKLIMG ARKATYTADM QGCGFANGVS NEDTSSSGVT ENPTSINASS GPSQILEELK 420 GLPEHLSSPN GGNGSKKSEI NGGDDQSRVK EKKRTRTMGA KNKRLLLHSE ESMELRVTWE 480 EAQELLRPSP NAKPTIVVIE EHEFEEFDEP PVFGKRTILT SNPSGSEQER WGTCDDCSKW 540 RRLPTLFSQQ SGHVQTMFGT RAEYKKRRIG VSQTARNEQE PSGLDALASA AVLGDTLDDS 600 EVATTTRHPR HRVGCSCIVC IQPPSGKGRH KPTCGCTVCS TVKRRFKTLM MRRKKKQLER 660 DGTAAAVDEE NKEGAEPDKK KEGKTGRIDL NSDPYNREDV EAVVAVEKQE ESKKSEEGMC 720 WGVSQGGDVV GETELEGGGE AEKTNSEEQK

Sequence ? help Back to Top

Protein Sequence Length: 750 aa Download sequence Send to blast

MIKFLIVVYR SAYETSRFCE TFHLEQSGWR ECYLCNKVSF CLLINFLFSS AMLRLHCGCI  60
ASKLMVEFMD YGGVGCTSCT NCNSKRGENP GVFSRLPMNT QHTNGESGVR SEANLFSQPP  120
VPVDDKKEEF KPHLGFSNLM KPDNNVTNTT TTTTGYRHES SSSSPSPSQP SLNMALATLP  180
YSPSFATPVA DGGKKLMGGG GGASSQPHLF QCSASSILQK PSKILLGPPP PGTSKSAQAR  240
IGRPPVEGRG KGHLLPRYWP KYTDKELQQI SGNLNLNIVP LFEKTLSASD AGRIGRLVLP  300
KACAESEGIP LKVQDVRGKE WTFQFRFWPN NNSRMYVLEG VTPCIQSMRL QAGDTVTFSR  360
VDPGGKLIMG ARKATYTADM QGCGFANGVS NEDTSSSGVT ENPTSINASS GPSQILEELK  420
GLPEHLSSPN GGNGSKKSEI NGGDDQSRVK EKKRTRTMGA KNKRLLLHSE ESMELRVTWE  480
EAQELLRPSP NAKPTIVVIE EHEFEEFDEP PVFGKRTILT SNPSGSEQER WGTCDDCSKW  540
RRLPTLFSQQ SGHVQTMFGT RAEYKKRRIG VSQTARNEQE PSGLDALASA AVLGDTLDDS  600
EVATTTRHPR HRVGCSCIVC IQPPSGKGRH KPTCGCTVCS TVKRRFKTLM MRRKKKQLER  660
DGTAAAVDEE NKEGAEPDKK KEGKTGRIDL NSDPYNREDV EAVVAVEKQE ESKKSEEGMC  720
WGVSQGGDVV GETELEGGGE AEKTNSEEQK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	3e-73	260	382	2	132	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	191	199	GGKKLMGGG
2	642	654	KRRFKTLMMRRKK

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK353502	0.0	AK353502.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-47-G20.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018441902.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	A0A3P6CG84	0.0	A0A3P6CG84_BRAOL; Uncharacterized protein
STRING	Bo4g058460.1	0.0	(Brassica oleracea)

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]