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_01618.1_g00003.1

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: 814aa MW: 88890.2 Da PI: 7.8552

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_01618.1_g00003.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	60.5	3e-19	314	413	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 ++ +L++gD+v+F Rsa1.0_01618.1_g00003.1 314 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKVQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMRLQAGDTVTF 398 99************************666678889***********99899999999.****************** PP EE-SSSEE..EEEEE- CS B3 83 kldgrsefelvvkvfr 98 ++++ +++l +++++ Rsa1.0_01618.1_g00003.1 399 SRVD-PGGKLIMGARK 413 *766.88888888776 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	3.3E-29	311	415	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.96E-20	311	409	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.34E-24	312	413	No hit	No description
Pfam	PF02362	2.2E-16	314	413	IPR003340	B3 DNA binding domain
SMART	SM01019	9.5E-23	314	415	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.884	314	415	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	13.582	564	614	IPR011124	Zinc finger, CW-type
Pfam	PF07496	2.6E-9	570	611	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: 814 aa Download sequence Send to blast
MGSKVCMNAS CGSSSSVEWK KGWPLRSGAL ADLCFRCGYL PSPSLIGLKV SVLVFIILSA 60 YETSRFCETF HLEQSGWREC YLCNKRLHCG CIASKLMVEF MDYGGVGCTS CTNCHSKRGE 120 NPGVFSRLPM NNTQHTNGES GVRSEANHFS QPPVPVDDKK EEFKPHLGFS NLMKPDNNVT 180 NTTTTTTGYR HESSSSSPSP SQPSLNMALA TLPYSPSFAT PVADGKKLMG GGGGASSQPH 240 LFQCSASSIL QKPSKILLGP PPPGTSKSAQ ARIGRPPVEG RGKGHLLPRY WPKYTDKELQ 300 QISGNLNLNI VPLFEKTLSA SDAGRIGRLV LPKACAEAYF PPISQSEGIP LKVQDVRGKE 360 WTFQFRFWPN NNSRMYVLEG VTPCIQSMRL QAGDTVTFSR VDPGGKLIMG ARKATYTADM 420 QGCGFANGVS NEDTSSSGVT ENPTSINATS CPSQILEELK GLPEHLSSPN GGNGSKKSEI 480 NGGDDQSRVK EKKRTRTMGA KNKRLLLHSE ESMELRVTWE EAQELLRPSP NAKPTIVVIE 540 EHEFEEFDEP PVFGKRTILT SNPSGEQERW GSCDDCSKWR RLPVDALLPA KWTCSDNVWD 600 QSRCSCSAPE ESLKELENGL RAGKEYKKRR IGVSQTARNE QEPSGLDALA SAAVLGDTLD 660 DSEVATTTRH PRHRVGCSCI VCIQPPSGKG RHKPTCGCTV CSTVKRRFKT LMMRRKKKQL 720 ERDGTAAVDE ENKEGAEPDK KKEGKTGRID LNSDPYNRED VEAVVAVEKQ EESKKSEEGM 780 CWGAAQGGDV LGETELEGGG EAEKTTSEEQ KVAS

Sequence ? help Back to Top

Protein Sequence Length: 814 aa Download sequence Send to blast

MGSKVCMNAS CGSSSSVEWK KGWPLRSGAL ADLCFRCGYL PSPSLIGLKV SVLVFIILSA  60
YETSRFCETF HLEQSGWREC YLCNKRLHCG CIASKLMVEF MDYGGVGCTS CTNCHSKRGE  120
NPGVFSRLPM NNTQHTNGES GVRSEANHFS QPPVPVDDKK EEFKPHLGFS NLMKPDNNVT  180
NTTTTTTGYR HESSSSSPSP SQPSLNMALA TLPYSPSFAT PVADGKKLMG GGGGASSQPH  240
LFQCSASSIL QKPSKILLGP PPPGTSKSAQ ARIGRPPVEG RGKGHLLPRY WPKYTDKELQ  300
QISGNLNLNI VPLFEKTLSA SDAGRIGRLV LPKACAEAYF PPISQSEGIP LKVQDVRGKE  360
WTFQFRFWPN NNSRMYVLEG VTPCIQSMRL QAGDTVTFSR VDPGGKLIMG ARKATYTADM  420
QGCGFANGVS NEDTSSSGVT ENPTSINATS CPSQILEELK GLPEHLSSPN GGNGSKKSEI  480
NGGDDQSRVK EKKRTRTMGA KNKRLLLHSE ESMELRVTWE EAQELLRPSP NAKPTIVVIE  540
EHEFEEFDEP PVFGKRTILT SNPSGEQERW GSCDDCSKWR RLPVDALLPA KWTCSDNVWD  600
QSRCSCSAPE ESLKELENGL RAGKEYKKRR IGVSQTARNE QEPSGLDALA SAAVLGDTLD  660
DSEVATTTRH PRHRVGCSCI VCIQPPSGKG RHKPTCGCTV CSTVKRRFKT LMMRRKKKQL  720
ERDGTAAVDE ENKEGAEPDK KKEGKTGRID LNSDPYNRED VEAVVAVEKQ EESKKSEEGM  780
CWGAAQGGDV LGETELEGGG EAEKTTSEEQ KVAS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	5e-82	292	422	2	132	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	704	716	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_01618.1_g00003.1

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	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]