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_009144302.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

Protein Properties

Length: 795aa MW: 86581.4 Da PI: 7.5647

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009144302.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	60.5	2.9e-19	299	398	1	98
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 f+k+l+ sd+++ grlvlpk +ae++ +++ e++ l+++d +g++W++++++ +++s++yvl+ G ++ +L++gD+v+F++++ +++ XP_009144302.1 299 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKVQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMRLQAGDTVTFSRVD-PGGK 391 99************************666678889***********99899999999.*******************766.8888 PP .EEEEE- CS B3 92 lvvkvfr 98 l +++++ XP_009144302.1 392 LIMGARK 398 8888776 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.83E-20	296	394	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	4.7E-29	296	399	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.27E-24	297	398	No hit	No description
PROSITE profile	PS50863	10.884	299	400	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.1E-16	299	398	IPR003340	B3 DNA binding domain
SMART	SM01019	9.5E-23	299	400	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	13.624	547	597	IPR011124	Zinc finger, CW-type
Pfam	PF07496	3.0E-9	553	594	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: 795 aa Download sequence Send to blast
MFEVKMGSKV CMNASCGSTS SVEWKKGWPL RSGALADLCF RCGSAYETSR FCETFHMEQS 60 GWRECYLCNK RLHCGCIASK LVVEFMDYGG VGCSTCTNSH SKRGENPGVF SRLPMNMQQT 120 NGESGMSIDG VVRSEANLFS QPLVSGDDKR EEFTPHRGFG NLMKQDNNVT TTGYTHESSS 180 SSPAQPSLNM ALATLPYSPS FATPVVDGNK LMGAGGGGVA SSQSRLFQCS ASSILQKPSK 240 SVLGTPPPGT SKSAQARIGR PPVEGRGKGH LLPRYWPKYT DKELQQISGN LNLNIVPLFE 300 KTLSASDAGR IGRLVLPKAC AEAYFPPISQ SEGIPLKVQD VRGKEWTFQF RFWPNNNSRM 360 YVLEGVTPCI QSMRLQAGDT VTFSRVDPGG KLIMGARKAT YTVDMQGCGF ANGASNEDTS 420 SSGVTENLTS INAPSCPSQM LEGLPEHLGS PHGGNGVKKS EINGGDDQSR GKEKKRTRTL 480 GAKNKRLLLH SEESMELRVT WEEAQELLRP SANAKPTVVV IEEHEFEEFE EPPVFGKRTI 540 VVTSRPSGEQ ERWGSCDDCS KWRRLPVDAL LPAKWTCSDN VWDSSRCSCS APEESLKELE 600 NVLRAGKEYK KRRIGVSQTA RNEQEPSGLD ALASAAVLGD ALDESEVATT TRHPRHRVGC 660 SCIVCIQPPS GKGRHKPTCG CTVCSTVKRR FKTLMMRRKK KQLECDGTAA VDEENKEGVE 720 PEKNEGEKEG RIDLNSDPYN REDAEAVAVE KREESKKSEG GVSWGVSQGG GVLGETEVGG 780 GEAEKTTSEE QKVTS

Sequence ? help Back to Top

Protein Sequence Length: 795 aa Download sequence Send to blast

MFEVKMGSKV CMNASCGSTS SVEWKKGWPL RSGALADLCF RCGSAYETSR FCETFHMEQS  60
GWRECYLCNK RLHCGCIASK LVVEFMDYGG VGCSTCTNSH SKRGENPGVF SRLPMNMQQT  120
NGESGMSIDG VVRSEANLFS QPLVSGDDKR EEFTPHRGFG NLMKQDNNVT TTGYTHESSS  180
SSPAQPSLNM ALATLPYSPS FATPVVDGNK LMGAGGGGVA SSQSRLFQCS ASSILQKPSK  240
SVLGTPPPGT SKSAQARIGR PPVEGRGKGH LLPRYWPKYT DKELQQISGN LNLNIVPLFE  300
KTLSASDAGR IGRLVLPKAC AEAYFPPISQ SEGIPLKVQD VRGKEWTFQF RFWPNNNSRM  360
YVLEGVTPCI QSMRLQAGDT VTFSRVDPGG KLIMGARKAT YTVDMQGCGF ANGASNEDTS  420
SSGVTENLTS INAPSCPSQM LEGLPEHLGS PHGGNGVKKS EINGGDDQSR GKEKKRTRTL  480
GAKNKRLLLH SEESMELRVT WEEAQELLRP SANAKPTVVV IEEHEFEEFE EPPVFGKRTI  540
VVTSRPSGEQ ERWGSCDDCS KWRRLPVDAL LPAKWTCSDN VWDSSRCSCS APEESLKELE  600
NVLRAGKEYK KRRIGVSQTA RNEQEPSGLD ALASAAVLGD ALDESEVATT TRHPRHRVGC  660
SCIVCIQPPS GKGRHKPTCG CTVCSTVKRR FKTLMMRRKK KQLECDGTAA VDEENKEGVE  720
PEKNEGEKEG RIDLNSDPYN REDAEAVAVE KREESKKSEG GVSWGVSQGG GVLGETEVGG  780
GEAEKTTSEE QKVTS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	1e-81	277	407	2	132	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	687	699	KRRFKTLMMRRKK

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in flowers and at lower levels in roots, stems and leaves. {ECO:0000269\|PubMed:15894743}.

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	XP_009144302.1

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_009144302.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	M4DP72	0.0	M4DP72_BRARP; Uncharacterized protein
STRING	Bra018313.1-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]