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_009141065.1

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: 783aa MW: 85759.5 Da PI: 7.138

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009141065.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	58.3	1.4e-18	295	394	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_009141065.1 295 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMMLQAGDTVTFSRVD-PGGK 387 99************************666678889***********99899999999.*******************766.7777 PP .EEEEE- CS B3 92 lvvkvfr 98 l +++++ XP_009141065.1 388 LIMGFRK 394 7777665 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	6.93E-20	292	394	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	3.9E-29	292	399	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	5.05E-24	293	394	No hit	No description
Pfam	PF02362	5.1E-16	295	394	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.814	295	396	IPR003340	B3 DNA binding domain
SMART	SM01019	5.9E-23	295	395	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	13.624	539	589	IPR011124	Zinc finger, CW-type
Pfam	PF07496	3.3E-9	545	586	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: 783 aa Download sequence Send to blast
MFQVKTGSKM CMNASCGSTS TVEWKKGWPL RSGALADLCF RCGSAYETSL FCETFHLDQS 60 GWRECYLCNK RLHCGCIASK LVVEFMDFGG VGCTTCTNCH QPNLNNRGEN PGLFSRLPMN 120 RQHTNGESGM NVGKADLFSQ PLVQGDDKRE EFMPHRGFSN LMKPDNATTT GYRHDANGTH 180 ESSPTPSQPP SLNMPMAALP YSLNFATATK KLMDAASQSH TVQSSASGIL QTPSKSVPGT 240 PSGPGTSKSA QARIGRPPNE GRGRSHLLPR YWPKYTDKEL QQISGNLNLN IVPLFEKTLS 300 ASDAGRIGRL VLPKACAEAY FPPISQSEGI PLKIQDVRGK EWTFQFRFWP NNNSRMYVLE 360 GVTPCIQSMM LQAGDTVTFS RVDPGGKLIM GFRKAAHTGV IQGCGLTNGT SNEDTSSSGV 420 TETPTSVNAS SCPAQTPEEL KGLPEHLNSN HGGSSLKKSE VNGVKDKKRT RTVGAKHKRM 480 LWRSEEAMEV RITWEETQEL IRPSPSEKPT VVVIEEHEFE EFNEPPVFGK RTIVTSRPSG 540 EQERWGSCDD CSKWRRLPVD ALLPAKWTCS DNVWDESRCS CSAPEESLKE LENVLRMSKE 600 YKKRRSGVSQ TVRTEEELTG LDALASAAAL GDTLGEEEEP ATTTRHPRHR VGCSCIVCIQ 660 PPSGKGRHNS SCLCTVCSTV KRRFKTLMMR RKKKQLEREE IEAAVAAAAD QENKEDGKTG 720 RIDLNSDPCN RGDVEAVGVE EKDESEKGEA GGCLGVAQAD DVVGVTELEG EGEKIGEESK 780 GSS

Sequence ? help Back to Top

Protein Sequence Length: 783 aa Download sequence Send to blast

MFQVKTGSKM CMNASCGSTS TVEWKKGWPL RSGALADLCF RCGSAYETSL FCETFHLDQS  60
GWRECYLCNK RLHCGCIASK LVVEFMDFGG VGCTTCTNCH QPNLNNRGEN PGLFSRLPMN  120
RQHTNGESGM NVGKADLFSQ PLVQGDDKRE EFMPHRGFSN LMKPDNATTT GYRHDANGTH  180
ESSPTPSQPP SLNMPMAALP YSLNFATATK KLMDAASQSH TVQSSASGIL QTPSKSVPGT  240
PSGPGTSKSA QARIGRPPNE GRGRSHLLPR YWPKYTDKEL QQISGNLNLN IVPLFEKTLS  300
ASDAGRIGRL VLPKACAEAY FPPISQSEGI PLKIQDVRGK EWTFQFRFWP NNNSRMYVLE  360
GVTPCIQSMM LQAGDTVTFS RVDPGGKLIM GFRKAAHTGV IQGCGLTNGT SNEDTSSSGV  420
TETPTSVNAS SCPAQTPEEL KGLPEHLNSN HGGSSLKKSE VNGVKDKKRT RTVGAKHKRM  480
LWRSEEAMEV RITWEETQEL IRPSPSEKPT VVVIEEHEFE EFNEPPVFGK RTIVTSRPSG  540
EQERWGSCDD CSKWRRLPVD ALLPAKWTCS DNVWDESRCS CSAPEESLKE LENVLRMSKE  600
YKKRRSGVSQ TVRTEEELTG LDALASAAAL GDTLGEEEEP ATTTRHPRHR VGCSCIVCIQ  660
PPSGKGRHNS SCLCTVCSTV KRRFKTLMMR RKKKQLEREE IEAAVAAAAD QENKEDGKTG  720
RIDLNSDPCN RGDVEAVGVE EKDESEKGEA GGCLGVAQAD DVVGVTELEG EGEKIGEESK  780
GSS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	3e-83	273	403	2	132	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	680	692	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_009141065.1

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_009141065.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	M4DYN9	0.0	M4DYN9_BRARP; Uncharacterized protein
STRING	Bra021635.1-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]