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_013633557.1

Organism

Brassica oleracea

Taxonomic ID

3712

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: 774aa MW: 85013.1 Da PI: 7.0929

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013633557.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	55.7	9.3e-18	286	385	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_013633557.1 286 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVRGKEWIFQFRFwpNNNSRMYVLE-GVTPCIQSMMLQAGDTVTFSRVD-PGGK 378 99************************666678889***********99899999999.*******************776.7777 PP .EEEEE- CS B3 92 lvvkvfr 98 l +++++ XP_013633557.1 379 LIMGFRK 385 7777776 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	2.09E-19	283	387	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	7.8E-29	283	395	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.05E-22	284	385	No hit	No description
PROSITE profile	PS50863	10.644	286	387	IPR003340	B3 DNA binding domain
SMART	SM01019	4.3E-21	286	386	IPR003340	B3 DNA binding domain
Pfam	PF02362	3.4E-15	286	385	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	13.939	530	580	IPR011124	Zinc finger, CW-type
Pfam	PF07496	5.3E-10	536	577	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: 774 aa Download sequence Send to blast
MFQVKTGSKM CMNASCGSTS TVEWKKGWPL RSGALADLCF RCGSAYETSL FCETFHLDQS 60 GWRECYLCNK RLHCGCIASK LVVEFMDYGG VGCSTCTNCH QPNLGKIGEN PGLFSRLPMN 120 RQHTNGENGM NVGKADLFSQ PLVQGDDKRE EFMPHRGFSN LIKTDRLDGG EILESSSTPS 180 QPPSLNMPLA ALPYSLNFAT ATKKLMDAAS QPHAVQSSSS SILQTPSKSV LGTPPGTSKS 240 AQARIGRPPN EGRGRSHLLP RYWPKYTDKE LQQISGNLNL NIVPLFEKTL SASDAGRIGR 300 LVLPKACAEA YFPPISQSEG IPLKIQDVRG KEWIFQFRFW PNNNSRMYVL EGVTPCIQSM 360 MLQAGDTVTF SRVDPGGKLI MGFRKATHTK DIQGCGLTNG TLNEDTSSSG VTETPTSINA 420 SSCPSQNPEE LKGLPEHLNS NHGGSSLKKS EVNGVKDKKR TRTVGAKSRR LLLHSEESME 480 VRITWEETQE LIRPSPSEKP TVVVIEEHEF EEFYEPPVFG KRTIITSKPS GEQERWASCD 540 DCSKWRKLPV EALLPAKWTC SDNVWDESRC SCSAPEESLK ELENVLRMSK EYKKRRTGVS 600 QTVRTEEELT GLDALASAAA LGDTLGEEEE PATTTRHPRH RVGCSCIVCI QPPSGKGRHN 660 SSCLCTVCST VKRRFKTLMM RRKKKQLERE EIEAAAAADQ ENKEDGKTGR IDLNSDPCNR 720 GEVEAVGVEE KEESGKGEAG ECLGVAQAGD VVGVTELEGE GEKIGEESKG SKLI

Sequence ? help Back to Top

Protein Sequence Length: 774 aa Download sequence Send to blast

MFQVKTGSKM CMNASCGSTS TVEWKKGWPL RSGALADLCF RCGSAYETSL FCETFHLDQS  60
GWRECYLCNK RLHCGCIASK LVVEFMDYGG VGCSTCTNCH QPNLGKIGEN PGLFSRLPMN  120
RQHTNGENGM NVGKADLFSQ PLVQGDDKRE EFMPHRGFSN LIKTDRLDGG EILESSSTPS  180
QPPSLNMPLA ALPYSLNFAT ATKKLMDAAS QPHAVQSSSS SILQTPSKSV LGTPPGTSKS  240
AQARIGRPPN EGRGRSHLLP RYWPKYTDKE LQQISGNLNL NIVPLFEKTL SASDAGRIGR  300
LVLPKACAEA YFPPISQSEG IPLKIQDVRG KEWIFQFRFW PNNNSRMYVL EGVTPCIQSM  360
MLQAGDTVTF SRVDPGGKLI MGFRKATHTK DIQGCGLTNG TLNEDTSSSG VTETPTSINA  420
SSCPSQNPEE LKGLPEHLNS NHGGSSLKKS EVNGVKDKKR TRTVGAKSRR LLLHSEESME  480
VRITWEETQE LIRPSPSEKP TVVVIEEHEF EEFYEPPVFG KRTIITSKPS GEQERWASCD  540
DCSKWRKLPV EALLPAKWTC SDNVWDESRC SCSAPEESLK ELENVLRMSK EYKKRRTGVS  600
QTVRTEEELT GLDALASAAA LGDTLGEEEE PATTTRHPRH RVGCSCIVCI QPPSGKGRHN  660
SSCLCTVCST VKRRFKTLMM RRKKKQLERE EIEAAAAADQ ENKEDGKTGR IDLNSDPCNR  720
GEVEAVGVEE KEESGKGEAG ECLGVAQAGD VVGVTELEGE GEKIGEESKG SKLI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	3e-82	264	394	2	132	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	671	683	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_013633557.1

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_013633557.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	A0A0D3C332	0.0	A0A0D3C332_BRAOL; Uncharacterized protein
STRING	Bo4g173060.1	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]