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

Araha.14380s0003.1.p

Organism

Arabidopsis halleri

Taxonomic ID

81970

Taxonomic Lineage

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

Family

Protein Properties

Length: 799aa MW: 87599.5 Da PI: 8.0376

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Araha.14380s0003.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	57.6	2.2e-18	300	395	1	94
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkld 85 f+k+l+ sd+++ grlvlpk +ae++ +++ e++ l+++d +g++W+++++y +++s++yvl+ G ++ L++gD+v+F+++ Araha.14380s0003.1.p 300 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVRGKEWTFQFRYwpNNNSRMYVLE-GVTPCIQSMMLQAGDTVTFSRV 387 99************************666678889*************899999999.*******************76 PP SSSEE..EE CS B3 86 grsefelvv 94 + +++l + Araha.14380s0003.1.p 388 D-PGGKLIM 395 5.6665555 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.6E-28	297	407	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	2.22E-19	297	395	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.68E-23	298	395	No hit	No description
PROSITE profile	PS50863	10.616	300	401	IPR003340	B3 DNA binding domain
SMART	SM01019	1.9E-22	300	400	IPR003340	B3 DNA binding domain
Pfam	PF02362	6.8E-16	300	395	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	13.224	546	596	IPR011124	Zinc finger, CW-type
Pfam	PF07496	1.1E-8	552	593	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: 799 aa Download sequence Send to blast
MFEVKMVSKM CMNASCGTTS TVEWKKGWAL RSGLLADLCY RCGSAYESSL FCEQFHKDQS 60 GWRECYLCNK RLHCGCIASK VTIELMDYGG VGCSTCTCCH QLNLNTRGEN PGVFSRLPMK 120 PLADRQHVNG ESGMNIDGGR NEAGLFSQPL VMGGDKREEF MPHRGLGQLM NSENTSTGYR 180 LDAAGEMHES SPSQPSLNMG LAVNPFSPSF ATEGLEGKKH IGASQPNMVH CSASNILQKP 240 SKPAISTPPV ASKSAQARIG RPPVEGRGKG HLLPRYWPKY TDKEVQQISG NLNLNIVPLF 300 EKTLSASDAG RIGRLVLPKA CAEAYFPPIS QSEGIPLKIQ DVRGKEWTFQ FRYWPNNNSR 360 MYVLEGVTPC IQSMMLQAGD TVTFSRVDPG GKLIMGSRKA ANAGDMQGCG LTNGTSTEDT 420 SSSGVTENPP SINGSSCPSL IPQELNGMPE NLSSQKSETN GGRIGDDPTR VKEKKRTRTI 480 GAKNKRLLLH SEESMELRLT WEEAQDLLRP SPSAKPTIVV IEEKEIEEYD EPPVFGKRTI 540 VTTRPSGEQE RWATCDDCSK WRRLPVDALL PFKWTCIDNV WDVSRCSCSA PEESLKELEN 600 VLKVGREYKK RRTGESQAAK SQQEPCGLDA LASAAVLGDT IGEPEVATTT RHPRHRAGCS 660 CIVCIQPPSG KGRHKPTCGC TVCSTVKRRF KTLMMRRKKK QLERDVTAAE DKKKKDMELA 720 ESDKSKEEKE VNTARIDLNS DPYNKEDAEA VAVEKEESRK RAIGQCSGVV TQGAGDVLGV 780 TELEGEAKKV GEEPRVSS*

Sequence ? help Back to Top

Protein Sequence Length: 799 aa Download sequence Send to blast

MFEVKMVSKM CMNASCGTTS TVEWKKGWAL RSGLLADLCY RCGSAYESSL FCEQFHKDQS  60
GWRECYLCNK RLHCGCIASK VTIELMDYGG VGCSTCTCCH QLNLNTRGEN PGVFSRLPMK  120
PLADRQHVNG ESGMNIDGGR NEAGLFSQPL VMGGDKREEF MPHRGLGQLM NSENTSTGYR  180
LDAAGEMHES SPSQPSLNMG LAVNPFSPSF ATEGLEGKKH IGASQPNMVH CSASNILQKP  240
SKPAISTPPV ASKSAQARIG RPPVEGRGKG HLLPRYWPKY TDKEVQQISG NLNLNIVPLF  300
EKTLSASDAG RIGRLVLPKA CAEAYFPPIS QSEGIPLKIQ DVRGKEWTFQ FRYWPNNNSR  360
MYVLEGVTPC IQSMMLQAGD TVTFSRVDPG GKLIMGSRKA ANAGDMQGCG LTNGTSTEDT  420
SSSGVTENPP SINGSSCPSL IPQELNGMPE NLSSQKSETN GGRIGDDPTR VKEKKRTRTI  480
GAKNKRLLLH SEESMELRLT WEEAQDLLRP SPSAKPTIVV IEEKEIEEYD EPPVFGKRTI  540
VTTRPSGEQE RWATCDDCSK WRRLPVDALL PFKWTCIDNV WDVSRCSCSA PEESLKELEN  600
VLKVGREYKK RRTGESQAAK SQQEPCGLDA LASAAVLGDT IGEPEVATTT RHPRHRAGCS  660
CIVCIQPPSG KGRHKPTCGC TVCSTVKRRF KTLMMRRKKK QLERDVTAAE DKKKKDMELA  720
ESDKSKEEKE VNTARIDLNS DPYNKEDAEA VAVEKEESRK RAIGQCSGVV TQGAGDVLGV  780
TELEGEAKKV GEEPRVSS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	3e-88	278	408	2	132	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	686	698	KRRFKTLMMRRKK
2	697	714	KKKQLERDVTAAEDKKKK

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	Araha.14380s0003.1.p

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	AB206553	0.0	AB206553.1 Arabidopsis thaliana HSI2 mRNA for transcription factor B3-EAR motif, complete cds.
GenBank	AY062492	0.0	AY062492.1 Arabidopsis thaliana putative VP1/ABI3 family regulatory protein (At2g30470; T6B20.17) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002881112.1	0.0	B3 domain-containing transcription repressor VAL1
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	D7LC55	0.0	D7LC55_ARALL; High-level expression of sugar-inducible gene 2
STRING	scaffold_401535.1	0.0	(Arabidopsis lyrata)

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

Link Out ? help Back to Top
Phytozome	Araha.14380s0003.1.p

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]