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

mrna28098.1-v1.0-hybrid

Organism

Fragaria vesca

Taxonomic ID

57918

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria

Family

Protein Properties

Length: 968aa MW: 106402 Da PI: 6.9531

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
mrna28098.1-v1.0-hybrid	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	58.9	9.1e-19	357	457	1	99
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvF 82 f+kvl+ sd+++ grlvlpk +ae++ +++ e+ l+++d +g++W++++++ +++s++yvl+ G ++ +L++gD+v+F mrna28098.1-v1.0-hybrid 357 FEKVLSASDAGRIGRLVLPKACAEAYfpPISHSEGLPLRIQDVKGNEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTF 441 99************************555556667***********99899999999.****************** PP EE-SSSEE..EEEEE-S CS B3 83 kldgrsefelvvkvfrk 99 ++++ + +lv++++++ mrna28098.1-v1.0-hybrid 442 SRID-PGNKLVIGFRKA 457 *887.777789988875 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.9E-29	353	461	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.14E-20	354	457	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.87E-23	355	456	No hit	No description
PROSITE profile	PS50863	10.828	357	458	IPR003340	B3 DNA binding domain
SMART	SM01019	4.2E-23	357	458	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.8E-16	357	457	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	14.811	617	667	IPR011124	Zinc finger, CW-type
Pfam	PF07496	3.5E-12	622	664	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: 968 aa Download sequence Send to blast
MGTKICMNVS CGTSNTHEWK NGWPLRSGGF AHLCYKCGAA YEKSVFCDTF HIGETGWRDC 60 SSCHKPLHCG CVASRSLYEC LDYGGVGCIG CANSSQPRVI PRNDVLNGFG GLALSNAGDR 120 NSSSVEYRTV GDTVDEGKFL QLCGTVDEGK LLQLCKIMEA NESTLLPQSP TGEESVFLES 180 NLLPQPQRDD KIESLGQTKG QEVIHQIGEV SPGFFSPTQS SIGSLTFAAQ PDNGRTMLEV 240 NHMSIPSSQP SLSMSLCAPS ATSNFIQPFS GGHMDIRDQS KTPSAFQQVK PRPILPRPLQ 300 PPLPPVSSET NRSVRIARPP TEGRGRNQLL PRYWPRITDQ ELQKLSGALN STIVPLFEKV 360 LSASDAGRIG RLVLPKACAE AYFPPISHSE GLPLRIQDVK GNEWTFQFRF WPNNNSRMYV 420 LEGVTPCIQS MQLQAGDTVT FSRIDPGNKL VIGFRKASQS VNMQGPQTSV LQNGTPGETS 480 FSSENLATGS GDSSLFHMNK GSKDPPLNSP SDHHLAEWDT YMQNRENSGH RTSEDLLQPA 540 SNSEKKRTRN IGPKSKRLLM HSEDVMELRL TWEEAQDLLR PPPSVKPSIV TIEDFEFEEY 600 DEPPVFGKRS IFTAGPSKRR EQWAQCDDCS KWRMLPVDVL LPPKWTCSEN SWDSSRSSCT 660 APEEMSSKQL DNLLSSSVSL KGLKKRRKII EKKNAEEQEP SGLDALASAA ILGDNVRESG 720 EQSVGATTKH PRHRPGCTCI VCIQPPSGKG KHKPSCKCNV CLTVKRRFTT MMQRKYEKRQ 780 LEREAENSQR NNGNNKDESE VNGTTSGDAM LHRNNSANNS QRNNNNHKDE SEINGTTSGD 840 AALHRNHSSE NGASSSQSRT QADAAESSSA GQIDLNCEPS GLFRNPTLQD LFKLAKAASA 900 ARPSEKYTNE NSLRTMMDEE QAGLASCSLK QANGDNERQL PNEAHLSSVS WDCPSIGDKV 960 YREPDLE*

Sequence ? help Back to Top

Protein Sequence Length: 968 aa Download sequence Send to blast

MGTKICMNVS CGTSNTHEWK NGWPLRSGGF AHLCYKCGAA YEKSVFCDTF HIGETGWRDC  60
SSCHKPLHCG CVASRSLYEC LDYGGVGCIG CANSSQPRVI PRNDVLNGFG GLALSNAGDR  120
NSSSVEYRTV GDTVDEGKFL QLCGTVDEGK LLQLCKIMEA NESTLLPQSP TGEESVFLES  180
NLLPQPQRDD KIESLGQTKG QEVIHQIGEV SPGFFSPTQS SIGSLTFAAQ PDNGRTMLEV  240
NHMSIPSSQP SLSMSLCAPS ATSNFIQPFS GGHMDIRDQS KTPSAFQQVK PRPILPRPLQ  300
PPLPPVSSET NRSVRIARPP TEGRGRNQLL PRYWPRITDQ ELQKLSGALN STIVPLFEKV  360
LSASDAGRIG RLVLPKACAE AYFPPISHSE GLPLRIQDVK GNEWTFQFRF WPNNNSRMYV  420
LEGVTPCIQS MQLQAGDTVT FSRIDPGNKL VIGFRKASQS VNMQGPQTSV LQNGTPGETS  480
FSSENLATGS GDSSLFHMNK GSKDPPLNSP SDHHLAEWDT YMQNRENSGH RTSEDLLQPA  540
SNSEKKRTRN IGPKSKRLLM HSEDVMELRL TWEEAQDLLR PPPSVKPSIV TIEDFEFEEY  600
DEPPVFGKRS IFTAGPSKRR EQWAQCDDCS KWRMLPVDVL LPPKWTCSEN SWDSSRSSCT  660
APEEMSSKQL DNLLSSSVSL KGLKKRRKII EKKNAEEQEP SGLDALASAA ILGDNVRESG  720
EQSVGATTKH PRHRPGCTCI VCIQPPSGKG KHKPSCKCNV CLTVKRRFTT MMQRKYEKRQ  780
LEREAENSQR NNGNNKDESE VNGTTSGDAM LHRNNSANNS QRNNNNHKDE SEINGTTSGD  840
AALHRNHSSE NGASSSQSRT QADAAESSSA GQIDLNCEPS GLFRNPTLQD LFKLAKAASA  900
ARPSEKYTNE NSLRTMMDEE QAGLASCSLK QANGDNERQL PNEAHLSSVS WDCPSIGDKV  960
YREPDLE*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	1e-69	335	465	2	132	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	683	687	KKRRK
2	764	778	KRRFTTMMQRKYEKR

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	mrna28098.1-v1.0-hybrid

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_011461406.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL2
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	A0A2P6QKW1	0.0	A0A2P6QKW1_ROSCH; Putative transcription factor & chromatin remodeling CW-Zn-B3/VAL family
STRING	XP_004294727.1	0.0	(Fragaria vesca)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF10323	30	39

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	mrna28098.1-v1.0-hybrid

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]