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_010522012.1

Organism

Tarenaya hassleriana

Taxonomic ID

28532

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Cleomaceae; Tarenaya

Family

Protein Properties

Length: 810aa MW: 88857.3 Da PI: 8.1179

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_010522012.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	61.7	1.2e-19	309	408	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_010522012.1 309 FEKTLSASDAGRIGRLVLPKACAEAYfpSIHQSEGIPLKIQDVKGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRID-PGGK 401 99************************667778899***********99899999999.*******************887.7888 PP .EEEEE- CS B3 92 lvvkvfr 98 lv+++++ XP_010522012.1 402 LVLGFRK 408 8888776 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	8.9E-31	306	414	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.09E-21	306	412	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	5.34E-24	307	408	No hit	No description
Pfam	PF02362	7.4E-17	309	408	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.955	309	410	IPR003340	B3 DNA binding domain
SMART	SM01019	4.3E-23	309	410	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	13.844	562	612	IPR011124	Zinc finger, CW-type
Pfam	PF07496	4.1E-10	567	609	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: 810 aa Download sequence Send to blast
MGQKICMNAS CATTNTVEWK KGWPLRAGGV ADLCFRCGSA YESSLFCDTF HKEQSGWREC 60 FLCHKRLHCG CIASKLMVEL LDFGGVGCTN CSSCYSSSLN KRSESQDLLG RLTMMLAERQ 120 PPNGESGILG NNIDSGRLSQ LCQVVEANEP DRFPQSQRGD PKTLLGGDKR EEFMPQPELG 180 KLFKPESTKS VMETRDMQES LSQPSLSMSL AVTPSGPPFP SGVVEGKKQS NVTRSPTVQS 240 SCSVLPKPSK SAVSTPGTSK AASCPLRSAR PPVEGRGRNH LLPRYWPRIT DQELQQISGN 300 LNSKIVPLFE KTLSASDAGR IGRLVLPKAC AEAYFPSIHQ SEGIPLKIQD VKGKEWTFQF 360 RFWPNNNSRM YVLEGVTPCI QSMQLQAGDT VTFSRIDPGG KLVLGFRKTA CGGEQQGSGL 420 TNGTSAEDTS SSGVTENPSS INDPAGPLQM PKEMKGLPEH LSSPDGEISL QKNKNNGVRT 480 GDGSPQIKEK KRTRNIGTKN KRLLLHNEES MELRLTWEEA QDLLRPSPSA KPTIVTIEDN 540 EFEEYDEPPV FGKKTVFTSR PSGGQEQWAQ CDDCSKWRRL PLDALLPSRW TCSDNVWDLD 600 RCSCSVPEKN LKELESFLGV GRETKKQRSG EKQREGRKEE ASGLEALASA AALGDSIGDG 660 SRGAAVAVAV ATTTRHPRHR EGCSCIVCIQ PPSGKGKHKP TCCCNVCMTV KRRFRTLMLR 720 KKKKQQQLDL RGKEEEEEEE EEAQKAEPDK NKPGKEGSTS GRIDLNSDPY NKEGVGIPLR 780 EKEDEAVESR GNGRGGLLGG VADQENRSKE

Sequence ? help Back to Top

Protein Sequence Length: 810 aa Download sequence Send to blast

MGQKICMNAS CATTNTVEWK KGWPLRAGGV ADLCFRCGSA YESSLFCDTF HKEQSGWREC  60
FLCHKRLHCG CIASKLMVEL LDFGGVGCTN CSSCYSSSLN KRSESQDLLG RLTMMLAERQ  120
PPNGESGILG NNIDSGRLSQ LCQVVEANEP DRFPQSQRGD PKTLLGGDKR EEFMPQPELG  180
KLFKPESTKS VMETRDMQES LSQPSLSMSL AVTPSGPPFP SGVVEGKKQS NVTRSPTVQS  240
SCSVLPKPSK SAVSTPGTSK AASCPLRSAR PPVEGRGRNH LLPRYWPRIT DQELQQISGN  300
LNSKIVPLFE KTLSASDAGR IGRLVLPKAC AEAYFPSIHQ SEGIPLKIQD VKGKEWTFQF  360
RFWPNNNSRM YVLEGVTPCI QSMQLQAGDT VTFSRIDPGG KLVLGFRKTA CGGEQQGSGL  420
TNGTSAEDTS SSGVTENPSS INDPAGPLQM PKEMKGLPEH LSSPDGEISL QKNKNNGVRT  480
GDGSPQIKEK KRTRNIGTKN KRLLLHNEES MELRLTWEEA QDLLRPSPSA KPTIVTIEDN  540
EFEEYDEPPV FGKKTVFTSR PSGGQEQWAQ CDDCSKWRRL PLDALLPSRW TCSDNVWDLD  600
RCSCSVPEKN LKELESFLGV GRETKKQRSG EKQREGRKEE ASGLEALASA AALGDSIGDG  660
SRGAAVAVAV ATTTRHPRHR EGCSCIVCIQ PPSGKGKHKP TCCCNVCMTV KRRFRTLMLR  720
KKKKQQQLDL RGKEEEEEEE EEAQKAEPDK NKPGKEGSTS GRIDLNSDPY NKEGVGIPLR  780
EKEDEAVESR GNGRGGLLGG VADQENRSKE

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	6e-74	287	417	2	132	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	710	721	KRRFRTLMLRKK

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_010522012.1

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_010522012.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like isoform X1
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	R0HB22	0.0	R0HB22_9BRAS; Uncharacterized protein
STRING	XP_010522011.1	0.0	(Tarenaya hassleriana)

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]