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_010558872.1

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: 712aa MW: 78840.9 Da PI: 5.81

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_010558872.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	62.3	8e-20	267	366	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++ ++++d +g++W++++++ +++s++yvl+ G ++ +Lk+gD+v+F++++ +++ XP_010558872.1 267 FEKILSASDAGRIGRLVLPKACAEAYfpSIDQPEGTCMKIQDVKGKEWTFQFRFwpNNNSRMYVLE-GVTPCMQSMKLKAGDTVTFSRID-PGGK 359 99************************777788999***********99899999999.*******************887.5665 PP .EEEEE- CS B3 92 lvvkvfr 98 lv++ ++ XP_010558872.1 360 LVMGCRK 366 5555544 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	9.55E-21	264	370	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	8.6E-30	264	371	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	9.15E-24	265	366	No hit	No description
SMART	SM01019	3.9E-22	267	367	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.602	267	368	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.6E-17	267	366	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	13.067	509	559	IPR011124	Zinc finger, CW-type
Pfam	PF07496	2.1E-9	514	556	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: 712 aa Download sequence Send to blast
MGQKICMNAS CATTTTVEWK KGWPLRTGGF ADLCFRCGSA YESSLFCDTF HKEQSGWREC 60 YMCHKLLHCG CIASKLMVDL LDFGGIGCTS CTNCCHNSSL TERSKNQGLL GRLTMMVADR 120 QTLNGESGVL GNDNDSEANE PSLFPQPQSG TQRGDPQMIH GGDKRDEFMT QPGSTVSVMD 180 TGDMQEPLSQ PSLSMSLAVT PSGPSSFPSG FVEGKMHILN HSTIVMKPSP AEGRGRNLLL 240 SRYCPRITDQ ELQQISGNLN SKIVPLFEKI LSASDAGRIG RLVLPKACAE AYFPSIDQPE 300 GTCMKIQDVK GKEWTFQFRF WPNNNSRMYV LEGVTPCMQS MKLKAGDTVT FSRIDPGGKL 360 VMGCRKTASG REQQGSGLKH TSWSGVTEIP SSMNCSSCPL QMPEEVEGLP EHMIILQKRE 420 SNGRGIADDE SSRIKEEKWT RNIGTKNKRL LLLNEEAMEL RLTWEEAQDL LCPPPTANPT 480 IVTVEEHRFE EYDEPPVFGK KTVFTSRPSG GHEQWAQCDN CSKWRRLPVD ALLPSRWTCS 540 YNVWDVGRCL CSAAEENLNE LDSFLRLGTE SKKQRTGESW KEGTEQEEGS GMDEVAGGVV 600 KGDSSGENGD GPEEEEEVAA TTRHPRHRPG CSCIVCIQPP SGRGRHEPGC SCNVCVAVKR 660 RFRTLMLRKR KKQLEREGGA EENHDINDNN GETVGIDLNS DPYNNRGEEM LL

Sequence ? help Back to Top

Protein Sequence Length: 712 aa Download sequence Send to blast

MGQKICMNAS CATTTTVEWK KGWPLRTGGF ADLCFRCGSA YESSLFCDTF HKEQSGWREC  60
YMCHKLLHCG CIASKLMVDL LDFGGIGCTS CTNCCHNSSL TERSKNQGLL GRLTMMVADR  120
QTLNGESGVL GNDNDSEANE PSLFPQPQSG TQRGDPQMIH GGDKRDEFMT QPGSTVSVMD  180
TGDMQEPLSQ PSLSMSLAVT PSGPSSFPSG FVEGKMHILN HSTIVMKPSP AEGRGRNLLL  240
SRYCPRITDQ ELQQISGNLN SKIVPLFEKI LSASDAGRIG RLVLPKACAE AYFPSIDQPE  300
GTCMKIQDVK GKEWTFQFRF WPNNNSRMYV LEGVTPCMQS MKLKAGDTVT FSRIDPGGKL  360
VMGCRKTASG REQQGSGLKH TSWSGVTEIP SSMNCSSCPL QMPEEVEGLP EHMIILQKRE  420
SNGRGIADDE SSRIKEEKWT RNIGTKNKRL LLLNEEAMEL RLTWEEAQDL LCPPPTANPT  480
IVTVEEHRFE EYDEPPVFGK KTVFTSRPSG GHEQWAQCDN CSKWRRLPVD ALLPSRWTCS  540
YNVWDVGRCL CSAAEENLNE LDSFLRLGTE SKKQRTGESW KEGTEQEEGS GMDEVAGGVV  600
KGDSSGENGD GPEEEEEVAA TTRHPRHRPG CSCIVCIQPP SGRGRHEPGC SCNVCVAVKR  660
RFRTLMLRKR KKQLEREGGA EENHDINDNN GETVGIDLNS DPYNNRGEEM LL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	3e-69	245	375	2	132	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	658	671	KRRFRTLMLRKRKK
2	667	671	RKRKK

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_010558872.1

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_010558872.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like
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	XP_010558872.1	0.0	(Tarenaya hassleriana)

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]