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_010542684.1

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: 687aa MW: 75285.1 Da PI: 8.6397

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_010542684.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	65.1	1e-20	239	338	1	98
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 f+kvl+ sd+++ grlvlpk +ae++ ++++ e++ l+++d +g++W+++++y +++s++yvl+ G +a +L++gD+v+F++++ +++ XP_010542684.1 239 FEKVLSASDAGRIGRLVLPKACAEAYfpSINQSEGIPLKIQDVKGKEWTFQFRYwpNNNSRMYVLE-GVTPCIQAMQLQAGDTVTFSRID-PGGK 331 99************************888889999*************899999999.*******************887.5555 PP .EEEEE- CS B3 92 lvvkvfr 98 +v+++++ XP_010542684.1 332 FVMGFRK 338 5666554 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-30	236	343	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.96E-21	236	340	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.18E-25	237	338	No hit	No description
SMART	SM01019	1.5E-23	239	339	IPR003340	B3 DNA binding domain
Pfam	PF02362	5.3E-18	239	337	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.35	239	340	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	12.541	493	543	IPR011124	Zinc finger, CW-type
Pfam	PF07496	3.7E-10	498	540	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: 687 aa Download sequence Send to blast
MVELLDFGGV GCSTCTSSCY NTSLSKRGEN HDLLGRLTMI LADRQPPHNG KGGILGNNID 60 GGRLSQLCQI AEDHEPDLLS RSQSGEPQTL LGGDKRAEGF MPHPGFGKHL EPDSTTSASV 120 TRDMQESLSQ PSLSMSLAVT PSAPSLSSEV TEGKKPSIAT QSPTVEPSFS VLPKPSKSTV 180 STAPGTSNPA SSSSQLRLVR PPAEGRGRNH LLPRYWPRIS DQELQQISGN LNSKIVPLFE 240 KVLSASDAGR IGRLVLPKAC AEAYFPSINQ SEGIPLKIQD VKGKEWTFQF RYWPNNNSRM 300 YVLEGVTPCI QAMQLQAGDT VTFSRIDPGG KFVMGFRKTA NSGEQQGSGL TNGVSAEDTL 360 SSGVTENPSS INGSSGPLQM LKEVKGLPEH LSSLDGSNRL QKSQNNGGRT GDEDSLLVKG 420 KKRTRNIGTK NKRLLLQNEE AMKLRLTWEE AQDLLRPPPN AKPTIVTVEE HEFEEYDEPP 480 VFGKNIVFTS RPSGGHEQWA QCGECYKWRR LPMGVHLIAR WKCSDNVWDV GRCSCSAPEE 540 NLKELESLRL GKESKKRRNW ERKREGMSGL DALASAAGLG EGREEEAEEA ITTRHPRHRP 600 GCSCIVCIQP PSGKGKHKPC CCCNVCMTVK RRFRTLMLRK KKKKKMNRNS EKEEGIDLNM 660 GLPIQEEIDE SRASGRDGQK QSVASSG

Sequence ? help Back to Top

Protein Sequence Length: 687 aa Download sequence Send to blast

MVELLDFGGV GCSTCTSSCY NTSLSKRGEN HDLLGRLTMI LADRQPPHNG KGGILGNNID  60
GGRLSQLCQI AEDHEPDLLS RSQSGEPQTL LGGDKRAEGF MPHPGFGKHL EPDSTTSASV  120
TRDMQESLSQ PSLSMSLAVT PSAPSLSSEV TEGKKPSIAT QSPTVEPSFS VLPKPSKSTV  180
STAPGTSNPA SSSSQLRLVR PPAEGRGRNH LLPRYWPRIS DQELQQISGN LNSKIVPLFE  240
KVLSASDAGR IGRLVLPKAC AEAYFPSINQ SEGIPLKIQD VKGKEWTFQF RYWPNNNSRM  300
YVLEGVTPCI QAMQLQAGDT VTFSRIDPGG KFVMGFRKTA NSGEQQGSGL TNGVSAEDTL  360
SSGVTENPSS INGSSGPLQM LKEVKGLPEH LSSLDGSNRL QKSQNNGGRT GDEDSLLVKG  420
KKRTRNIGTK NKRLLLQNEE AMKLRLTWEE AQDLLRPPPN AKPTIVTVEE HEFEEYDEPP  480
VFGKNIVFTS RPSGGHEQWA QCGECYKWRR LPMGVHLIAR WKCSDNVWDV GRCSCSAPEE  540
NLKELESLRL GKESKKRRNW ERKREGMSGL DALASAAGLG EGREEEAEEA ITTRHPRHRP  600
GCSCIVCIQP PSGKGKHKPC CCCNVCMTVK RRFRTLMLRK KKKKKMNRNS EKEEGIDLNM  660
GLPIQEEIDE SRASGRDGQK QSVASSG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	3e-75	217	347	2	132	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	629	640	KRRFRTLMLRKK
2	629	644	KRRFRTLMLRKKKKKK
3	638	644	RKKKKKK

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_010542684.1

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_010542684.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	R0HB22	0.0	R0HB22_9BRAS; Uncharacterized protein
STRING	XP_010542684.1	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]