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

Ciclev10000225m

Common Name

CICLE_v10000225mg

Organism

Citrus clementina

Taxonomic ID

85681

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus

Family

Protein Properties

Length: 894aa MW: 99095.7 Da PI: 7.198

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Ciclev10000225m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	58.1	1.6e-18	331	430	1	98
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 f+k+l+ sd+++ grlvlpk +ae++ +++ e++ l+++d +g++W +++++ +++s++yvl+ G ++ +L++gD+++F++++ ++ Ciclev10000225m 331 FEKILSASDAGRIGRLVLPKACAEAYfpHISQSEGVPLRVQDVKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTITFSRID-PGG 422 99************************777778999***********99899999999.*******************887.788 PP ..EEEEE- CS B3 91 elvvkvfr 98 +lv+++++ Ciclev10000225m 423 KLVMGFRK 430 78887776 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	7.1E-29	327	431	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	2.88E-20	328	430	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.69E-23	329	430	No hit	No description
PROSITE profile	PS50863	10.856	331	432	IPR003340	B3 DNA binding domain
SMART	SM01019	6.4E-21	331	431	IPR003340	B3 DNA binding domain
Pfam	PF02362	8.2E-16	331	430	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	13.518	595	645	IPR011124	Zinc finger, CW-type
Pfam	PF07496	8.4E-9	600	642	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: 894 aa Download sequence Send to blast
MGPRICMNPK CRTANTHEWK KGWLLRSGVC ADLCYDCGSA YENFIFCNTF HLEEPGWREC 60 NFCSKRLHCG CRASNSFLEL LDYGGVGCRS CAMSPRLHLI QRDEIPNGFG ALTKKDSDDT 120 QTPMLENRVV GDGTAEGKLT QLCRIMEANE PSFLAPFQRG DTIVSLGQEK REELRLPFVE 180 VGTGFSSPTK LSSRSSKFTK PDGSRSMLDV RDMPESLAQR SSSMSLGVPA GCSNFVPPFS 240 NGAADGREPC KAHPSFQQGQ RSRPILPKPS KTGLTISSET KKSTASQLRI ARPPAEGRGK 300 NHLLPRYWPR ITDQELQQLS GDLNSTIVPL FEKILSASDA GRIGRLVLPK ACAEAYFPHI 360 SQSEGVPLRV QDVKGKEWVF QFRFWPNNNS RMYVLEGVTP CIQSMQLQAG DTITFSRIDP 420 GGKLVMGFRK APIPGDMQDA QTSAITNGCP GESSLSGVTE NLPTVSGYSG HFQMLKGSKD 480 PHIDALSEHL SLAEGDNGWH KSENHGQKTN EDSPQKSLLG MEKKRTRNIG SKSKRLLMHS 540 EEAMELRLTW EEAQDLLRPS PSARPNIVTI EDHEFEEYDE PPVFGKRTVF TARPSGEQEQ 600 WAPCDDCSKW RKLPTDALLP PKWTCSDNVW DSIRCSCSAA EEMIQKDLEN LLRVGRESKK 660 RKIVESQRRD QQNEPSGLDA LATAAVLGDY AGDSGEPSSV GATTTRHPRH RPGCTCIVCI 720 QPPSGKGKHK PTCTCNVCMT VKRRFKTLML RKKRRQSERE VEVAQKNHSD QMGDSEMNGS 780 VKQESVPTSH TDNEISQTKS QTEVAESSSA QIGLDLNCYP NREDMQPEES RVSIMTLDRV 840 ASVPLEDCHP NGLASLSSCM LQQVNNGDHE RLLSDERFLA SVGWGRDQEP NLD*

Sequence ? help Back to Top

Protein Sequence Length: 894 aa Download sequence Send to blast

MGPRICMNPK CRTANTHEWK KGWLLRSGVC ADLCYDCGSA YENFIFCNTF HLEEPGWREC  60
NFCSKRLHCG CRASNSFLEL LDYGGVGCRS CAMSPRLHLI QRDEIPNGFG ALTKKDSDDT  120
QTPMLENRVV GDGTAEGKLT QLCRIMEANE PSFLAPFQRG DTIVSLGQEK REELRLPFVE  180
VGTGFSSPTK LSSRSSKFTK PDGSRSMLDV RDMPESLAQR SSSMSLGVPA GCSNFVPPFS  240
NGAADGREPC KAHPSFQQGQ RSRPILPKPS KTGLTISSET KKSTASQLRI ARPPAEGRGK  300
NHLLPRYWPR ITDQELQQLS GDLNSTIVPL FEKILSASDA GRIGRLVLPK ACAEAYFPHI  360
SQSEGVPLRV QDVKGKEWVF QFRFWPNNNS RMYVLEGVTP CIQSMQLQAG DTITFSRIDP  420
GGKLVMGFRK APIPGDMQDA QTSAITNGCP GESSLSGVTE NLPTVSGYSG HFQMLKGSKD  480
PHIDALSEHL SLAEGDNGWH KSENHGQKTN EDSPQKSLLG MEKKRTRNIG SKSKRLLMHS  540
EEAMELRLTW EEAQDLLRPS PSARPNIVTI EDHEFEEYDE PPVFGKRTVF TARPSGEQEQ  600
WAPCDDCSKW RKLPTDALLP PKWTCSDNVW DSIRCSCSAA EEMIQKDLEN LLRVGRESKK  660
RKIVESQRRD QQNEPSGLDA LATAAVLGDY AGDSGEPSSV GATTTRHPRH RPGCTCIVCI  720
QPPSGKGKHK PTCTCNVCMT VKRRFKTLML RKKRRQSERE VEVAQKNHSD QMGDSEMNGS  780
VKQESVPTSH TDNEISQTKS QTEVAESSSA QIGLDLNCYP NREDMQPEES RVSIMTLDRV  840
ASVPLEDCHP NGLASLSSCM LQQVNNGDHE RLLSDERFLA SVGWGRDQEP NLD*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	6e-71	309	438	2	131	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	741	752	KRRFKTLMLRKK
2	741	753	KRRFKTLMLRKKR

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in flowers and at lower levels in roots, stems and leaves. {ECO:0000269\|PubMed:15894743}.

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}.

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_006432020.1	0.0	B3 domain-containing transcription repressor VAL1
Refseq	XP_006491930.1	0.0	B3 domain-containing transcription repressor VAL1
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	V4T1N2	0.0	V4T1N2_9ROSI; Uncharacterized protein
STRING	XP_006491930.1	0.0	(Citrus sinensis)
STRING	XP_006432020.1	0.0	(Citrus clementina)

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	Ciclev10000225m
Entrez Gene	18040251

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]