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

Glyma.18G052100.3.p

Common Name

GLYMA_18G052100

Organism

Glycine max

Taxonomic ID

3847

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja

Family

Protein Properties

Length: 909aa MW: 100380 Da PI: 7.4155

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.18G052100.3.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	63	4.9e-20	336	436	1	99
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldg 86 f+kvl+ sd+++ grlvlpk +ae++ +++ e++ l+++d +g++W++++++ +++s++yvl+ G +a +L++gD+v+F++++ Glyma.18G052100.3.p 336 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQSEGVPLRMQDVKGNEWTFQFRFwpNNNSRMYVLE-GVTPCIQAMQLCAGDTVTFSRID 424 99************************666778999***********99899999999.*******************887 PP SSEE..EEEEE-S CS B3 87 rsefelvvkvfrk 99 +++lv++++++ Glyma.18G052100.3.p 425 -PGGKLVMGFRKA 436 .788888887765 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.4E-30	332	443	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.27E-20	334	436	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	5.97E-23	334	435	No hit	No description
PROSITE profile	PS50863	10.532	336	437	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.6E-16	336	435	IPR003340	B3 DNA binding domain
SMART	SM01019	7.5E-23	336	437	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	14.181	597	647	IPR011124	Zinc finger, CW-type
Pfam	PF07496	2.3E-9	602	644	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: 909 aa Download sequence Send to blast
MGSNICVVNG SCTHEWRKGW PLRSGGFAQL CCKCGFMEEW KGDILDPLSA YENSVFCNKF 60 HCQQTGWREC NFCNKPIHCG CIVSRSLFEY LDFGGIGCVS CVNTTQLSMM RNMENPNVTV 120 LSIKNNAGDR HSAHFDGRLP VGGVDEGKLM QFCKIIEASE SSRWNHAQRD GIIAHRGQKN 180 QEAKSSFREV EIGFSNVMNP SVQSLTFATL ENNRSTWEIK NMHESNTKPS LSMYLGNASG 240 NNSVPPSAGE AVEGRLDGKT SPPFQGSRSI FPKPLKNGLT MNMETNKGTM SQSRVARPPA 300 DGRGKNQLLP RYWPRITDEE LERLAGDLKS TVVPLFEKVL SASDAGRIGR LVLPKACAEA 360 YFPPISQSEG VPLRMQDVKG NEWTFQFRFW PNNNSRMYVL EGVTPCIQAM QLCAGDTVTF 420 SRIDPGGKLV MGFRKASNST DTQDASTSAQ SNSAKGTVSS GTENLPSGSN NADLLHSLTG 480 NVECHLNGHT EHLHLGTGTA GLLKTENNEM TNSSSPQQQI SVLEKKRTRN IGPKSKRLLI 540 DNEDAMELKL TWEEAQDLLR PPPSVKPSIV TIEDQVIEEY DEPPVFGKRT IFSACSSGGK 600 EQWAQCDDCS KWRKLPVDAL LPPKWTCCEN VWDSSRCSCS APEELSSREI ENLLKNNKDF 660 KKRRIVESSK SIQEHEPSGL DALASAAVLG ENLIDTAESS AGVTTKHPRH RPGCSCIVCI 720 QPPSGKGRHK PTCTCNVCMT VKRRFKTLML RKKKRQSERE ADAAQKDQTL PKDELDTNGA 780 SRDDTSQLEK EAGLKSQHEV GGSSAGQIDL NSHPNREDMQ VETTGLNMSS HLEPATNHTV 840 GEFMNQNGLR NFNNEVQTGQ NSSLHTPKSN GEGQRYFSDG RCFASIMWNQ ERKDEVHSQT 900 NQSQNNLS*

Sequence ? help Back to Top

Protein Sequence Length: 909 aa Download sequence Send to blast

MGSNICVVNG SCTHEWRKGW PLRSGGFAQL CCKCGFMEEW KGDILDPLSA YENSVFCNKF  60
HCQQTGWREC NFCNKPIHCG CIVSRSLFEY LDFGGIGCVS CVNTTQLSMM RNMENPNVTV  120
LSIKNNAGDR HSAHFDGRLP VGGVDEGKLM QFCKIIEASE SSRWNHAQRD GIIAHRGQKN  180
QEAKSSFREV EIGFSNVMNP SVQSLTFATL ENNRSTWEIK NMHESNTKPS LSMYLGNASG  240
NNSVPPSAGE AVEGRLDGKT SPPFQGSRSI FPKPLKNGLT MNMETNKGTM SQSRVARPPA  300
DGRGKNQLLP RYWPRITDEE LERLAGDLKS TVVPLFEKVL SASDAGRIGR LVLPKACAEA  360
YFPPISQSEG VPLRMQDVKG NEWTFQFRFW PNNNSRMYVL EGVTPCIQAM QLCAGDTVTF  420
SRIDPGGKLV MGFRKASNST DTQDASTSAQ SNSAKGTVSS GTENLPSGSN NADLLHSLTG  480
NVECHLNGHT EHLHLGTGTA GLLKTENNEM TNSSSPQQQI SVLEKKRTRN IGPKSKRLLI  540
DNEDAMELKL TWEEAQDLLR PPPSVKPSIV TIEDQVIEEY DEPPVFGKRT IFSACSSGGK  600
EQWAQCDDCS KWRKLPVDAL LPPKWTCCEN VWDSSRCSCS APEELSSREI ENLLKNNKDF  660
KKRRIVESSK SIQEHEPSGL DALASAAVLG ENLIDTAESS AGVTTKHPRH RPGCSCIVCI  720
QPPSGKGRHK PTCTCNVCMT VKRRFKTLML RKKKRQSERE ADAAQKDQTL PKDELDTNGA  780
SRDDTSQLEK EAGLKSQHEV GGSSAGQIDL NSHPNREDMQ VETTGLNMSS HLEPATNHTV  840
GEFMNQNGLR NFNNEVQTGQ NSSLHTPKSN GEGQRYFSDG RCFASIMWNQ ERKDEVHSQT  900
NQSQNNLS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	6e-69	314	443	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	754	KRRFKTLMLRKKKR

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Glyma.18G052100.3.p

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_006602061.2	0.0	B3 domain-containing transcription repressor VAL1 isoform X2
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	K7MQ28	0.0	K7MQ28_SOYBN; Uncharacterized protein
STRING	GLYMA18G05840.2	0.0	(Glycine max)

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	Glyma.18G052100.3.p

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]