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.11G197900.1.p

Common Name

GLYMA_11G197900, LOC100789848

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: 912aa MW: 100739 Da PI: 7.459

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.11G197900.1.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.11G197900.1.p 336 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQSEGVPLRMQDVKGNEWTFQFRFwpNNNSRMYVLE-GVTPCIQAMQLCAGDTVTFSRID 424 99************************666778999***********99899999999.*******************887 PP SSEE..EEEEE-S CS B3 87 rsefelvvkvfrk 99 +++lv++++++ Glyma.11G197900.1.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	6.01E-23	334	435	No hit	No description
Pfam	PF02362	1.6E-16	336	435	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.532	336	437	IPR003340	B3 DNA binding domain
SMART	SM01019	7.5E-23	336	437	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	14.611	597	647	IPR011124	Zinc finger, CW-type
Pfam	PF07496	8.9E-11	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: 912 aa Download sequence Send to blast
MGSDICVVNG SCTHEWRKGW PLRSGGFAQL CCKCGFMEEW KGDILDRLSA YENSVFCNKF 60 HRQQTGWREC NFCNKPIHSG CIVSRSLFGY LDFGGIGCVS CVNTTQLSMM RNTENPNVSV 120 SSIKNNASDR HSAHFDGRLL VGGVDEGKLM QFCKIIEASE SSHWNHAQSD GIIAHHGQNN 180 QEAKCSFREG DIGFSNVRKP SVQSLTFATL ENNRSTWEIK NMHESNAQPS FSMYLGNASG 240 NDSVPPSAGE AVEGRLEGKT SPPFQRSRPI CPKPLKSGLT MNVETDKGAI SQSRVARPPA 300 DGRGKNQLLP RYWPRITDQE LERLAGDLKS TVVPLFEKVL SASDAGRIGR LVLPKACAEA 360 YFPPISQSEG VPLRMQDVKG NEWTFQFRFW PNNNSRMYVL EGVTPCIQAM QLCAGDTVTF 420 SRIDPGGKLV MGFRKASNST DTQDASTSAQ SNSAKGTISS GTENLPSGSN HANLLHSLTG 480 NVETHLNGHT EHLHLGTGTA GLLKTENNEM TNSSSPQQQI SVLEKKRTRN IGPKSKRLLI 540 DNEDAMELKL TWEEAQDLLR PPPSVKPNIV TIEDQVFEEY DEPPVFGKRT IFSACSSGGK 600 EQWAQCDDCS KWRKLPVDAL LPPKWTCSEN VWDSSRCSCS VPEELSSKEL ENLLKTNKDF 660 KKRRIAESSK SIQEHEASGL DALASAAVLG ENLVDTAESS AGATTKHPRH RPGCSCIVCI 720 QPPSGKGRHK PTCTCNVCMT VKRRFKTLML RKKKRQSERE ADTAQKDQTL LKDEPDTNGA 780 PRDDTSRLEK EVGLNKSQHQ VGESSTGQID LNSHPNREDM QVETTGLNMS SHLEPATNHT 840 VGEFMDKNDL RRSFNNEVQT GQNSSLHTPP QSSGEGQRYF SDGRCFASIV WNQERKDEVH 900 SQPNQSQNNL S*

Sequence ? help Back to Top

Protein Sequence Length: 912 aa Download sequence Send to blast

MGSDICVVNG SCTHEWRKGW PLRSGGFAQL CCKCGFMEEW KGDILDRLSA YENSVFCNKF  60
HRQQTGWREC NFCNKPIHSG CIVSRSLFGY LDFGGIGCVS CVNTTQLSMM RNTENPNVSV  120
SSIKNNASDR HSAHFDGRLL VGGVDEGKLM QFCKIIEASE SSHWNHAQSD GIIAHHGQNN  180
QEAKCSFREG DIGFSNVRKP SVQSLTFATL ENNRSTWEIK NMHESNAQPS FSMYLGNASG  240
NDSVPPSAGE AVEGRLEGKT SPPFQRSRPI CPKPLKSGLT MNVETDKGAI SQSRVARPPA  300
DGRGKNQLLP RYWPRITDQE LERLAGDLKS TVVPLFEKVL SASDAGRIGR LVLPKACAEA  360
YFPPISQSEG VPLRMQDVKG NEWTFQFRFW PNNNSRMYVL EGVTPCIQAM QLCAGDTVTF  420
SRIDPGGKLV MGFRKASNST DTQDASTSAQ SNSAKGTISS GTENLPSGSN HANLLHSLTG  480
NVETHLNGHT EHLHLGTGTA GLLKTENNEM TNSSSPQQQI SVLEKKRTRN IGPKSKRLLI  540
DNEDAMELKL TWEEAQDLLR PPPSVKPNIV TIEDQVFEEY DEPPVFGKRT IFSACSSGGK  600
EQWAQCDDCS KWRKLPVDAL LPPKWTCSEN VWDSSRCSCS VPEELSSKEL ENLLKTNKDF  660
KKRRIAESSK SIQEHEASGL DALASAAVLG ENLVDTAESS AGATTKHPRH RPGCSCIVCI  720
QPPSGKGRHK PTCTCNVCMT VKRRFKTLML RKKKRQSERE ADTAQKDQTL LKDEPDTNGA  780
PRDDTSRLEK EVGLNKSQHQ VGESSTGQID LNSHPNREDM QVETTGLNMS SHLEPATNHT  840
VGEFMDKNDL RRSFNNEVQT GQNSSLHTPP QSSGEGQRYF SDGRCFASIV WNQERKDEVH  900
SQPNQSQNNL S*

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.11G197900.1.p

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AP015038	1e-158	AP015038.1 Vigna angularis var. angularis DNA, chromosome 5, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006591264.2	0.0	B3 domain-containing transcription repressor VAL1
Refseq	XP_014619648.1	0.0	B3 domain-containing transcription repressor VAL1
Refseq	XP_014619649.1	0.0	B3 domain-containing transcription repressor VAL1
Refseq	XP_014619650.1	0.0	B3 domain-containing transcription repressor VAL1
Refseq	XP_028189970.1	0.0	B3 domain-containing transcription repressor VAL1-like
Refseq	XP_028189971.1	0.0	B3 domain-containing transcription repressor VAL1-like
Refseq	XP_028189972.1	0.0	B3 domain-containing transcription repressor VAL1-like
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	A0A445I4E8	0.0	A0A445I4E8_GLYSO; Uncharacterized protein
TrEMBL	K7LR55	0.0	K7LR55_SOYBN; Uncharacterized protein
STRING	GLYMA11G31234.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF10323	30	39
Representative plant	OGRP1236	14	46

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.11G197900.1.p
Entrez Gene	100789848

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]