PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Gorai.003G152700.1
Common NameB456_003G152700
Organism
Gossypium raimondii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family B3
Protein Properties Length: 886aa    MW: 97711.2 Da    PI: 6.7946
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.003G152700.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B359.55.8e-19353452198
                         EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                         f+kvl+ sd+++ grlvlpk +ae++   +++ e+  l+++d +g++W++++++  +++s++yvl+ G     ++ +L++gD+v+F++++ 
  Gorai.003G152700.1 353 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQSEGLPLRIQDVNGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMQLRAGDTVTFSRID- 441
                         99**************************555556677***************9989999999***9.********************887. PP

                         SEE..EEEEE- CS
                  B3  88 sefelvvkvfr 98 
                          +++lv+++++
  Gorai.003G152700.1 442 PGGKLVMGFRK 452
                         77777777765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.9E-30350455IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.97E-21350453IPR015300DNA-binding pseudobarrel domain
CDDcd100172.81E-24351452No hitNo description
PROSITE profilePS5086311.152353454IPR003340B3 DNA binding domain
PfamPF023623.5E-16353452IPR003340B3 DNA binding domain
SMARTSM010192.5E-23353453IPR003340B3 DNA binding domain
PROSITE profilePS5105014.275581631IPR011124Zinc finger, CW-type
PfamPF074962.1E-10586628IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010030Biological Processpositive regulation of seed germination
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:2000034Biological Processregulation of seed maturation
GO:0005634Cellular Componentnucleus
GO:0005739Cellular Componentmitochondrion
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 886 aa     Download sequence    Send to blast
MTLKGDLILI FDFDLSSLCW MGSKICMNSS CGAATSNEWK KGWPLRSGGF AHLCYPCGSA  60
YEDGVYCDTF HLEESGWREC RICGNHLHCG CIASNYLLEL LDYGGVGCIS CAKSSRLHTV  120
KRIQTHGDEI PEGVGAVPMN NAGSSAVEGK AVSDHVDERT LAPLCKSMEA NECNLLPQSQ  180
RGDANASLGQ HRGEEVICPT EKVGAGFSNA TQPYVRPANF AKLDNARSAL DVRDIQDSLP  240
QPYLSMSLGG SSANPNFLLP FSSGLADGKE PSKTWSSFQQ GQQSRRILPK PSKNGLTTSS  300
ELNKGMIPQA RITRPPVEGR GKNHLLPRYW PRITDQELQK LSGDLKSTIV PLFEKVLSAS  360
DAGRIGRLVL PKACAEAYFP PISQSEGLPL RIQDVNGKEW TFQFRFWPNN NSRMYVLEGV  420
TPCIQSMQLR AGDTVTFSRI DPGGKLVMGF RKAANSDTQT PKGGKDLLGN ALSEHFGLPD  480
GNISRSRDED HGVRANENSV HQLAMNAEKK KTRNIGSKSK RLLMHSVDAL ELRLTWEEAQ  540
DLLRPPPSVR PSIVTIEDHE FEEYDEPPVF GKRTIFGAWP SGEQEQWAQC DDCSKWRRLP  600
VDVLLPSKWK CSDNVWDSSR CACSAPEETG PKELENILKV GTDLKKAKVQ ESPKVAPEPE  660
PTGLDALASA AVLGDKMGDV GESSVGATTK HPRHRPGCTC IVCIQPPSGK GKHKANCTCN  720
VCLTVKRRFK TLMLRKKKRQ SEREAEISER DNKKQMDETE LKDTRNDHSE NEGSRSRIEG  780
EVAEASTGEI DLNCHPIRED VQLEGGLNMM SFVEATSLPV ENYIKQNGIE SLKTEQQQQG  840
SLGSHFQSKV NRENERPLSD EEFLASVGWE HVGHKEPCLE RNSLQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A5e-703314562127B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1725736KRRFKTLMLRKK
2725738KRRFKTLMLRKKKR
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE 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
UniProtTranscriptional 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
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJX5814785e-78JX581478.1 Gossypium hirsutum clone NBRI_GE14122 microsatellite sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012471733.10.0PREDICTED: B3 domain-containing transcription repressor VAL1-like
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A0D2P1Z80.0A0A0D2P1Z8_GOSRA; Uncharacterized protein
STRINGGorai.003G152700.10.0(Gossypium raimondii)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM72032639
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G30470.10.0high-level expression of sugar-inducible gene 2
Publications ? help Back to Top
  1. Paterson AH, et al.
    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Nature, 2012. 492(7429): p. 423-7
    [PMID:23257886]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]
  9. 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]
  10. 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]
  11. 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]