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 Tp57577_TGAC_v2_mRNA5141
Organism
Trifolium pratense
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium
Family B3
Protein Properties Length: 865aa    MW: 96069.5 Da    PI: 7.2143
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp57577_TGAC_v2_mRNA5141genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B356.55.2e-18321420198
                               EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEE CS
                        B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvv 81 
                               f+k l+ sd+++ grlvlpk +ae++   ++++e+  l+++d +g++W +++++  +++s++yvl+ G     ++ +L++gD+v+
  Tp57577_TGAC_v2_mRNA5141 321 FEKMLSASDAGRIGRLVLPKACAEAYfpPISQPEGLPLRIQDVKGKEWMFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVT 404
                               89**************************555567778***************9989999999***9.****************** PP

                               EEE-SSSEE..EEEEE- CS
                        B3  82 Fkldgrsefelvvkvfr 98 
                               F++++  e++l +++++
  Tp57577_TGAC_v2_mRNA5141 405 FSRMD-PEGKLIMGFRK 420
                               **876.77777777765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.5E-29313429IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.2E-18318420IPR015300DNA-binding pseudobarrel domain
CDDcd100179.76E-22319420No hitNo description
PfamPF023621.5E-15321420IPR003340B3 DNA binding domain
PROSITE profilePS5086311.166321422IPR003340B3 DNA binding domain
SMARTSM010191.2E-19321421IPR003340B3 DNA binding domain
PROSITE profilePS5105013.298550600IPR011124Zinc finger, CW-type
PfamPF074969.0E-10555597IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010030Biological Processpositive regulation of seed germination
GO:2000034Biological Processregulation of seed maturation
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 865 aa     Download sequence    Send to blast
MESRCCMNVL CGTSTSIRWR KGWLLRSGEF SDLCDKCGSA YDQSAFCDIF HAKDSGWREC  60
TSCGKRLHCG CVASKSQLEI LDTGGVSCIT CTSYSGLQPI AGNEKPNESE TAKVKHVSVQ  120
QYLSLANQLN ARGMQVGNYT ENDGLRCWLK PHNVNMDGPS TEIKPEVLPS VGEFGSTLVS  180
QFHRESNGSS RTAKGENYKA GDMQDIYESL TQTNLSMTLA APLVNSNPFH NVLVDEREQS  240
KMSAPLLLAS RSRHLLPKPP RPTLSPGLEA NAGMVSQVRI ARPPAEGRGR NQLLPRYWPR  300
ITDQELQQIS GDSNSTIVPL FEKMLSASDA GRIGRLVLPK ACAEAYFPPI SQPEGLPLRI  360
QDVKGKEWMF QFRFWPNNNS RMYVLEGVTP CIQSMQLQAG DTVTFSRMDP EGKLIMGFRK  420
ATNSASVQSQ KGCSETHLNA LSKKWNSVGG DMDWHNVEMP ESRKRDALSL PPVLVPEKKR  480
TRNIGSKSKR LLIDSQDALE LKLTWEEAQD LLRPPPEVKP SVVMIEDHLF EEYEEPPVFG  540
KKSIFVVRSN GINEQWTQCD SCLKWRKLPV DVLIPPKWTC MENFWDQSRC SCAAPNELNP  600
RELDNLLRMN KEFKKQRLAA ASQRPALERE SPGLDALANA AVLGDDASES GTTPVMTTTK  660
HPRHRPGCSC IVCIQPPSGK GKHKPTCTCN VCMTVKRRFK TLMMRKKKRQ SEREAEIAQK  720
NQLSYRTKDE SEVDSTSRHL TPVNGSENGA RVPNELDSRS QDQVAEAATG QLDLNCQPDR  780
DDVQSGPNTL SMMTLLEEAN LPLETYLKQN GLSSLISEQQ TNSASNVQAQ TTNESEGRQN  840
EDCNTASVVH EQEGSPEENS NSVS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A9e-702994292132B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1695706KRRFKTLMMRKK
2695708KRRFKTLMMRKKKR
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 VAL1/HSI2. {ECO:0000269|PubMed:17158584, ECO:0000269|PubMed:17267611}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapTp57577_TGAC_v2_mRNA5141
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1475370.0AC147537.39 Medicago truncatula clone mth2-133k2, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013455146.10.0B3 domain-containing transcription repressor VAL2 isoform X4
SwissprotQ5CCK40.0VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBLA0A2K3NLM20.0A0A2K3NLM2_TRIPR; B3 domain-containing protein
STRINGAES874860.0(Medicago truncatula)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G32010.10.0HSI2-like 1
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]
  4. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]