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 29915.m000469
Common NameRCOM_1057510
Organism
Ricinus communis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus
Family B3
Protein Properties Length: 891aa    MW: 98497.2 Da    PI: 7.078
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
29915.m000469genomeJCVIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B358.51.2e-18336436199
                    EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
             B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                    f+kvl+ sd+++ grlvlpk +ae++   ++++e+  l+++d +g++W +++++  +++s++yvl+ G     ++ +L++gD+v+F++++  e++l
  29915.m000469 336 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQPEGLPLRIQDVKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRMD-PEGKL 429
                    99**************************555567778***************9989999999***9.********************876.77778 PP

                    EEEEE-S CS
             B3  93 vvkvfrk 99 
                    v++++++
  29915.m000469 430 VMGFRKA 436
                    8877765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.8E-30327440IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.36E-20333437IPR015300DNA-binding pseudobarrel domain
CDDcd100179.80E-23334435No hitNo description
PfamPF023623.7E-16336436IPR003340B3 DNA binding domain
PROSITE profilePS5086311.152336437IPR003340B3 DNA binding domain
SMARTSM010195.0E-21336437IPR003340B3 DNA binding domain
PROSITE profilePS5105013.035565615IPR011124Zinc finger, CW-type
PfamPF074969.2E-7570612IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010030Biological Processpositive regulation of seed germination
GO:2000034Biological Processregulation of seed maturation
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 891 aa     Download sequence    Send to blast
MESKKTCMNA LCGATSNDWR KGWPLRSGDF ALLCDNCGTA YEQSTFCDLF HSKDSGWREC  60
VSCGKRLHCG CIASRFLLEL LDGGGVNCIN CIKSSGINSV SSNHLYGLAN LFYVWDEKPN  120
GFGMSKLDNV SELQSSDNQL DVERKFLRLG NSTEVIATRH LLQLQNDETS VSFRQMKQED  180
NFPPVGEIGS TSFSNLNQAS NGLSLTAKPE TRKATIAAKE LYESLTQTNL SITLGSTFGN  240
PIPFPGAVVD ERTQSKASSP LQQGSRCRHL LPKPPKSALV TGLETNAGMV SQIRVARPPA  300
EGRGRNQLLP RYWPRITDQE LQQISADSNS TIVPLFEKVL SASDAGRIGR LVLPKACAEA  360
YFPPISQPEG LPLRIQDVKG KEWVFQFRFW PNNNSRMYVL EGVTPCIQSM QLQAGDTVTF  420
SRMDPEGKLV MGFRKASNSM AVQSLKGSTD THLSALSKHL HSANGDISWH KSEKHEERTR  480
ESLLLTSLLV PERKRARNIG SKSKRLLIDS LDALELKLTW EEAQDFLRPP PTVKPSIVTI  540
EDHDFEEYEE PPVFGKRSIF IVRAVGGQEQ WTPCDSCCKW RKLPVDILLP PKWTCADNLG  600
DQSRCSCSAP DELTPRELEN LLRLNKDFKK RRITTILRPA QEQESSGLDA LANAAILGDE  660
ADPGTTAVAT TTKHPRHRPG CSCIVCIQPP SGKGKHKPSC TCNVCMTVKR RFKTMMLRKK  720
KRQSEREAEI AQRNQHISGL RDEAEVESSS KHASTPQDPS ENEARSMNEL ESKSQSNNLS  780
NKMVDAGKGH IDLNCQPDRE EESQAGVARM SMMSLLQVAS LPLETYLKQN GLTSLVSEQQ  840
GSSASHVPPQ AGESEGRLPE DCQIASAVQE QESGGEDNYG HGPEESQNDP V
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A2e-683144432131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1708719KRRFKTMMLRKK
2708721KRRFKTMMLRKKKR
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
PlantRegMap29915.m000469
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015580571.10.0B3 domain-containing transcription repressor VAL2 isoform X2
SwissprotQ5CCK40.0VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBLB9SRS40.0B9SRS4_RICCO; Transcription factor, putative
STRINGXP_002528687.10.0(Ricinus communis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF110183239
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]