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 RrC1722_p2
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family bHLH
Protein Properties Length: 304aa    MW: 33825.4 Da    PI: 7.7604
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1722_p2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH35.22.2e-1185128855
                 HHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
         HLH   8 rErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  Er RR+++++ f++L  llP++     +K +K++i+ +Av  IksL+
  RrC1722_p2  85 TERERRKKMRDMFSKLHALLPQL----PPKADKSTIVDEAVSSIKSLE 128
                 6*********************6....39*****************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088813.33877127IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474593.01E-1478138IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.103.1E-1481139IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000835.82E-1382132No hitNo description
SMARTSM003536.5E-885133IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000101.1E-885128IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009793Biological Processembryo development ending in seed dormancy
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 304 aa     Download sequence    Send to blast
MSIQFNMTNA QELGQEGFVW GISSSDDSGG GCRRIEKQLP LPQPSVLLEN PILMDKKSAK  60
GKKRTKRNGK NHAEDSPDHE IHIWTERERR KKMRDMFSKL HALLPQLPPK ADKSTIVDEA  120
VSSIKSLEQT LQKLQMKKLE KLQYSSASNT TASPTTLLTP ILNHSQILPV GAAPADCYSR  180
EAFLADQISS SITNLPYPCN DPTAAFDIWS SRNVVLNICG NEAFFNICCP KDKSGVFTNV  240
CYLFEKYNIE VVFANVSSNV YRSTYVIQAQ VSPTYENQLL GDGFGVGDIF KQAANELALY  300
FSST
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that controls embryo growth (PubMed:18567831, PubMed:18849529, PubMed:23318634). Regulates endosperm breakdown and embryonic epidermal development. Regulates the expression of SBT2.4/ALE1 (PubMed:18849529, PubMed:23318634). Involved in embryonic cuticle formation upstream of SBT2.4/ALE1 (PubMed:23318634). Does not seem to be a general regulator of endosperm patterning. May control specific signaling pathways that coordinate embryo invasion and breakdown of surrounding endosperm tissues (PubMed:18849529). Required for the production the embryo sheath, an extracuticular endosperm-derived structure at the surface of the embryo. Acts upstream of KRS (PubMed:28696222). {ECO:0000269|PubMed:18567831, ECO:0000269|PubMed:18849529, ECO:0000269|PubMed:23318634, ECO:0000269|PubMed:28696222}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF4886238e-87AF488623.1 Arabidopsis thaliana clone bHLH095 putative bHLH transcription factor mRNA, partial sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018488206.10.0PREDICTED: transcription factor bHLH95
SwissprotQ9FXA31e-154BH095_ARATH; Transcription factor bHLH95
TrEMBLA0A0D3CPI20.0A0A0D3CPI2_BRAOL; Uncharacterized protein
STRINGBo6g018390.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM50742549
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G49770.11e-114bHLH family protein
Publications ? help Back to Top
  1. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
    [PMID:20219281]
  2. Zhang Y, et al.
    Reduced function of the RNA-binding protein FPA rescues a T-DNA insertion mutant in the Arabidopsis ZHOUPI gene by promoting transcriptional read-through.
    Plant Mol. Biol., 2016. 91(4-5): p. 549-61
    [PMID:27164978]
  3. Fourquin C, et al.
    Mechanical stress mediated by both endosperm softening and embryo growth underlies endosperm elimination in Arabidopsis seeds.
    Development, 2016. 143(18): p. 3300-5
    [PMID:27287798]
  4. Du Q,Wang H
    Retarded Embryo Development 1 (RED1) regulates embryo development, seed maturation and plant growth in Arabidopsis.
    J Genet Genomics, 2016. 43(7): p. 439-49
    [PMID:27477025]
  5. Moussu S, et al.
    ZHOUPI and KERBEROS Mediate Embryo/Endosperm Separation by Promoting the Formation of an Extracuticular Sheath at the Embryo Surface.
    Plant Cell, 2017. 29(7): p. 1642-1656
    [PMID:28696222]