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 Rsa1.0_03012.1_g00002.1
Organism
Raphanus sativus
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 YABBY
Protein Properties Length: 237aa    MW: 26178.7 Da    PI: 8.5067
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_03012.1_g00002.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1YABBY275.75.5e-85171982170
                    YABBY   2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee.......lleelkveee 80 
                              d+ sss+q+Cyv+C+fC+t+lavsvP +slfk+vtvrCGhC++llsv++++++ ll+++s++++s+ ++       llee+++ ++
  Rsa1.0_03012.1_g00002.1  17 DHISSSDQLCYVHCSFCDTVLAVSVPPSSLFKTVTVRCGHCSNLLSVTVNMRALLLPSVSNIGHSYLPSpsppppnLLEEMRNGGQ 102
                              7899***************************************************************999999************* PP

                    YABBY  81 nlksnvekeesastsvssekl......senedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknW 160
                              n+++n+++++++ +++s+e++       + + +e+pr+pp++rPPekrqrvPsaynrfikeeiqrika+nPdishreafsaaaknW
  Rsa1.0_03012.1_g00002.1 103 NINMNMMMNHQPAAHHSNESFvmatrnGRVDLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNW 188
                              **************9999887778776666889***************************************************** PP

                    YABBY 161 ahfPkihfgl 170
                              ahfP+ihfgl
  Rsa1.0_03012.1_g00002.1 189 AHFPHIHFGL 198
                              ********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046905.1E-6921198IPR006780YABBY protein
SuperFamilySSF470957.2E-8143192IPR009071High mobility group box domain
Gene3DG3DSA:1.10.30.108.8E-5146192IPR009071High mobility group box domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0010154Biological Processfruit development
GO:0010158Biological Processabaxial cell fate specification
GO:1902183Biological Processregulation of shoot apical meristem development
GO:2000024Biological Processregulation of leaf development
Sequence ? help Back to Top
Protein Sequence    Length: 237 aa     Download sequence    Send to blast
MSSMSMSSSS APTYPPDHIS SSDQLCYVHC SFCDTVLAVS VPPSSLFKTV TVRCGHCSNL  60
LSVTVNMRAL LLPSVSNIGH SYLPSPSPPP PNLLEEMRNG GQNINMNMMM NHQPAAHHSN  120
ESFVMATRNG RVDLQEMPRP PPANRPPEKR QRVPSAYNRF IKEEIQRIKA GNPDISHREA  180
FSAAAKNWAH FPHIHFGLMP DHPPTKKANV RQQEGEEVMM GREGFYGSAA NVGVTHN
Functional Description ? help Back to Top
Source Description
UniProtInvolved in the abaxial cell fate determination during embryogenesis and organogenesis. Regulates the initiation of embryonic shoot apical meristem (SAM) development (PubMed:10457020, PubMed:12417699, PubMed:19837869). Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity (PubMed:10457020, PubMed:12417699). {ECO:0000269|PubMed:10457020, ECO:0000269|PubMed:12417699, ECO:0000269|PubMed:19837869}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_03012.1_g00002.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1365400.0AF136540.1 Arabidopsis thaliana YABBY3 (YABBY3) mRNA, complete cds.
GenBankAY0371860.0AY037186.1 Arabidopsis thaliana AT4g00180/F6N15_22 mRNA, complete cds.
GenBankBT0026620.0BT002662.1 Arabidopsis thaliana At4g00180/F6N15_22 gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018454386.11e-177PREDICTED: axial regulator YABBY 3 isoform X2
RefseqXP_018454387.11e-177PREDICTED: axial regulator YABBY 3 isoform X2
RefseqXP_018455886.11e-177PREDICTED: axial regulator YABBY 3 isoform X2
RefseqXP_018455887.11e-177PREDICTED: axial regulator YABBY 3 isoform X2
SwissprotQ9XFB11e-136YAB3_ARATH; Axial regulator YABBY 3
TrEMBLA0A078JBF71e-144A0A078JBF7_BRANA; BnaAnng18530D protein
TrEMBLA0A397XXC61e-144A0A397XXC6_BRACM; Uncharacterized protein
TrEMBLM4F8A81e-144M4F8A8_BRARP; Uncharacterized protein
STRINGBra037320.1-P1e-145(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM22172877
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G00180.11e-125YABBY family protein
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Yadav RK, et al.
    Plant stem cell maintenance involves direct transcriptional repression of differentiation program.
    Mol. Syst. Biol., 2013. 9: p. 654
    [PMID:23549482]