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 XP_009111512.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family YABBY
Protein Properties Length: 239aa    MW: 26281.9 Da    PI: 8.5152
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009111512.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1YABBY2711.5e-83172002170
           YABBY   2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee........lleelkveeenlksnvek 88 
                     d+ sss+q+Cyv+C+fC+t+lavsvP +slfk+vtvrCGhC++llsv++++++ ll+++s++++s+ ++        llee+++ ++n+++n+++
  XP_009111512.1  17 DHISSSDQLCYVHCSFCDTVLAVSVPPSSLFKTVTVRCGHCSNLLSVTVNMRALLLPSVSNIGHSFLPSpppppppnLLEEMRNGGQNINMNMMM 111
                     7899***************************************************************99999*********************** PP

           YABBY  89 eesastsvssekl......senedeevprvppvirP.PekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170
                     +++a +++s+e++       + + +e+pr+pp++rP PekrqrvPsaynrfikeeiqrika+nPdishreafsaaaknWahfP+ihfgl
  XP_009111512.1 112 SHHAAAHHSNESFvmatrvRSVDLQEMPRPPPANRPaPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 200
                     ********99887778887777899**********999*************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046901.2E-6721200IPR006780YABBY protein
SuperFamilySSF470959.69E-8143194IPR009071High mobility group box domain
Gene3DG3DSA:1.10.30.101.2E-4149194IPR009071High 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: 239 aa     Download sequence    Send to blast
MSSMSMSSSS APAYPPDHIS SSDQLCYVHC SFCDTVLAVS VPPSSLFKTV TVRCGHCSNL  60
LSVTVNMRAL LLPSVSNIGH SFLPSPPPPP PPNLLEEMRN GGQNINMNMM MSHHAAAHHS  120
NESFVMATRV RSVDLQEMPR PPPANRPAPE KRQRVPSAYN RFIKEEIQRI KAGNPDISHR  180
EAFSAAAKNW AHFPHIHFGL MPDHPPTKKA NVRQQEGEEV MMGREGFYGS AANVGVTHN
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in subepidermal cells of anlagen regions, then in abaxial part of primordia and finally in differentiating organs. Levels decrease in differentiated organs. In embryo the expression starts during the heart stage in the cotyledon anlagen. Later, expression expands to abaxial domain of the cotyledon primordia and decrease as the embryo matures. In stamen, expression restricted to the abaxial region differentiating into the connective. In gynoecium, expressed in the abaxial cell layers differentiating into the valves. {ECO:0000269|PubMed:10457020}.
UniprotTISSUE SPECIFICITY: Expressed in abaxial regions of lateral aerial organ primordia leading to cotyledons, leaves, flower meristems, sepals, petals, stamen and carpels, but not in roots. {ECO:0000269|PubMed:10457020, ECO:0000269|PubMed:12417699}.
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
PlantRegMapXP_009111512.1
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_009111509.11e-177PREDICTED: axial regulator YABBY 3 isoform X1
RefseqXP_009111510.11e-177PREDICTED: axial regulator YABBY 3 isoform X1
RefseqXP_009111511.11e-177PREDICTED: axial regulator YABBY 3 isoform X1
RefseqXP_009111512.11e-177PREDICTED: axial regulator YABBY 3 isoform X1
RefseqXP_013693633.11e-177axial regulator YABBY 3 isoform X1
RefseqXP_013693636.11e-177axial regulator YABBY 3 isoform X1
RefseqXP_013693637.21e-177axial regulator YABBY 3 isoform X3
RefseqXP_013693638.11e-177axial regulator YABBY 3 isoform X1
RefseqXP_013693644.11e-177axial regulator YABBY 3 isoform X1
RefseqXP_013693645.11e-177axial regulator YABBY 3 isoform X1
RefseqXP_013693646.21e-177axial regulator YABBY 3 isoform X3
RefseqXP_013693647.11e-177axial regulator YABBY 3 isoform X1
SwissprotQ9XFB11e-137YAB3_ARATH; Axial regulator YABBY 3
TrEMBLA0A078JBF71e-150A0A078JBF7_BRANA; BnaAnng18530D protein
TrEMBLA0A397XXC61e-150A0A397XXC6_BRACM; Uncharacterized protein
TrEMBLM4F8A81e-150M4F8A8_BRARP; Uncharacterized protein
STRINGBra037320.1-P1e-151(Brassica rapa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G00180.11e-119YABBY 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]