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_009142321.1
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: 233aa    MW: 26094.8 Da    PI: 6.9322
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009142321.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1YABBY274.51.2e-84251945170
           YABBY   5 ssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee.......lleelkveeenlksnvekeesa 92 
                     s seq+CyvqCn+C+tilavsvP+ts+fk+vtvrCG+Ct+l+s  ++++s +l+a+++l+ +l ++       +leelk++ +n+++++++++ +
  XP_009142321.1  25 SPSEQLCYVQCNYCETILAVSVPYTSMFKTVTVRCGCCTNLIS--VNMRSLVLPASNQLQLQLGPHsyftpqnILEELKDAPSNMNMMMMNQHPN 117
                     789****************************************..5678999******************************************* PP

           YABBY  93 stsvsseklsenedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170
                     +++++s+ ++ ++++e+p++ppv+rPPekrqrvPsaynrfikeeiqrika+nPdishreafsaaaknWahfP+ihfgl
  XP_009142321.1 118 MNDIPSF-MDLHQQHEIPKAPPVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 194
                     ******6.5*******************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046901.3E-7026194IPR006780YABBY protein
SuperFamilySSF470957.59E-8140187IPR009071High mobility group box domain
Gene3DG3DSA:1.10.30.108.6E-5142188IPR009071High mobility group box domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009909Biological Processregulation of flower development
GO:0009933Biological Processmeristem structural organization
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0010093Biological Processspecification of floral organ identity
GO:0010154Biological Processfruit development
GO:0010158Biological Processabaxial cell fate specification
GO:0010159Biological Processspecification of organ position
GO:0010450Biological Processinflorescence meristem growth
GO:1902183Biological Processregulation of shoot apical meristem development
GO:2000024Biological Processregulation of leaf development
Sequence ? help Back to Top
Protein Sequence    Length: 233 aa     Download sequence    Send to blast
MSMSSMSSPS SAVFSPENLS PDPLSPSEQL CYVQCNYCET ILAVSVPYTS MFKTVTVRCG  60
CCTNLISVNM RSLVLPASNQ LQLQLGPHSY FTPQNILEEL KDAPSNMNMM MMNQHPNMND  120
IPSFMDLHQQ HEIPKAPPVN RPPEKRQRVP SAYNRFIKEE IQRIKAGNPD ISHREAFSAA  180
AKNWAHFPHI HFGLAPDNQP VKKTNMPQQE GEDNMGMKEG FYAPAANVGV IPY
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.107720.0bud
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 transition between globular and heart stages in the cotyledon anlagen. From the heart stage, 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 young lateral aerial organs, and in primordia leading to cotyledons, leaves, flower meristems, sepals, petals, stamen and carpels, but not in roots. {ECO:0000269|PubMed:10323860, ECO:0000269|PubMed:10457020, ECO:0000269|PubMed:14555697, ECO:0000269|Ref.3}.
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:10323860, PubMed:10331982, PubMed:10457020, PubMed:11812777, PubMed:12417699, PubMed:9878633, Ref.3, Ref.6, PubMed:19837869). Required during flower formation and development, particularly for the patterning of floral organs. Positive regulator of class B (AP3 and PI) activity in whorls 2 and 3. Negative regulator of class B activity in whorl 1 and of SUP activity in whorl 3. Interacts with class A proteins (AP1, AP2 and LUG) to repress class C (AG) activity in whorls 1 and 2. Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity. In vitro, can compete and displace the AP1 protein binding to DNA containing CArG box (PubMed:10323860, PubMed:10331982, PubMed:10457020, PubMed:11812777, PubMed:12417699, PubMed:9878633, Ref.3, Ref.6). {ECO:0000269|PubMed:10323860, ECO:0000269|PubMed:10331982, ECO:0000269|PubMed:10457020, ECO:0000269|PubMed:11812777, ECO:0000269|PubMed:12417699, ECO:0000269|PubMed:19837869, ECO:0000269|PubMed:9878633, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00620PBMTransfer from AT2G45190Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009142321.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJQ8289870.0JQ828987.1 Brassica rapa var. parachinensis YABBY1 (YABBY1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009142321.11e-175PREDICTED: axial regulator YABBY 1 isoform X1
RefseqXP_013688135.11e-175axial regulator YABBY 1-like isoform X1
SwissprotO221521e-141YAB1_ARATH; Axial regulator YABBY 1
TrEMBLA0A397ZR051e-173A0A397ZR05_BRACM; Uncharacterized protein
TrEMBLI1VHY71e-173I1VHY7_BRARP; Putative male sterile protein
TrEMBLI3QKS11e-173I3QKS1_BRARC; YABBY1
STRINGBra040322.1-P1e-174(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
AT2G45190.11e-137YABBY 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. Lian H,Li X,Liu Z,He Y
    HYL1 is required for establishment of stamen architecture with four microsporangia in Arabidopsis.
    J. Exp. Bot., 2013. 64(11): p. 3397-410
    [PMID:23918970]
  3. Tameshige T, et al.
    Pattern dynamics in adaxial-abaxial specific gene expression are modulated by a plastid retrograde signal during Arabidopsis thaliana leaf development.
    PLoS Genet., 2013. 9(7): p. e1003655
    [PMID:23935517]
  4. Boter M, et al.
    FILAMENTOUS FLOWER Is a Direct Target of JAZ3 and Modulates Responses to Jasmonate.
    Plant Cell, 2015. 27(11): p. 3160-74
    [PMID:26530088]
  5. Douglas SJ,Li B,Kliebenstein DJ,Nambara E,Riggs CD
    A novel Filamentous Flower mutant suppresses brevipedicellus developmental defects and modulates glucosinolate and auxin levels.
    PLoS ONE, 2017. 12(5): p. e0177045
    [PMID:28493925]
  6. Tanaka W,Toriba T,Hirano HY
    Three TOB1-related YABBY genes are required to maintain proper function of the spikelet and branch meristems in rice.
    New Phytol., 2017. 215(2): p. 825-839
    [PMID:28556940]
  7. Silverblatt-Buser EW,Frick MA,Rabeler C,Kaplinsky NJ
    Genetic Interactions Between BOB1 and Multiple 26S Proteasome Subunits Suggest a Role for Proteostasis in Regulating Arabidopsis Development.
    G3 (Bethesda), 2018. 8(4): p. 1379-1390
    [PMID:29487187]