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 Ciclev10021834m
Common NameCICLE_v10021834mg
Organism
Citrus clementina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family YABBY
Protein Properties Length: 253aa    MW: 28589 Da    PI: 8.8657
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10021834mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1YABBY228.71.5e-70141783170
            YABBY   3 vfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkeelleelkveeenlksnvekeesastsv 96 
                       f +seq+Cyv+Cn C+t+lavsvP tslfk+vtvrCGhCt+ll vn++      a + hl++++  + ++  + e  n + n   +++++++ 
  Ciclev10021834m  14 QFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHNFFSPSHNL-REEIPNPSPNFLINQTNTNDF 106
                      6889*****************************************999999999999999999998875543.333333333333333333333 PP

            YABBY  97 sseklsenedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170
                       +   ++   +e+pr+p + rPPekrqrvPsaynrfik+eiqrika+nPdishreafsaaaknWahfP+ihfgl
  Ciclev10021834m 107 IVP--TRGVVDELPRPPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 178
                      332..3567889************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046904.7E-6917178IPR006780YABBY protein
SuperFamilySSF470951.07E-7123171IPR009071High mobility group box domain
Gene3DG3DSA:1.10.30.102.4E-4127170IPR009071High mobility group box domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0007275Biological Processmulticellular organism development
GO:0016021Cellular Componentintegral component of membrane
Sequence ? help Back to Top
Protein Sequence    Length: 253 aa     Download sequence    Send to blast
MSMSSSSTTL SLDQFPTSEQ LCYVHCNLCD TVLAVSVPCT SLFKTVTVRC GHCTNLLPVN  60
MRGLLLPSAN QFHLGHNFFS PSHNLREEIP NPSPNFLINQ TNTNDFIVPT RGVVDELPRP  120
PATSRPPEKR QRVPSAYNRF IKDEIQRIKA GNPDISHREA FSAAAKNWAH FPHIHFGLVP  180
DHQPVKKANV RQQIDLVHAG RRRCSDERWF FRFSKRGCLA LLRMACHCIL LVLNLSYVLC  240
YDLCLCRPLS LQ*
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}.
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_006440374.11e-141axial regulator YABBY 1
SwissprotO221522e-72YAB1_ARATH; Axial regulator YABBY 1
TrEMBLV4TPH40.0V4TPH4_9ROSI; Uncharacterized protein
STRINGXP_006440375.10.0(Citrus clementina)
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
AT2G45190.13e-74YABBY 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]