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 orange1.1g006550m
Common NameCISIN_1g006550mg, LOC102618434
Organism
Citrus sinensis
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 TALE
Protein Properties Length: 642aa    MW: 70329.1 Da    PI: 6.8836
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g006550mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox29.81e-094384751954
                        HHH..SSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHH CS
           Homeobox  19 Fek..nrypsaeereeLAkklgLterqVkvWFqNrRak 54 
                        Fe   ++yp+ +e+  LAk++gL+ +qV++WF N R +
  orange1.1g006550m 438 FEHflHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVR 475
                        554459******************************88 PP
2BELL104.85.9e-34303372372
               BELL   3 qelqkkkakLlslleeVdkrYkqyveqlqtvissFeavaglgsakpYtslAlkaiSrhFrcLkdaiaeqi 72 
                         ++++kk++L+s+l+eV++rYkqy++q+q+ ++sFe vaglg+a+p+++lAlka+S+hFr+Lk+ai++q+
  orange1.1g006550m 303 SDNRRKKSRLISMLDEVYRRYKQYYQQMQAAVASFEYVAGLGNAAPFANLALKAMSKHFRSLKNAITDQL 372
                        5799***************************************************************997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005743.3E-50241370IPR006563POX domain
PfamPF075262.9E-37246369IPR006563POX domain
PROSITE profilePS5007112.26416479IPR001356Homeobox domain
CDDcd000863.84E-13419480No hitNo description
SMARTSM003891.5E-10419483IPR001356Homeobox domain
SuperFamilySSF466892.05E-17421485IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.606.4E-28422483IPR009057Homeodomain-like
PfamPF059202.0E-18436475IPR008422Homeobox KN domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010051Biological Processxylem and phloem pattern formation
GO:0010076Biological Processmaintenance of floral meristem identity
GO:0010077Biological Processmaintenance of inflorescence meristem identity
GO:0010089Biological Processxylem development
GO:0010154Biological Processfruit development
GO:0010223Biological Processsecondary shoot formation
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048457Biological Processfloral whorl morphogenesis
GO:0048645Biological Processorgan formation
GO:0080006Biological Processinternode patterning
GO:0005634Cellular Componentnucleus
GO:0005829Cellular Componentcytosol
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 642 aa     Download sequence    Send to blast
MAEGFEPYHV PQQSRRDKLR IVAQNHPSVV CVESSSSAPA PAAGLLPLYD ASSLLSSSDL  60
LTAHEFQHQQ QQDNKATNPV CVVKEEGVNL MGFVGGASTS SHHNHHPYLD PHSTLHNLNP  120
SSILDINNNN NPFLFTAPHN LQNQLRDFDQ SYNGGEGSSE VVLFKPEPLA LSLSSHHTTQ  180
NNSLPLELNL QRYGSAIYGD HRVTSTGYVV PSSSTVAAGA SGSTSNEVSR STSSLPFGPF  240
TGYASILKGS RFLKPAQQLL EEFCDVGQGV FAEKNYTVDS SLMDPPLVNL NASGIVVDDG  300
DGSDNRRKKS RLISMLDEVY RRYKQYYQQM QAAVASFEYV AGLGNAAPFA NLALKAMSKH  360
FRSLKNAITD QLQFTNKAQI QANRGKDEAS TFGSTDRGPY GHRPVLNSGF IERQSQPVWR  420
PQRGLPERAV TVLRAWLFEH FLHPYPTDTE KLMLAKQTGL SRSQVSNWFI NARVRLWKPM  480
VEEIHMLETR QGQKATQREE QSANRSSDHL PSSNSLPSEN PSTSTQRVQE TPSKRSRDEF  540
PDIPVGNEEP PNLSYNSLSN HPHVGVGVSM AGGNSGVSLT LGLYQNNGIG LSEPYPISAA  600
QRFGLVHETS SEGFVLSGYE AQSRIFGRDV IGGQLLHDFV G*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3k2a_A4e-16425483563Homeobox protein Meis2
3k2a_B4e-16425483563Homeobox protein Meis2
4xrm_A4e-16425483563Homeobox protein Meis2
4xrm_B4e-16425483563Homeobox protein Meis2
4xrs_A3e-16425482158Homeobox protein Meis1
4xrs_B3e-16425482158Homeobox protein Meis1
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed during late heart stage embryo in the SAM region between the two developing cotyledons. Expression is initially down-regulated in incipient floral primordia but a strong expression is subsequently detected in the central region of young floral primordia and the inner whorl of developing flowers. In fruit, is expressed in the replum of developing ovaries. {ECO:0000269|PubMed:12874117}.
UniprotTISSUE SPECIFICITY: Predominantly expressed in stems, inflorescences and flowers. {ECO:0000269|PubMed:12874117, ECO:0000269|PubMed:12897247, ECO:0000269|PubMed:13678595, ECO:0000269|PubMed:15019989}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that is involved in the preservation of the spiral phyllotactic arrangement leading to a regular pattern of organ initiation. Required for maintenance of stem cell fate in the shoot apical meristem, and is essential for specifying floral primordia and establishing early internode patterning events during inflorescence development. Acts as transcription repressor of AG expression in floral and inflorescence meristems. Is also responsive of the nuclear import of SHOOT MERISTEMLESS (STM). In the fruit, plays a central role in patterning by negatively regulating SHP expression in order to prevent replum cells from adopting a valve margin cell fate. {ECO:0000269|PubMed:12874117, ECO:0000269|PubMed:12897247, ECO:0000269|PubMed:13678595, ECO:0000269|PubMed:15019989, ECO:0000269|PubMed:15120075, ECO:0000269|PubMed:15155890, ECO:0000269|PubMed:16741748}.
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_006480898.10.0BEL1-like homeodomain protein 9
SwissprotQ9LZM81e-124BLH9_ARATH; BEL1-like homeodomain protein 9
TrEMBLA0A067EVK50.0A0A067EVK5_CITSI; Uncharacterized protein
STRINGXP_006480898.10.0(Citrus sinensis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM56882746
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G02030.11e-109TALE family protein
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. Pabón-Mora N,Wong GK,Ambrose BA
    Evolution of fruit development genes in flowering plants.
    Front Plant Sci, 2014. 5: p. 300
    [PMID:25018763]
  3. Khan M, et al.
    Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis.
    Plant Physiol., 2015. 169(3): p. 2166-86
    [PMID:26417006]
  4. Andrés F, et al.
    Floral Induction in Arabidopsis by FLOWERING LOCUS T Requires Direct Repression of BLADE-ON-PETIOLE Genes by the Homeodomain Protein PENNYWISE.
    Plant Physiol., 2015. 169(3): p. 2187-99
    [PMID:26417007]
  5. Bencivenga S,Serrano-Mislata A,Bush M,Fox S,Sablowski R
    Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis.
    Dev. Cell, 2016. 39(2): p. 198-208
    [PMID:27666746]
  6. Sehra B,Franks RG
    Redundant CArG Box Cis-motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development.
    Front Plant Sci, 2017. 8: p. 1712
    [PMID:29085379]
  7. Simonini S,Stephenson P,Østergaard L
    A molecular framework controlling style morphology in Brassicaceae.
    Development, 2018.
    [PMID:29440299]