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 orange1.1g048287m
Common NameCISIN_1g048287mg
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 C2H2
Protein Properties Length: 365aa    MW: 39942.9 Da    PI: 9.4347
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g048287mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.23.1e-056383323
                       ETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                       C++Cgk F r  nL+ H r H
  orange1.1g048287m 63 CEICGKGFQRDQNLQLHRRGH 83
                       *******************88 PP
2zf-C2H213.90.00016137159123
                        EEETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                        +kC++C+k++  +s+ k H +t+
  orange1.1g048287m 137 WKCEKCSKRYAVQSDWKAHSKTC 159
                        58*****************9998 PP
3zf-C2H211.90.0007167185523
                        TTTEEESSHHHHHHHHHHT CS
            zf-C2H2   5 dCgksFsrksnLkrHirtH 23 
                        dCg++Fsr++++ +H   +
  orange1.1g048287m 167 DCGTVFSRRDSFITHRAFC 185
                        8**************8765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.87E-66083No hitNo description
Gene3DG3DSA:3.30.160.603.0E-56083IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0766183IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.4896183IPR007087Zinc finger, C2H2
PROSITE patternPS0002806383IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.1E-4125158IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.87E-6132157No hitNo description
SMARTSM00355130137157IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 365 aa     Download sequence    Send to blast
MLDKMPEDTI PNGFVQNSVI AGSNNPPNTA AKKKRNLPGT PDPEAEVIAL SPKTLMATNR  60
FLCEICGKGF QRDQNLQLHR RGHNLPWKLK QRTSKEVRKR VYVCPEKTCV HHHPSRALGD  120
LTGIKKHFCR KHGEKKWKCE KCSKRYAVQS DWKAHSKTCG TREYKCDCGT VFSRRDSFIT  180
HRAFCDALAE ETARVNAASS MNSLANGSIS YHFMGTPLGP SVAQHFSSIF KPIPGGGADE  240
TIDQTRRGLS LWMAPGSQGH ETVGSNLTEI QQLGSVSSEA MYGDHPPPSD YHFNWVFGNN  300
KQSSNNAAEA PAIASASLPL TGVKEAAATA SHHHQLVSVN VPSLYSSQQQ QTTTHQTQAA  360
AAAAN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-37133202372Zinc finger protein JACKDAW
5b3h_F4e-37133202372Zinc finger protein JACKDAW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of embryos and 2-days post-germination roots but not in the quiescent center (PubMed:17785527). Detected only in cells that perform asymmetric cell divisions (PubMed:17785527). In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:25829440}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00125DAPTransfer from AT1G03840Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {ECO:0000269|PubMed:21935722}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006446712.10.0zinc finger protein NUTCRACKER
SwissprotQ9ZWA61e-131IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLA0A067EF640.0A0A067EF64_CITSI; Uncharacterized protein (Fragment)
STRINGXP_006446712.10.0(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM37102660
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G03840.11e-130C2H2 family protein
Publications ? help Back to Top
  1. Muñoz-Strale D,León G
    Identification of two highly specific pollen promoters using transcriptomic data.
    Plant Physiol. Biochem., 2014. 83: p. 292-9
    [PMID:25208507]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]