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 orange1.1g037502m
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: 426aa    MW: 47956.1 Da    PI: 8.7659
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g037502mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H218.64.9e-065779123
                       EEETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                       y+C++C++ F r  nL+ H r+H
  orange1.1g037502m 57 YVCEICNQGFQRDQNLQMHRRRH 79
                       9*********************9 PP
2zf-C2H216.13.1e-05134156123
                        EEETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                        ++C++C+k +  +s++k H++t+
  orange1.1g037502m 134 WVCEKCSKGYAVQSDYKAHLKTC 156
                        58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576674.41E-55480No hitNo description
Gene3DG3DSA:3.30.160.601.7E-55679IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.975779IPR007087Zinc finger, C2H2
SMARTSM003550.00525779IPR015880Zinc finger, C2H2-like
PROSITE patternPS01359059139IPR019786Zinc finger, PHD-type, conserved site
PROSITE patternPS0002805979IPR007087Zinc finger, C2H2
SMARTSM0035521098128IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.8E-4125155IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM0035560134161IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 426 aa     Download sequence    Send to blast
MLANNSPSAI PCSSEPFSCL ENGISHNKRK RRPAGTPDPD AEVVSLSPKT LLESDRYVCE  60
ICNQGFQRDQ NLQMHRRRHK VPWKLLKRET PVVRKRVFVC PEPSCLHHDP CHALGDLVGI  120
KKHFRRKHSN HKQWVCEKCS KGYAVQSDYK AHLKTCGTRG HSCDCGRVFS RVESFIEHQD  180
ACSKGHIRSE QQGLQQQPAA CLSRTASSPS PSSDTNFSAS HWPNLMVPKV PTIDTMFLNR  240
IHQGDKSTRN VKHHNLELQL LTTSNPIDVS DDSPKRDHDH NHSTQLQLSI GSSDISEKNE  300
LNVTYLSSTT NGKPAMDIAS RLKEQAREQL RLAMAEKACA EEARQAAKRQ IELAEQEFAN  360
AKRIRQQAQA ELDKAQALKE HAIKQINSTI LRVTCHACKQ QFQSRLPPDE NSLVLSYMSS  420
ATTEGE
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C7e-18132182555Zinc finger protein JACKDAW
5b3h_F7e-18132182555Zinc finger protein JACKDAW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expression levels gradually decrease with aging in both the shoot and root vasculature. {ECO:0000269|PubMed:16813575}.
UniprotTISSUE SPECIFICITY: Mainly expressed in the endodermis, the gravity-sensing tissue in inflorescence stems. Mostly present in stems and flowers, and, to a lower extent, in seedlings, hypocotyls, roots and the shoot apical meristem (SAM). {ECO:0000269|PubMed:16813575}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in inflorescence stems gravitropism, probably by regulating starch accumulation in amyloplasts of graviperceptive cells. Required for stem circumnutation movements. Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Acts cooperatively with IDD16 to control silique and branche orientation (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269|PubMed:16813575, ECO:0000269|PubMed:18259878, ECO:0000269|PubMed:24039602, ECO:0000269|PubMed:9210330}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by auxin. {ECO:0000269|PubMed:24039602}.
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_006441329.10.0protein SHOOT GRAVITROPISM 5
SwissprotF4IPE31e-149IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLV4VNQ80.0V4VNQ8_9ROSI; Uncharacterized protein
STRINGXP_006441329.10.0(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM69328131
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G68130.11e-137indeterminate(ID)-domain 14
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. Kim JY,Ryu JY,Baek K,Park CM
    High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis.
    New Phytol., 2016. 209(1): p. 265-79
    [PMID:26256266]
  3. Ryu JY,Kim JY,Park CM
    Adaptive thermal control of stem gravitropism through alternative RNA splicing in Arabidopsis.
    Plant Signal Behav, 2015. 10(11): p. e1093715
    [PMID:26452406]
  4. Qu Y, et al.
    Peroxisomal CuAOζ and its product H2O2 regulate the distribution of auxin and IBA-dependent lateral root development in Arabidopsis.
    J. Exp. Bot., 2017. 68(17): p. 4851-4867
    [PMID:28992128]
  5. Shi H, et al.
    Zinc finger of Arabidopsis thaliana 6 is involved in melatonin-mediated auxin signaling through interacting INDETERMINATE DOMAIN15 and INDOLE-3-ACETIC ACID 17.
    J. Pineal Res., 2018. 65(2): p. e12494
    [PMID:29607541]