PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Niben101Scf06687g00001.1
Organism
Nicotiana benthamiana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana
Family C2H2
Protein Properties Length: 426aa    MW: 47822.5 Da    PI: 9.0943
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Niben101Scf06687g00001.1genomeBTI-
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H218.64.9e-065072123
                              EEETTTTEEESSHHHHHHHHHHT CS
                   zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                              y+C++C++ F r  nL+ H r+H
  Niben101Scf06687g00001.1 50 YVCEICNQGFQRDQNLQMHRRRH 72
                              9*********************9 PP
2zf-C2H216.13.1e-05127149123
                               EEETTTTEEESSHHHHHHHHHHT CS
                   zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                               ++C++C+k +  +s++k H++t+
  Niben101Scf06687g00001.1 127 WVCEKCSKGYAVQSDYKAHLKTC 149
                               58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576674.41E-54773No hitNo description
Gene3DG3DSA:3.30.160.601.7E-54972IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00525072IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.975072IPR007087Zinc finger, C2H2
PROSITE patternPS0002805272IPR007087Zinc finger, C2H2
PROSITE patternPS01359052132IPR019786Zinc finger, PHD-type, conserved site
SMARTSM0035519091121IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.4E-4118148IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM0035560127154IPR015880Zinc 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
MLSNNPSSSS DPFTSSENGN RRKRRPAGTP DPDAEVVSLS PKTLLESDRY VCEICNQGFQ  60
RDQNLQMHRR RHKVPWKLLK RETPIIRKRV FVCPEPTCLH HDPCHALGDL VGIKKHFRRK  120
HSNHKQWVCE KCSKGYAVQS DYKAHLKTCG TRGHSCDCGR VFSRVESFIE HQDACSMGRL  180
RSESQSLHPS NCLSRTASSP SPSSDTNLST TPWPSTLLKN LSSSTATHPV NPNIIKNSTK  240
QRHNLELQLL TTTTSSSSPF DVSVSSKPNE DHSTYNLQLS IGSSDFNERN ESSENATALD  300
ALKLKDEARE QLKLAMAEKA YAEEARQQAK RQIELAEQEF ANAKRIRQQA QVELDKANAL  360
KQQAIKQINS TLSQITCHSC KQKFQAPPSD ENNSLTLSYI SSGLTEGQHE VANNINQTNH  420
LKLSQR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C5e-18123175355Zinc finger protein JACKDAW
5b3h_F5e-18123175355Zinc finger protein JACKDAW
Search in ModeBase
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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_016494721.10.0PREDICTED: protein SHOOT GRAVITROPISM 5-like
SwissprotF4IPE31e-153IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A1S4C0N80.0A0A1S4C0N8_TOBAC; protein SHOOT GRAVITROPISM 5-like
STRINGXP_009777609.10.0(Nicotiana sylvestris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA10222482
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G68130.11e-139indeterminate(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]