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 Gorai.009G128000.1
Common NameB456_009G128000, LOC105767848
Organism
Gossypium raimondii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family C2H2
Protein Properties Length: 379aa    MW: 43224.1 Da    PI: 8.3738
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.009G128000.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H218.74.8e-0680101223
                         EETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   2 kCpdCgksFsrksnLkrHirtH 23 
                         +C+ Cg +F+ + +Lk+H+++H
  Gorai.009G128000.1  80 ECQECGATFRKPAHLKQHLQSH 101
                         5*******************99 PP
2zf-C2H2163.5e-05107131123
                         EEET..TTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                         ++C   dC+ s++rk++L+rH+  H
  Gorai.009G128000.1 107 FVCLvdDCHASYRRKDHLNRHLLQH 131
                         899999***************9887 PP
3zf-C2H212.20.00057136161123
                         EEET..TTTEEESSHHHHHHHHHH.T CS
             zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                         ++Cp   C+  F  + n+krH +  H
  Gorai.009G128000.1 136 FSCPieTCNSKFAFQGNMKRHVKEfH 161
                         89********************9988 PP
4zf-C2H218.65.2e-06176200123
                         EEET..TTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                         y C+   Cgk+F+ +s L++H  +H
  Gorai.009G128000.1 176 YICQevGCGKVFKFSSKLRKHEDSH 200
                         89*******************9888 PP
5zf-C2H215.64.6e-05267291223
                         EET..TTTEEESSHHHHHHHHHH.T CS
             zf-C2H2   2 kCp..dCgksFsrksnLkrHirt.H 23 
                         kC    C  +Fs+ksnL++H +  H
  Gorai.009G128000.1 267 KCDfgGCLHTFSTKSNLRQHVKAvH 291
                         688889**************99877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS501579.2243865IPR007087Zinc finger, C2H2
SMARTSM00355283860IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.71379106IPR007087Zinc finger, C2H2
SMARTSM003550.01279101IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.6E-880105IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028081101IPR007087Zinc finger, C2H2
SuperFamilySSF576677.5E-1091133No hitNo description
Gene3DG3DSA:3.30.160.603.3E-9106133IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.016107136IPR007087Zinc finger, C2H2
SMARTSM003550.025107131IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280109131IPR007087Zinc finger, C2H2
SuperFamilySSF576676.07E-5134162No hitNo description
Gene3DG3DSA:3.30.160.605.1E-5134162IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.598136166IPR007087Zinc finger, C2H2
SMARTSM003550.16136161IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280138161IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.1E-7171200IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.17E-5172200No hitNo description
PROSITE profilePS5015710.928176205IPR007087Zinc finger, C2H2
SMARTSM003550.018176200IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280178200IPR007087Zinc finger, C2H2
SMARTSM003559.9208233IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280210233IPR007087Zinc finger, C2H2
SMARTSM0035518236257IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.0E-5247288IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576678.44E-7248304No hitNo description
PROSITE profilePS5015711.614266296IPR007087Zinc finger, C2H2
SMARTSM003550.0017266291IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280268291IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.605.5E-5290319IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003553.8297323IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280299323IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005730Cellular Componentnucleolus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008097Molecular Function5S rRNA binding
GO:0046872Molecular Functionmetal ion binding
GO:0080084Molecular Function5S rDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 379 aa     Download sequence    Send to blast
MITCSENPLS SEKNKCNQMD EEKGERVSGP IFKDIRRYFC DHCGICRSKK SLITTHILTH  60
HPEKIDNGGK EEEEVSTSNE CQECGATFRK PAHLKQHLQS HSLERPFVCL VDDCHASYRR  120
KDHLNRHLLQ HQGKLFSCPI ETCNSKFAFQ GNMKRHVKEF HDEDSSSTDA ASQKQYICQE  180
VGCGKVFKFS SKLRKHEDSH VKLDSVEAFC SEPSCLKYFS NEQCLKAHVQ SCHQYINCQI  240
CGAKQLKKNI KRHLRSHESG VASERIKCDF GGCLHTFSTK SNLRQHVKAV HEELKPFACS  300
FSGCGMRFSY KHVRDNHEKS ALHVYVPGDF IESDEQFQSR PRGGRKRTCP TVEMLIRKRV  360
APPQMDTMMD PGPIQGCS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tf6_A1e-158322819155PROTEIN (TRANSCRIPTION FACTOR IIIA)
1tf6_D1e-158322819155PROTEIN (TRANSCRIPTION FACTOR IIIA)
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Both isoforms 1 and 2 transcripts are expressed in seedlings and both TFIIIA and TFIIIA-C are present at similar ratios in 10-day-old seedlings (at protein level). In correlation with the reorganization of 5S rDNA chromatin to a mature state, full-length isoform 1 protein TFIIIA with transcriptional activity accumulates and permits de novo transcription of 5S rRNA. Isoforms 1 and 2 transcripts accumulate in various tissues of the reproductive phase, including flowers and siliques, but only isoform 2 is present in mature seeds. In flowers, both TFIIIA and TFIIIA-C are present at similar ratios (at protein level). Very low amounts of TFIIIA are found in extracts from fresh siliques compared to TFIIIA-C. The amount of full-length TFIIIA protein progressively increases from fresh siliques to seeds concomitant with lower proportions of the shorter TFIIIA-C protein (at protein level) thus leading to 5S rRNA accumulation in the seed. {ECO:0000269|PubMed:22353599}.
UniprotTISSUE SPECIFICITY: Expressed in seedlings, flowers, siliques and seeds. {ECO:0000269|PubMed:22353599}.
Functional Description ? help Back to Top
Source Description
UniProtEssential protein (PubMed:22353599). Isoform 1 is a transcription activator the binds both 5S rDNA and 5S rRNA and stimulates the transcription of 5S rRNA gene (PubMed:12711688, PubMed:22353599). Isoform 1 regulates 5S rRNA levels during development (PubMed:22353599). {ECO:0000269|PubMed:12711688, ECO:0000269|PubMed:22353599}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00229DAPTransfer from AT1G72050Download
Motif logo
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_012442876.10.0PREDICTED: putative zinc finger protein 66 isoform X1
SwissprotQ84MZ41e-151TF3A_ARATH; Transcription factor IIIA
TrEMBLA0A0D2QEX00.0A0A0D2QEX0_GOSRA; Uncharacterized protein
STRINGGorai.009G128000.10.0(Gossypium raimondii)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM47142852
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G72050.21e-154transcription factor IIIA
Publications ? help Back to Top
  1. Paterson AH, et al.
    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Nature, 2012. 492(7429): p. 423-7
    [PMID:23257886]