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 Gorai.009G288800.6
Common NameB456_009G288800, LOC105770407
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: 303aa    MW: 34852.9 Da    PI: 8.5345
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.009G288800.6genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.62.2e-053054123
                        EEET..TTTEEESSHHHHHHHHHHT CS
             zf-C2H2  1 ykCp..dCgksFsrksnLkrHirtH 23
                        ++C   dC+ s++rk++L+rH+  H
  Gorai.009G288800.6 30 FVCLveDCHASYRRKDHLTRHLLQH 54
                        789999***************9887 PP
2zf-C2H214.10.000145984123
                        EEET..TTTEEESSHHHHHHHHHH.T CS
             zf-C2H2  1 ykCp..dCgksFsrksnLkrHirt.H 23
                        +kC   +C++ F  + n+krH++  H
  Gorai.009G288800.6 59 FKCLieNCNREFAFQGNMKRHLKEfH 84
                        799999*****************988 PP
3zf-C2H2193.9e-0699123123
                         EEET..TTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                         y+C+   Cgk+F  ks Lk+H  +H
  Gorai.009G288800.6  99 YVCQevGCGKVFEFKSKLKKHEDSH 123
                         99*******************9888 PP
4zf-C2H216.22.9e-05191215223
                         EET..TTTEEESSHHHHHHHHHH.T CS
             zf-C2H2   2 kCp..dCgksFsrksnLkrHirt.H 23 
                         kC+   C  +Fs+ksnL++H +  H
  Gorai.009G288800.6 191 KCNfeGCLHTFSTKSNLRQHVKAvH 215
                         79999***************99877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.43E-71956No hitNo description
Gene3DG3DSA:3.30.160.601.9E-92756IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0473054IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.0583059IPR007087Zinc finger, C2H2
PROSITE patternPS0002803254IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.608.9E-55781IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.85E-65785No hitNo description
SMARTSM003550.0955984IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.725989IPR007087Zinc finger, C2H2
PROSITE patternPS0002806184IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.7E-795123IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.08E-596123No hitNo description
PROSITE profilePS5015711.05399128IPR007087Zinc finger, C2H2
SMARTSM003550.0199123IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280101123IPR007087Zinc finger, C2H2
SMARTSM003551.4131156IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280133156IPR007087Zinc finger, C2H2
SMARTSM0035518159180IPR015880Zinc finger, C2H2-like
SuperFamilySSF576677.42E-8172228No hitNo description
SMARTSM003550.0021190215IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.635190220IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.604.7E-6191215IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280192215IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.3E-4216243IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003558.7221247IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280223247IPR007087Zinc finger, C2H2
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: 303 aa     Download sequence    Send to blast
MDQYQVGRPP EKLHQVSLNH AVWYTFERPF VCLVEDCHAS YRRKDHLTRH LLQHQGKLFK  60
CLIENCNREF AFQGNMKRHL KEFHDEESSD LDAGSQKQYV CQEVGCGKVF EFKSKLKKHE  120
DSHVKLDSVE AFCSEPGCMK YFTNEQCLKA HVLSSHAYIN CQICGAKQLK KNIKRHLRSH  180
EPGGVESERI KCNFEGCLHT FSTKSNLRQH VKAVHEELKP FACSFFGCGM RFSYKHVRDN  240
HEKSGCHVYT PGNFLETDEQ FRSKPRGGLK RTCPTVEMLV RKRVTPPQMD ATMDLGPAPA  300
CS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tf6_A2e-122015133155PROTEIN (TRANSCRIPTION FACTOR IIIA)
1tf6_D2e-122015133155PROTEIN (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}.
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_012447056.10.0PREDICTED: transcription factor IIIA isoform X2
SwissprotQ84MZ41e-118TF3A_ARATH; Transcription factor IIIA
TrEMBLA0A0D2TWK50.0A0A0D2TWK5_GOSRA; Uncharacterized protein
STRINGGorai.009G288800.10.0(Gossypium raimondii)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G72050.11e-121transcription 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]