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.003G119600.2
Common NameB456_003G119600
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 Trihelix
Protein Properties Length: 623aa    MW: 68700.2 Da    PI: 6.9675
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.003G119600.2genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix681.9e-21530610186
            trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                         +W+ +ev++Li++r ++++r++  k +++lWee+s  + e g++rsp qCk+ w +l ++y++ k+ ++++     +++pyf++++
  Gorai.003G119600.2 530 KWKPEEVKKLIKMRGDLHSRFQVVKGRMALWEEISTSLLEDGITRSPAQCKSLWASLVQKYEESKNEKRSH-----KSWPYFEDMN 610
                         7****************************************************************999996.....57******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.104.1E-82588IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.48E-2125253IPR001279Metallo-beta-lactamase
PfamPF075211.0E-5194225IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.909523587IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.608.3E-5526589IPR009057Homeodomain-like
PfamPF138374.8E-18528611No hitNo description
CDDcd122031.43E-22529594No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009658Biological Processchloroplast organization
GO:0009942Biological Processlongitudinal axis specification
GO:0060918Biological Processauxin transport
GO:0009507Cellular Componentchloroplast
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 623 aa     Download sequence    Send to blast
MKITLVIPAL DPHTPIYASS FTMEMMSDST NVLSPGRTIS ESAVADALSR HISGAKGRII  60
TTQFASNIHR LGSIKAAADV TGRKLVFIGM SLRTYLDAAW KDGKAPIDPS TLVKAEDIDA  120
YAPKDLIIVT TGSQAEPRAA LNLASYGSSH SFKLNKEDVI LYSAKVIPGN ESRVMKMLNR  180
ISEIGSTIVM GKNEGLHTSG HGYRGELEEV LQIVKPQHFL PIHGELLFLK EHELLGKSTG  240
IRHTTVIKNG EMLGVSHLRN RRVLSNGFSS LGKENLQLMY SDGDKAFGTS TELCVDERLR  300
IASDGIIVVS MEILRPQKID GMVENTLKGK IKITTRCLWL DKGKLLDTLH KAAHATLSSC  360
PVNCPLAHME RTVSEVLRKT VRKYSGKRPE VIAIALENPA GVLSDELNEN LSGNYNAGFG  420
LPTLRKVVDG HPRRGPPNKM KVEDDGILHL ENASEHSLLD DDAEAERFLP VEDTSTSIPD  480
YTERLTPNTD DSDELEEHEP EVKGDGTASN GDDSEMTGSQ PKSSKPKRNK WKPEEVKKLI  540
KMRGDLHSRF QVVKGRMALW EEISTSLLED GITRSPAQCK SLWASLVQKY EESKNEKRSH  600
KSWPYFEDMN KVLSDFEATA TT*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3zq4_A1e-3525313192473RIBONUCLEASE J 1
3zq4_C1e-3525313192473RIBONUCLEASE J 1
3zq4_D1e-3525313192473RIBONUCLEASE J 1
3zq4_E1e-3525313192473RIBONUCLEASE J 1
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During the early stages of embryo development, first observed at the transition stage. In the heart and torpedo stages, predominantly present in the upper part of embryos. In seedlings, strongly expressed in shoot meristems, hypocotyls, in the vascular bundles of cotyledons, and in the veins of mature leaves. In reproductive organs, detected in inflorescences, especially in sepals, filaments, and stigmas, as well as in mature siliques and seeds. {ECO:0000269|PubMed:25871650}.
UniprotTISSUE SPECIFICITY: Moslty expressed in inflorescences, seedlings, leaves, flowers and flower buds, and, to a lower extent, in stems, siliques and roots. {ECO:0000269|PubMed:25871650}.
Functional Description ? help Back to Top
Source Description
UniProtEssential protein required during embryogenesis, especially in initiating and maintaining the organization of shoot apical meristems (SAMs), cotyledons, and hypocotyls (PubMed:15266054, PubMed:25871650). Involved in auxin-mediated pathways during embryogenesis (PubMed:25871650). RNase that has both endonuclease and 5'-3' exonuclease activities. Involved in RNA surveillance to prevent overaccumulation of antisense RNA (PubMed:22033332). Probably involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay (By similarity). {ECO:0000250|UniProtKB:Q72JJ7, ECO:0000269|PubMed:15266054, ECO:0000269|PubMed:22033332, ECO:0000269|PubMed:25871650}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. {ECO:0000269|PubMed:25871650}.
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_012471114.10.0PREDICTED: uncharacterized protein LOC105788673 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A0D2MMS30.0A0A0D2MMS3_GOSRA; Uncharacterized protein
STRINGGorai.003G119600.10.0(Gossypium raimondii)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G63420.10.0Trihelix family protein
Publications ? help Back to Top
  1. Bryant N,Lloyd J,Sweeney C,Myouga F,Meinke D
    Identification of nuclear genes encoding chloroplast-localized proteins required for embryo development in Arabidopsis.
    Plant Physiol., 2011. 155(4): p. 1678-89
    [PMID:21139083]
  2. 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]
  3. Halpert M,Liveanu V,Glaser F,Schuster G
    The Arabidopsis chloroplast RNase J displays both exo- and robust endonucleolytic activities.
    Plant Mol. Biol., 2019. 99(1-2): p. 17-29
    [PMID:30511330]