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 Gh_D03G1080
Organism
Gossypium hirsutum
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: 860aa    MW: 95390.3 Da    PI: 8.0605
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gh_D03G1080genomeNAU-NBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix67.43e-21768848186
     trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                  +W+ +ev++Li++r ++++r++  k +++lWee+s  + e g++rsp qCk+ w +l ++y++ k+ ++++     +++pyf++++
  Gh_D03G1080 768 KWKPEEVKKLIKMRGDLHSRFQVVKGRMALWEEISTSLLEDGITRSPAQCKSLWASLVQKYEESKNEKRSH-----KSWPYFEDMN 848
                  7****************************************************************999996.....57******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.1E-6876326IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.14E-7277491IPR001279Metallo-beta-lactamase
SMARTSM008493.7E-2789286IPR001279Metallo-beta-lactamase
PfamPF127063.5E-11101236IPR001279Metallo-beta-lactamase
PfamPF075211.6E-5432463IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.909761825IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.601.3E-4764827IPR009057Homeodomain-like
PfamPF138377.5E-18766849No hitNo description
CDDcd122032.26E-22767832No 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: 860 aa     Download sequence    Send to blast
MAASTSLSLC PYILCRKAGP RNRYISCSVG SPTPISTRRT KVPRKSSGRL DGARKSMEDS  60
VQRKMEQFYE GTAGPPLRVL PIGGLGEIGM NCMLVGHYDR YILIDAGVMF PDYDELGVQK  120
IIPDTTFIKK WSHKIEAVVI THGHEDHIGA LPWVIPALDP HTPIYASSFT MELIKKRLKE  180
NGIFVPSRLK VFKIRRRFKA GPFEIEPLRV THSIPDCCGL VLRCADGTIL HTGDWKIDES  240
PLDGKTFDRQ FLEELSKEGV TLMMSDSTNV LSPGRTISES AVADALLRHI SGAKGRIITT  300
QFASNIHRLG SIKAAADVTG RKLVFIGMSL RTYLDAAWKD GKAPIDPSTL VKAEDIDAYA  360
PKDLIIVTTG SQAEPRAALN LASYGSSHSF KLNKEDVILY SAKVIPGNES RVMKMLNRIS  420
EIGSTIVIGK NEGLHTSGHG YRGELEEVLQ IVKPQHFLPI HGELLFLKEH ELLGKSTGIR  480
HTTVIKNGEM LGVSHLRNRR VLSNGFSSLG KENLQLMYSD GDKAFGTSTE LCVDERLRIA  540
SDGIIVVSME ILRPQKIDGM VENTLKGKIK ITTRCLWLDK GKLLDTLHKA AHATLSSCPV  600
NCPLAHMERT VSEVLRKTVR KYSGKRPEVI AIALENPAGV LSDELNENLS GNYNAGFGLP  660
TLRKVVDGHP RRGPPNKMKV EDDGILHLEN ASEQSLLDDD AEAERFLPVE DTSTSIPDYT  720
ERLTPNTDDS DELEEHEPEV KSDGTASNGD DSEMTGSQPK SSKPKRNKWK PEEVKKLIKM  780
RGDLHSRFQV VKGRMALWEE ISTSLLEDGI TRSPAQCKSL WASLVQKYEE SKNEKRSHKS  840
WPYFEDMNKV LSDFEATATT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A1e-867763519560RIBONUCLEASE J
5a0t_B1e-867763519560RIBONUCLEASE J
5a0v_A1e-867763519560RIBONUCLEASE J
5a0v_B1e-867763519560RIBONUCLEASE J
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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_016730285.10.0PREDICTED: ribonuclease J-like isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A1U8MTY90.0A0A1U8MTY9_GOSHI; ribonuclease J-like isoform X1
STRINGGorai.003G119600.10.0(Gossypium raimondii)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95392634
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. 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]