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 XP_016475718.1
Organism
Nicotiana tabacum
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 Trihelix
Protein Properties Length: 705aa    MW: 78235.5 Da    PI: 7.3824
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_016475718.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix64.13.1e-20613693186
        trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                     rW+++e+++Li++r e+++r++  + +++lWee+s+++ ++ ++rsp qCk+ w +l ++y++ k  +k+     ++++pyf++++
  XP_016475718.1 613 RWKHDEIKKLIKLRGELHSRFQVVRGRMALWEEISSNLLSTEVNRSPAQCKSLWASLVQKYEESKSDKKS-----QEKWPYFEEMN 693
                     8****************************************************************99998.....578*******7 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-359180IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.67E-4415345IPR001279Metallo-beta-lactamase
PfamPF075214.3E-7288317IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.188606670IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.607.4E-5607672IPR009057Homeodomain-like
PfamPF138372.2E-17611695No hitNo description
CDDcd122031.37E-20612677No 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: 705 aa     Download sequence    Send to blast
MDMKTTLVIP ALDSHTPIFA SSFTMELIKK RLKEFGIFVP SRLKVFKTRR KFTAGPFEVE  60
PITVTHSIPD CSGIVLRCSD GTILHTGDWK IDESPLDGKV FDREGLEELS KEGVTLMMSD  120
STNVLSPGRT LSETVVADSL LRHISAAKGR IITTQFASNI HRLGSVKAAA DLTGRKLVFV  180
GMSLRTYLDA AWKDGKAPID PSTLVKVEDI DAYAPKDLLI VTTGSQAEPR AALNLASYGS  240
SHSLKLNKED IVLYSAKVIP GNETRVMEML NRISDIGSTI VMGKNELLHT SGHAHREELE  300
EVLKIVKPQH FLPIHGELLF LKEHELLGKS TGIRHTAVIK NGEMLGVSHL RNRKVLSNGF  360
ISLGKENLQL MYSDGDKAFG TAAELCIDER QRIASDGIIV VSMEILRPQS TDGATEKALK  420
GKIRITTRCL WLDKGKLLDA LHKAAHAALS SCPLSCPLPH MERTVSEVLR KMVRKYSSKR  480
PEVIAIAFEN PAGVLADEIN GKLSGKSHVG FGISALRNVM DEDQKGKQAS EARAEEGHGP  540
GYPIDDAAEQ VEGDDMDIER LTHDRATTSS SNSRDEYSTT KEESESSREE SIQIDSGFPE  600
SMMKSSKPLK RNRWKHDEIK KLIKLRGELH SRFQVVRGRM ALWEEISSNL LSTEVNRSPA  660
QCKSLWASLV QKYEESKSDK KSQEKWPYFE EMNEILSDLE ATAQK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A1e-6217489104560RIBONUCLEASE J
5a0t_B1e-6217489104560RIBONUCLEASE J
5a0v_A1e-6217489104560RIBONUCLEASE J
5a0v_B1e-6217489104560RIBONUCLEASE J
Search in ModeBase
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9754421e-160HG975442.1 Solanum pennellii chromosome ch03, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_016475718.10.0PREDICTED: ribonuclease J-like isoform X2
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A1S4AH080.0A0A1S4AH08_TOBAC; ribonuclease J-like isoform X2
STRINGXP_009774848.10.0(Nicotiana sylvestris)
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]