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_009774848.1
Organism
Nicotiana sylvestris
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: 880aa    MW: 97391.2 Da    PI: 7.5565
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009774848.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix63.74.2e-20788868186
        trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                     rW+++e+++Li++r e+++r++  + +++lWee+s+++ ++ ++rsp qCk+ w +l ++y++ k  +k+     ++++pyf++++
  XP_009774848.1 788 RWKHDEIKKLIKLRGELHSRFQVVRGRMALWEEISSNLLSTEVNRSPAQCKSLWASLVQKYEESKSDKKS-----QEKWPYFEEMN 868
                     8****************************************************************99998.....578*******7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.4E-6676326IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.03E-7177491IPR001279Metallo-beta-lactamase
SMARTSM008491.8E-2589286IPR001279Metallo-beta-lactamase
PfamPF127064.9E-10101236IPR001279Metallo-beta-lactamase
PfamPF075215.6E-7434463IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.188781845IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.609.9E-5782847IPR009057Homeodomain-like
PfamPF138372.9E-17786870No hitNo description
CDDcd122035.14E-21787852No 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: 880 aa     Download sequence    Send to blast
MAAFSAISLC PYKLCHQLNP SKRYISCYTP SSSTIGVRGS KGPRRRPAKT EGAGRSIDDS  60
VQRRMEHFYE GADGPPLRIL PIGGLGEIGM NCMLVGNYDR YILIDAGIMF PGYEDLGVQK  120
IIPDTTFIKK WSHKIEAVVI THGHEDHIGA LPWVIPALDS HTPIFASSFT MELIKKRLKE  180
FGIFVPSRLK VFKTRRKFTA GPFEVEPITV THSIPDCSGI VLRCSDGTIL HTGDWKIDES  240
PLDGKVFDRE GLEELSKEGV TLMMSDSTNV LSPGRTLSET VVADSLLRHI SAAKGRVITT  300
QFASNIHRLG SVKAAADLTG RKLVFVGMSL RTYLDAAWKD GKAPIDPSTL VKVEDIDAYA  360
PKDLLIVTTG SQAEPRAALN LASYGSSHSL KLNKEDIVLY SAKVIPGNET RVMEMLNRIS  420
DIGSTIVMGK NELLHTSGHA HREELEEVLK IVKPQHFLPI HGELLFLKEH ELLGKSTGIR  480
HTAVIKNGEM LGVSHLRNRK VLSNGFISLG KENLQLMYSD GDKAFGTAAE LCIDERQRIA  540
SDGIIVVSME ILRPQSTDGA TEKALKGKIR ITTRCLWLDK GKLLDALHKA AHAALSSCPL  600
SCPLPHMERT VSEVLRKMVR KYSSKRPEVI AIAFENPAGV LADEINGKLS GKSHVGFGIS  660
ALRNVMDEDQ KGKQASEARA EEGHGPGYPI DDAAEQVEGD DMDIERLTHD RATTSSSNSR  720
DEYSTTKVLL DDSLKPFVSS XLLAQLQEGS FGALTQEESE SSREESIQID SGFPESMMKS  780
SKPLKRNRWK HDEIKKLIKL RGELHSRFQV VRGRMALWEE ISSNLLSTEV NRSPAQCKSL  840
WASLVQKYEE SKSDKKSQEK WPYFEEMNEI LSDLEATAQK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A4e-877763519560RIBONUCLEASE J
5a0t_B4e-877763519560RIBONUCLEASE J
5a0v_A4e-877763519560RIBONUCLEASE J
5a0v_B4e-877763519560RIBONUCLEASE 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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009774848.10.0PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein LOC104224837
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A1U7W8910.0A0A1U7W891_NICSY; LOW QUALITY PROTEIN: uncharacterized protein LOC104224837
STRINGXP_009774848.10.0(Nicotiana sylvestris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA58742331
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]