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 Niben101Scf19230g01024.1
Organism
Nicotiana benthamiana
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: 851aa    MW: 94127.8 Da    PI: 7.5213
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Niben101Scf19230g01024.1genomeBTI-
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix67.72.3e-21759839186
                  trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdql 85 
                               rW+++e+++Li++r e+++r++  + +++lWee+s+++  +g++rsp+qCk+ w +l ++y++ k  +k+     ++++pyf+++
  Niben101Scf19230g01024.1 759 RWKHDEIKKLIKLRGELHSRFQVVRGRMALWEEISSNLLCTGVNRSPVQCKSLWASLVQKYEESKSDKKS-----QEKWPYFEEM 838
                               8****************************************************************99998.....578******* PP

                  trihelix  86 e 86 
                               +
  Niben101Scf19230g01024.1 839 N 839
                               7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.9E-6676326IPR001279Metallo-beta-lactamase
SuperFamilySSF562814.17E-7177491IPR001279Metallo-beta-lactamase
SMARTSM008491.8E-2589286IPR001279Metallo-beta-lactamase
PfamPF127065.2E-10101236IPR001279Metallo-beta-lactamase
PfamPF075215.8E-7434463IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.107752816IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.607.0E-5753818IPR009057Homeodomain-like
PfamPF138374.0E-18757841No hitNo description
CDDcd122033.64E-23758823No 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: 851 aa     Download sequence    Send to blast
MAAFSAISLC PYKLCHQLSP SKRYISCYTP SSSTIGVRGS KGPRRGPAKT EGAGRSIDDS  60
VQRRMEHFYE GADGPPLRVL PIGGLGEIGM NCMLVGNYDR YILIDAGIMF PGYEDLGVQK  120
IIPDTTFIKK WSHKIEAVVI THGHEDHIGA LPWVIPALDS HTPIFASSFT MELIKKRLKE  180
FGIFVPSRLK VFKARRKFTA 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
NIGSTIVMGK NELLHTSGHA HREELEEVLK IVKPQHFLPI HGELLFLKEH ELLGKSAGIR  480
HTAVIKNGEM LGVSHLRNRK VLSNGFISLG KENLQLMYSD GDKAFGTAAE LCIDERQRIA  540
SDGIIVVSME ILRPQSMDGA TEKALKGKIR ITTRCLWLDK GKLLDALHKA AHAALSSCPL  600
SCPLPHMERT VSEVLRKMVR KYSSKRPEVI AIAFENPAGV LADEINGKLS GKSDVGFGIS  660
ALRNVMDEDQ KGKQASEARA EEGDGPDYPI DDAAEQVEGD DMDIERLTHD RATTSSSNSR  720
DEYSTTKEES ESSREESIQI DSGFPESMMK SSKPLKRNRW KHDEIKKLIK LRGELHSRFQ  780
VVRGRMALWE EISSNLLCTG VNRSPVQCKS LWASLVQKYE ESKSDKKSQE KWPYFEEMNE  840
ILSDLEATAQ K
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A3e-887763519560RIBONUCLEASE J
5a0t_B3e-887763519560RIBONUCLEASE J
5a0v_A3e-887763519560RIBONUCLEASE J
5a0v_B3e-887763519560RIBONUCLEASE 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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_016475717.10.0PREDICTED: ribonuclease J-like isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A1S4AGA70.0A0A1S4AGA7_TOBAC; ribonuclease J-like isoform X1
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]