PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID NNU_004135-RA
Organism
Nelumbo nucifera
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; stem eudicotyledons; Proteales; Nelumbonaceae; Nelumbo
Family Trihelix
Protein Properties Length: 886aa    MW: 98109.3 Da    PI: 9.0353
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
NNU_004135-RAgenomeCASView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix62.21.2e-19794874186
       trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                    +W+ +e+++Li++r e+++r++  k ++ lW+e+s+++   g++r+p qCk+ w +l ++y++i+ g+k++     +++pyfd++e
  NNU_004135-RA 794 KWMPEEIMKLIKMRGELDSRFQVVKGRMVLWKEISANLLVYGINRTPGQCKSLWASLIQKYEEIRIGKKSK-----KSWPYFDEME 874
                    7****************************************************************999984.....56*******8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.102.0E-6776326IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.46E-7377491IPR001279Metallo-beta-lactamase
SMARTSM008496.6E-2789286IPR001279Metallo-beta-lactamase
PfamPF007533.5E-1190234IPR001279Metallo-beta-lactamase
PfamPF075211.0E-5432463IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.049787851IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.602.9E-5789853IPR009057Homeodomain-like
PfamPF138371.2E-16792876No hitNo description
CDDcd122031.42E-19793858No 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: 886 aa     Download sequence    Send to blast
MAALSALSLC PSRFSCRPNP RRASICCSVD APIVTGTRGS KIPHKRSGRM EGPGKSMEDS  60
VQRKMEQFYE GSNGPPLRVL PIGGLGEIGM NCMLVGNHDR YILIDAGVMF PDYDELGVQK  120
IIPDTAFIKR WSHKIEAVVI THGHEDHIGA LPWVIPALDP NTPIFASSFT MELIKKRLKE  180
FGIFVPSRLK MFRTRKKFIA GPFEVEPIRV THSIPDCCGL VLRCADGTIL HTGDWKIDES  240
PLDGKTFDRE ALEELSKEGV TLMMSDSTNV LSPGRTISEA VVADALLRHI SAAKGRVITT  300
QFASNIHRLG SVKAAADLTG RKLVFVGMSL RTYLDAAWKD GKAPIDPSTL VKVEDIDTYN  360
PKDLLIVTTG SQAEPRAALN LASYGSSHSL KLNKEDVILY SAKVIPGNEI RVMKMMNRIA  420
ELGSTIVMGK NEGLHTSGHG YRGELEEVLK IVKPQHFLPI HGELLFLKEH ELLGKSTGIR  480
HTAVIKNGEM LGVSHLRNRR VLSNGFISLG KENLQLMYND GDKAFGTSTE LCIDERLRIA  540
LDGIIVVSME VLRPQNVDGL LERKIKGKIR ITTRCLWLDK GKLLDALYKA AHAALSSCPV  600
NCPLAHMERT VSEVLRKMVR KYSSKRPEVI AIAVESTTGV LSDEINVRSS SKSHVGFGLL  660
GLNKIVDEHP RKRRSSRKLE EAGSGNTHLE KDISVQHEIA GEVDGQLLSE EEEATMSSSD  720
LEVSSSPTAE NSDDFWNLFV TPSPLEHLGK VENGSIRKEE HLELNKDGTK SRGEGSAELA  780
SPQSASSKPA KRNKWMPEEI MKLIKMRGEL DSRFQVVKGR MVLWKEISAN LLVYGINRTP  840
GQCKSLWASL IQKYEEIRIG KKSKKSWPYF DEMEKILLGR EATSTK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A1e-857763519560RIBONUCLEASE J
5a0t_B1e-857763519560RIBONUCLEASE J
5a0v_A1e-857763519560RIBONUCLEASE J
5a0v_B1e-857763519560RIBONUCLEASE 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_010250772.10.0PREDICTED: uncharacterized protein LOC104592923 isoform X2
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A1U7ZQ210.0A0A1U7ZQ21_NELNU; uncharacterized protein LOC104592923 isoform X2
STRINGXP_010250771.10.0(Nelumbo nucifera)
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]