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 evm_27.model.AmTr_v1.0_scaffold00009.218
Common NameAMTR_s00009p00241540, LOC18422873
Organism
Amborella trichopoda
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella
Family Trihelix
Protein Properties Length: 867aa    MW: 96183.2 Da    PI: 8.2215
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00009.218genomeTAGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix67.13.6e-21776856186
                                  trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegek 69 
                                               +W  +e+ +Li++r em++r+r+ k+++ lWeevs+k+ e g++r+p qCk+ w +l ++y+  + g+k
  evm_27.model.AmTr_v1.0_scaffold00009.218 776 KWEPEEISKLIQLRGEMDSRFRAVKARMVLWEEVSSKLLESGVKRTPGQCKSIWASLVQKYEDNRVGNK 844
                                               7******************************************************************** PP

                                  trihelix  70 krtsessstcpyfdqle 86 
                                               ++     + +p+f++++
  evm_27.model.AmTr_v1.0_scaffold00009.218 845 GK-----KGWPFFEEMD 856
                                               85.....57*******8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.2E-6680330IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.5E-7081495IPR001279Metallo-beta-lactamase
SMARTSM008493.0E-2493294IPR001279Metallo-beta-lactamase
PfamPF127069.1E-11106240IPR001279Metallo-beta-lactamase
PfamPF075216.5E-6436467IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.933769833IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.605.4E-6769835IPR009057Homeodomain-like
SMARTSM007170.003773835IPR001005SANT/Myb domain
PfamPF138376.5E-18774858No hitNo description
CDDcd122031.61E-20775838No 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: 867 aa     Download sequence    Send to blast
MGALSAFSIC PCRFSFNPNF NGETRKSFIS NAIGTPSVTG AKESRLRQKR SGRLEGPSKS  60
MEDSVQRKME EFYEGSSGPP LRVLPIGGLG EIGMNCMLVG HYDRYILVDA GVMFPDYDEL  120
GVQKIIPDTT FIKRWSHKIE AVVITHGHED HIGALPWVIP ALDSHTPIFA SSFTMELIKK  180
RLKEFSIFVP SRLKLFKIRK RFNAGPFEVE PIRVTHSIPD CCGLVLRCAD GTIFHTGDWK  240
IDESPLDGKI FDRQALEELA KEGVTLMMSD STNVLSPGRS MSEAVVKDAL LRNITAAQGR  300
VITTQFASNI HRLGSVKAAA DITGRKLVFV GMSLRTYLDA AWKDGKAPMD PSTLIKVEDI  360
DAYAPKDLLI VTTGSQAEPR AALNLASFGG SHSLKLTTED LILYSAKVIP GNETRVMKML  420
NRISEIGSTI VMGKNEGLHT SGHGYRGELE EVLRIVKPQH FLPIHGELLF LKEHELLGKS  480
TGIHHTTVIK NGEMLGVSHL RNRRVLSNGF TSLGKENLQL MYSDGDKAFG TSEELCINER  540
MRIASDGIIV VSMEIMRPPK VDGFFSQPSL KGRIKITTRC LWLDKGKLLE ALHKAAHAAL  600
SSCPVNCPVA HMERIVSEVL RKIVRKYSSK RPEVIAVAVE NANAVLAEEL KAKLSKSRGS  660
LTTLLNQSGD DGPAKERAYI ETDEVQTTTS TTAEFDNSLR EEEYINDEDA NELFLEDNVD  720
TSSETAIPAS DPKPADFNKF WERKEDNGSI SNVNVKNAEN KTLANNSSTK SAKRNKWEPE  780
EISKLIQLRG EMDSRFRAVK ARMVLWEEVS SKLLESGVKR TPGQCKSIWA SLVQKYEDNR  840
VGNKGKKGWP FFEEMDKILS VHHAEK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A1e-858164019560RIBONUCLEASE J
5a0t_B1e-858164019560RIBONUCLEASE J
5a0v_A1e-858164019560RIBONUCLEASE J
5a0v_B1e-858164019560RIBONUCLEASE 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
GenBankAC1355055e-35AC135505.15 Medicago truncatula chromosome 8 clone mth2-24j8, complete sequence.
GenBankLN6818145e-35LN681814.1 Cucumis melo genomic scaffold, anchoredscaffold00089.
GenBankLN7132565e-35LN713256.1 Cucumis melo genomic chromosome, chr_2.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006827615.10.0uncharacterized protein LOC18422873 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLW1NHR90.0W1NHR9_AMBTC; Uncharacterized protein
STRINGERM950310.0(Amborella trichopoda)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP30821521
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. Amborella Genome Project
    The Amborella genome and the evolution of flowering plants.
    Science, 2013. 342(6165): p. 1241089
    [PMID:24357323]
  3. 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]