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 Neem_27341_f_2
Organism
Azadirachta indica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta
Family Trihelix
Protein Properties Length: 863aa    MW: 95626 Da    PI: 7.2018
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_27341_f_2genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix61.32.3e-19770849186
        trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                     +W+ +ev++Li++r e++++++  k +++lW+e+s +++ +g++rsp qCk+ w +l ++y++ k g++++      ++pyf+++ 
  Neem_27341_f_2 770 KWKPDEVRQLIKMRGELHSKFQVVKGRMALWREISTHLMNEGINRSPGQCKSLWTSLLQKYEENKSGKNRN------SWPYFEEMS 849
                     7*************************************************************999999984......5******96 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-6412278IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.98E-6413342IPR001279Metallo-beta-lactamase
SMARTSM008492.2E-2025242IPR001279Metallo-beta-lactamase
PfamPF127061.1E-737188IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.98E-64373473IPR001279Metallo-beta-lactamase
PfamPF075214.2E-6412445IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
Gene3DG3DSA:1.10.10.602.6E-6763829IPR009057Homeodomain-like
PROSITE profilePS500908.142763827IPR017877Myb-like domain
CDDcd122031.45E-21769834No hitNo description
PfamPF138372.3E-18769851No 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: 863 aa     Download sequence    Send to blast
MEQFYEGSNG PPLRVLPIGG LGEIGMNCML VGNYDRYILI DAGVMFPDYD ELGVQKIIPD  60
TTFIKRWSHK IEAVVITHGH EDHIGALPWI ECKFNETDSH GDLRCVIPAL DSHTPIFASS  120
FTMELIKKRL KENGIFVPSR LKTFKTRRKF MAGPFEIEPI RVTHSIPDCC GLVLRCADGT  180
ILHTGDWKID ESPLDGKVFD REALEELSKE GVTLMMSDST NVLSPGRTIS ESVVKDALLR  240
NISAAKGRVI TTQFASNIHR LGSVKAAADL TGRKLVFVGM SLRTYLDAAW KDGKAPIDPS  300
TLVKVEDIDA YAPKDLLIVT TGSQAEPRAA LNLASYGGSH SLKLTKEDLI LYSAKMARAA  360
LNLASYGGSH SLKLTKEDLI LYSAKVIPGN ESRVMKMLNR ISEIGSTIVM GRNEGLHTSG  420
HGYRGELEEV LKLVKPQHFL PIHGELLFLK EHELLGRSTG IRHSTVIKNG EMLGVSHLRN  480
RRVLSNGFIS LGRENLQLMY SDGDKAFGTS TELCIDERLR IASDGIIVVS MEILRPQHGD  540
GRTANSLKGK IRITTRCLWL DKGKLLDALH KAAHAALSSC PVNSPLAHME KTVSEVLRKI  600
VRKYSGKRPE VIAIAMENPA AVLSDELNAR LSGNSHVGFG ISALRNMVDA HPKRSQPNKM  660
QAEEGNGHQQ SLQVDGIEVE ELPEEDATTS SSSFGERLSV DSQDTDDFWK SFLTAASPSD  720
NLVKDNSTLV PQEDQKMSEP ENDDNESSKD DSSERSSSRS KSSKGVKQNK WKPDEVRQLI  780
KMRGELHSKF QVVKGRMALW REISTHLMNE GINRSPGQCK SLWTSLLQKY EENKSGKNRN  840
SWPYFEEMSE ILSDSDSEAM TSK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A7e-791361719560RIBONUCLEASE J
5a0t_B7e-791361719560RIBONUCLEASE J
5a0v_A7e-791361719560RIBONUCLEASE J
5a0v_B7e-791361719560RIBONUCLEASE 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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankFR6923696e-68FR692369.1 Citrus reshni microsatellite DNA, locus mCrCIR04F12.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_024955087.10.0uncharacterized protein LOC102606767 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A2H5PFA60.0A0A2H5PFA6_CITUN; Uncharacterized protein
STRINGXP_006477010.10.0(Citrus sinensis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95392634
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]