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_1770_f_5
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: 889aa    MW: 98447.3 Da    PI: 7.3223
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_1770_f_5genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix61.32.4e-19796875186
       trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                    +W+ +ev++Li++r e++++++  k +++lW+e+s +++ +g++rsp qCk+ w +l ++y++ k g++++      ++pyf+++ 
  Neem_1770_f_5 796 KWKPDEVRQLIKMRGELHSKFQVVKGRMALWREISTHLMNEGINRSPGQCKSLWTSLLQKYEENKSGKNRN------SWPYFEEMS 875
                    7*************************************************************999999984......5******96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.5E-6412278IPR001279Metallo-beta-lactamase
SuperFamilySSF562814.46E-5513357IPR001279Metallo-beta-lactamase
SMARTSM008492.2E-2025242IPR001279Metallo-beta-lactamase
PfamPF127061.1E-737188IPR001279Metallo-beta-lactamase
SuperFamilySSF562814.43E-9388499IPR001279Metallo-beta-lactamase
PfamPF075214.3E-6438471IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.142789853IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.602.7E-6789855IPR009057Homeodomain-like
CDDcd122031.48E-21795860No hitNo description
PfamPF138372.4E-18795877No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 889 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 LYSAKVMQAR  360
AALNLASYGG SHSLKLTKED LILYSAKMVA SYGGSHSLKL TKEDLILYSA KVIPGNESRV  420
MKMLNRISEI GSTIVMGRNE GLHTSGHGYR GELEEVLKLV KPQHFLPIHG ELLFLKEHEL  480
LGRSTGIRHS TVIKNGEMLG VSHLRNRRVL SNGFISLGRE NLQLMYSDGD KAFGTSTELC  540
IDERLRIASD GIIVVSMEIL RPQHGDGRTA NSLKGKIRIT TRCLWLDKGK LLDALHKAAH  600
AALSSCPVNS PLAHMEKTVS EVLRKIVRKY SGKRPEVIAI AMENPAAVLS DELNARLSGN  660
SHVGFGISAL RNMVDAHPKR SQPNKMQAEE GNGHQQSLQV DGIEVEELPE EDATTSSSSF  720
GERLSVDSQD TDDFWKSFLT AASPSDNLVK DNSTLVPQED QKMSEPENDD NESSKDDSSE  780
RSSSRSKSSK GVKQNKWKPD EVRQLIKMRG ELHSKFQVVK GRMALWREIS THLMNEGINR  840
SPGQCKSLWT SLLQKYEENK SGKNRNSWPY FEEMSEILSD SDSEAMTSK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A9e-741364319560RIBONUCLEASE J
5a0t_B9e-741364319560RIBONUCLEASE J
5a0v_A9e-741364319560RIBONUCLEASE J
5a0v_B9e-741364319560RIBONUCLEASE 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]