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 Araha.39620s0009.1.p
Organism
Arabidopsis halleri
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family Trihelix
Protein Properties Length: 913aa    MW: 100911 Da    PI: 7.9404
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araha.39620s0009.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix681.8e-21820900186
              trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                           +W+ +e+++Li++r e+++r++  k +++lWee+s+++++ g++rsp qCk+ w +l ++y+++k+ e+++     +++p+f++++
  Araha.39620s0009.1.p 820 KWKPEEIKKLIRMRGELHSRFQVVKGRMALWEEISSNLSADGINRSPGQCKSLWASLIQKYEECKADERRK-----TSWPHFEDMN 900
                           7********************************************************************95.....36******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.107.7E-67108358IPR001279Metallo-beta-lactamase
SuperFamilySSF562817.49E-72109523IPR001279Metallo-beta-lactamase
SMARTSM008492.6E-25121318IPR001279Metallo-beta-lactamase
PfamPF127064.1E-10133268IPR001279Metallo-beta-lactamase
PfamPF075215.5E-7463495IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.107813877IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.607.9E-6815879IPR009057Homeodomain-like
CDDcd122031.76E-22819884No hitNo description
PfamPF138375.0E-18819901No 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: 913 aa     Download sequence    Send to blast
MMKPASLQGF SPQASSIYSD VLRPATTPSK MAAFSALSLC PYTFTFRQSS RIKSTVSCSV  60
TSAPASGTSP SSKTPRRRSG RPEGVGKSME DSVKRKMEQF YEGTDGPPLR VLPIGGLGEI  120
GMNCMLVGNY DRYILIDAGI MFPDYDEPGV QKIMPDTGFI RRWKHKIEAV VITHGHEDHI  180
GALPWVIPAL DPNTPIFASS FTMELIKKRL KEHGIFVQSR LKTFSTRRRF MAGPFEIEPI  240
TVTHSIPDCS GLFLRCADGN ILHTGDWKID EAPLDGKVFD REALEELSKE GVTLMMSDST  300
NVLSPGRTIS EKVVADALVR NVMAAKGRVI TTQFASNIHR LGSIKAAADL TGRKLVFVGM  360
SLRTYLEAAW RDGKAPIDPS SLIKVEDIEA YAPKDLLIVT TGSQAEPRAA LNLASYGSSH  420
AFKLTKEDII LYSAKVIPGN ESRVMKMMNR IADIGPNIIM GKNEMLHTSG HAYRGELEEV  480
LKIVKPQHFL PIHGELLFLK EHELLGKSTG IRHTTVIKNG EMLGVSHLRN RRVLSNGFSS  540
LGRENLQLMY SDGDKAFGTS SELCIDERLR ISSDGIIVLS MEIMRPGVSE NTLKGKIRIT  600
TRCMWLDKGR LLDALHKAAH AALSSCPVNC PLSHMERTVS EVLRKIVRKY SGKRPEVIAI  660
ATENPMAVRA DEVSARLSGD PSVGSGVAAL RKVVEGNNKR SRPKKAPSQE DSPKEVDRTL  720
EDDIIDSDAR LLAEEETAAS TYTEEVDMPV GSSSEDSDDF WKSFINPSSS PSPSETENVN  780
KVTDTEPKTE DKESSRDDDD PSDASDSETK SSPKRVRKNK WKPEEIKKLI RMRGELHSRF  840
QVVKGRMALW EEISSNLSAD GINRSPGQCK SLWASLIQKY EECKADERRK TSWPHFEDMN  900
DILSELDTSA SK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A4e-8710966319560RIBONUCLEASE J
5a0t_B4e-8710966319560RIBONUCLEASE J
5a0v_A4e-8710966319560RIBONUCLEASE J
5a0v_B4e-8710966319560RIBONUCLEASE 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapAraha.39620s0009.1.p
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
GenBankAK2212720.0AK221272.1 Arabidopsis thaliana mRNA for putative protein, complete cds, clone: RAFL24-15-P14.
GenBankBT0042100.0BT004210.1 Arabidopsis thaliana clone RAFL16-01-C03 (R50172) unknown protein (At5g63420) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020882456.10.0uncharacterized protein LOC9302627
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLD7MP090.0D7MP09_ARALL; EMB2746
STRINGBostr.0568s0468.1.p0.0(Boechera stricta)
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]