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 Pahal.A02043.1
Organism
Panicum hallii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family Trihelix
Protein Properties Length: 876aa    MW: 96094.3 Da    PI: 8.867
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pahal.A02043.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix66.36.4e-21783863186
        trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                     +W+ +e++ Li++r em+e++++ k ++ lWe++s  ++ +g++r+p qCk+ w +l ++y++ k+ e++      +t+pyf+ ++
  Pahal.A02043.1 783 KWKPEEIKSLIQMRGEMNEKFQSVKGRMVLWEDISGSLMNQGISRTPAQCKSLWTSLVQKYEESKKDEES-----MKTWPYFSAMD 863
                     7******************************************************************998.....579*******8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.7E-6686336IPR001279Metallo-beta-lactamase
SuperFamilySSF562813.15E-7287501IPR001279Metallo-beta-lactamase
SMARTSM008494.7E-2499296IPR001279Metallo-beta-lactamase
PfamPF127062.8E-10111246IPR001279Metallo-beta-lactamase
PfamPF075212.4E-7444473IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.666776840IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.604.4E-5779842IPR009057Homeodomain-like
PfamPF138373.4E-17782865No hitNo description
CDDcd122031.55E-20782847No 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: 876 aa     Download sequence    Send to blast
MVALASLSSL CPCGLARRRA ASASASASAS VSISCCAVAT PSSGKGPQES RTPRKRLRRT  60
EGATKSLEDS VKRKMEQFYE GVDGPPLRVL PIGGLGEIGM NCMLVGNYDR YILIDAGVMF  120
PDYDEFGVQK IIPDTTFIKK WSHKIEAVII THGHEDHIGA LPWVIPALDS STPIFASSFT  180
MELIKKRLKE FGIFLSSRLK VLRIKKRFQA GPFEVEPIRV THSIPDCCGL VLRCADGIIF  240
HTGDWKIDES PVDGKIFDRE ALEELSKEGV TLMMSDSTNV LSPGRSISES VVAGSLLRHI  300
SEAKGRVITT QFASNIHRIG SIKAAADLTG RKMVFVGMSL RTYLEAAFKD GKAPLDPSTL  360
VKAEDMDAYA PKDLLVVTTG SQGEPRAALN LASYGGSHAL KLSKEDVLLY SAKVIPGNET  420
RVMKMMNRLT DLGPKIIMGK DSGLHTSGHA YRDELEEVLR IVKPQHFLPV HGELLFLKEH  480
ELLGRSTGIR HTTVIKNGEM LGVSHLRNRR VLSNGFVSLG KEDFQLMYSD GDKAFGTSTD  540
LCIDERLRIA SDGIIFVSME IFRPQKEHAS VQSGLKGKFK ITTRCLWLDN GRLLDALYKA  600
AYAALSSCPV NCPLSHMERM VSEILRKMVR KYSGKRPDVI AVATENTTAG FSEHLEAKSS  660
GNFGASSATS HLSRSPARSL EGSYKTHPDN PDVDSEETLP EAVGTTPDDA TTSSNGGEAF  720
FSSDLHQPKT LEHFWESFKS PTAVKIARIV NGGNKQNIGK IGIMSKDSTQ SAPASVKSSK  780
KNKWKPEEIK SLIQMRGEMN EKFQSVKGRM VLWEDISGSL MNQGISRTPA QCKSLWTSLV  840
QKYEESKKDE ESMKTWPYFS AMDRILSCEG EMAAK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A4e-848764519560RIBONUCLEASE J
5a0t_B4e-848764519560RIBONUCLEASE J
5a0v_A4e-848764519560RIBONUCLEASE J
5a0v_B4e-848764519560RIBONUCLEASE 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_025800212.10.0ribonuclease J isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A2S3GPP80.0A0A2S3GPP8_9POAL; Uncharacterized protein
STRINGPavir.Ab01874.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP49963542
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]