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 Pavir.1KG323800.3.p
Organism
Panicum virgatum
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: 845aa    MW: 92756.6 Da    PI: 9.0373
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.1KG323800.3.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix544.5e-17779840162
             trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkryk 62 
                          +W+ +ev+ Li++r em+e++++ k ++ lWee+s  ++ +g++r+p qCk+ w +l ++y+
  Pavir.1KG323800.3.p 779 KWKPEEVKSLIQMRGEMNEKFQSVKGRMVLWEEISGSLMNEGISRTPAQCKSLWTSLVQKYE 840
                          7**********************************************************996 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.109.0E-6782332IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.78E-7283497IPR001279Metallo-beta-lactamase
SMARTSM008494.5E-2495292IPR001279Metallo-beta-lactamase
PfamPF127062.0E-10107242IPR001279Metallo-beta-lactamase
PfamPF075212.3E-7440469IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.851772836IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.601.1E-5775838IPR009057Homeodomain-like
CDDcd122032.01E-20778840No hitNo description
PfamPF138378.3E-12778840No 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: 845 aa     Download sequence    Send to blast
MVALASLSAL CPCGLARRRA ASASASVSIS CCAVATPSSG KGPQESRTPR KRLRRTEGAT  60
KSLEDSVKRK MEQFYEGVDG PPLRVLPIGG LGEIGMNCML VGNYDRYILI DAGVMFPDYD  120
EFGVQKIIPD TTFIKKWSHK IEAVIITHGH EDHIGALPWV IPALDSSTPI FASSFTMELI  180
KKRLKEFGIF LSSRLKVLRI KKRFQAGPFE VEPIRVTHSI PDCCGLVVRC ADGIIFHTGD  240
WKIDESPVDG KIFDREALEE LSKEGVTLMM SDSTNVLSPG RSISESVVAG SLLRHISEAK  300
GRVITTQFAS NIHRIGSIKA AADLTGRKMV FVGMSLRTYL EAAFKDGKAP LDPSTLVKAE  360
DMDAYAPKDL LVVTTGSQGE PRAALNLASY GGSHALKLSK DDVLLYSAKV IPGNETRVMK  420
MMNRLTDLGP KIIMGKDSGL HTSGHAYRDE LEEVLRIVKP QHFLPVHGEL LFLKEHELLG  480
RSTGIRHTTV IKNGEMLGVS HLRNRRVLSN GFVSLGKEDF QLMYSDGDKA FGTSTDLCID  540
ERLRIASDGI IFVSMEIFRP QKEHASAQSG LKGKFKITTR CLWLDNGRLL DALYKAAHAA  600
LSSCPVNCPL SHMERMVSEI LRKMVRKYSG KRPDVIAVAT ENTMAGFSEH LEAKSSGNLG  660
PSSTTSHLNR SPARSLEGSY KTHPDNPDVE PEETLLEAVS TTPDDATTSS NGGEAFFSSD  720
LHQPKTLEHF WESFKSPTAV KIARIVNGGN KQNIGKIGIM GKDSTQSAPA PVKSSKKNKW  780
KPEEVKSLIQ MRGEMNEKFQ SVKGRMVLWE EISGSLMNEG ISRTPAQCKS LWTSLVQKYE  840
VHQY*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A4e-858364119560RIBONUCLEASE J
5a0t_B4e-858364119560RIBONUCLEASE J
5a0v_A4e-858364119560RIBONUCLEASE J
5a0v_B4e-858364119560RIBONUCLEASE J
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.107500.0callus| leaf
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During the early stages of embryo development, first observed at the transition stage. In the heart and torpedo stages, predominantly present in the upper part of embryos. In seedlings, strongly expressed in shoot meristems, hypocotyls, in the vascular bundles of cotyledons, and in the veins of mature leaves. In reproductive organs, detected in inflorescences, especially in sepals, filaments, and stigmas, as well as in mature siliques and seeds. {ECO:0000269|PubMed:25871650}.
UniprotTISSUE SPECIFICITY: Moslty expressed in inflorescences, seedlings, leaves, flowers and flower buds, and, to a lower extent, in stems, siliques and roots. {ECO:0000269|PubMed:25871650}.
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
PlantRegMapPavir.1KG323800.3.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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004952679.10.0uncharacterized protein LOC101761263 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLK3YPU20.0K3YPU2_SETIT; Uncharacterized protein
STRINGPavir.Ab01874.1.p0.0(Panicum virgatum)
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]