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 Pp3c20_9790V3.2.p
Organism
Physcomitrella patens
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Bryophyta; Bryophytina; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrella
Family Trihelix
Protein Properties Length: 989aa    MW: 109002 Da    PI: 6.9615
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pp3c20_9790V3.2.pgenomeCOSMOSSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix605.9e-19842931186
           trihelix   1 rWtkqevlaLiearremeerlr.rgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrt...sessstcpyfdqle 86 
                        +W ++e+ +Lie+r+ m++ l  +gk++ p W+++++ ++e gfersp+qC + w++l k+y+++ e ++ r    +  +++++yf+ ++
  Pp3c20_9790V3.2.p 842 KWRHDETIKLIEVRSTMGDLLVkEGKKRRPSWKDIAASLSESGFERSPEQCSSMWSSLLKKYEAVVEEKRTRDssvPAPKKEWAYFELMD 931
                        7****************998763699**************************************999988884133556789****9998 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-65104355IPR001279Metallo-beta-lactamase
SuperFamilySSF562816.1E-73105520IPR001279Metallo-beta-lactamase
SMARTSM008493.4E-25117314IPR001279Metallo-beta-lactamase
PfamPF127063.3E-12130264IPR001279Metallo-beta-lactamase
PfamPF075211.6E-8460500IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
Gene3DG3DSA:1.10.10.601.2E-6833902IPR009057Homeodomain-like
PROSITE profilePS500908.792835900IPR017877Myb-like domain
SMARTSM007174.5E-4839902IPR001005SANT/Myb domain
PfamPF138372.2E-16840932No hitNo description
CDDcd122033.15E-14842904No hitNo description
PROSITE profilePS510298.743847938IPR006578MADF domain
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: 989 aa     Download sequence    Send to blast
MQSLQIRLGL NSLQGGGEAA GAPGALLKSE WKGVGQLFGF NPLTVPVSSR NCVTRAGGPT  60
VHQQSRSRQH RGGYGGHYEG PKRSRDDAVT RKMKSFHEGS DGPPLRVLPI GGLGEIGMNC  120
MLVGNYDRYI MIDAGLMFPD YDDLGIQKVL PDTQFIHRWR DKIEAVIITH GHEDHIGALP  180
WVIPALDPKT PIYATGFTMQ LIKRRLKEYN IPAEGRLRTF SMRARFDAGP FEIEPIRVTH  240
SIPDCCGLVL RCADGTIFHT GDWKIDESPV DGNVFDRVAL EQLQKEGVTL MMSDSTNVLS  300
PGRTTSEADV AEALMRKIVE AKGRRVITTQ FASNVHRLGC VKAAAEVSGR KLVFIGLSLK  360
TYLEAAWRDG QAPFDPAILV KAEDMDAYAP SQLLIVTTGS QAEPRAALNL ASMGSSRLLK  420
LHKDDVILYS AKMIPGNETR VMKMMNRIAE LGPNLVMGRG ENLHTSGHAY RGELEEVLRL  480
VKPQHFLPVH GEFAFLKEHE LLGKAQGIRH TAVIKNGEML GVAPLRNGRV LSSGFSQLGR  540
EKLKLMYNDG DKAFGTAADL CIQERMNIAL EGLVIASVEV IREETKYLNE DEVYEDKILR  600
DDDDGDELGL QGRVRITTRC LWTDNGKLLE SLQRAADVAL ASSRKDARLP TIERHVSVVL  660
RKVVQKYSNK RPDVIVIATD ASDGVVPNRS SPESINNYDQ PRNKPQPWKR AADSMSSFSR  720
GAVVGTVEPV DEVTSRSFVA EETSERNKVV ISSRVQSETV SAKAQRLSSE GDATQKNERV  780
KAGDGGEISA TSSGFSDPEE FESDEESGDS DQEADSVASD GAASSLSQES TEEIEPQKKR  840
QKWRHDETIK LIEVRSTMGD LLVKEGKKRR PSWKDIAASL SESGFERSPE QCSSMWSSLL  900
KKYEAVVEEK RTRDSSVPAP KKEWAYFELM DAVMQKLAKT AGSQDVVIEK AKSKKPKRKS  960
KKPKVDATAA IDSTEVELPD SEDRQTAQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A8e-8110558519485RIBONUCLEASE J
5a0t_B8e-8110558519485RIBONUCLEASE J
5a0v_A8e-8110558519485RIBONUCLEASE J
5a0v_B8e-8110558519485RIBONUCLEASE J
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1953961KKPKRKSKK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Ppa.172340.0protonema
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}.
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_024358144.10.0uncharacterized protein LOC112273491
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A2K1IUS10.0A0A2K1IUS1_PHYPA; Uncharacterized protein
STRINGPP1S192_99V6.10.0(Physcomitrella patens)
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]