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 Tp57577_TGAC_v2_mRNA27049
Organism
Trifolium pratense
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium
Family Trihelix
Protein Properties Length: 697aa    MW: 77685.9 Da    PI: 9.2341
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp57577_TGAC_v2_mRNA27049genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix60.15.6e-19604684186
                   trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdq 84 
                                +W+ +ev++Li++r+++ +r++  k +++lWee+s+ + + g++rsp qCk+ w +l  +y+ ik+g+  r     ++++y+++
  Tp57577_TGAC_v2_mRNA27049 604 KWKAEEVKKLIDLRSDLRDRFKVVKGRMALWEEISQSLLADGISRSPAQCKSLWTSLVLKYEDIKNGKDTR-----KNWQYLED 682
                                7******************************************************************9986.....79****** PP

                   trihelix  85 le 86 
                                +e
  Tp57577_TGAC_v2_mRNA27049 683 ME 684
                                *8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF562812.26E-432321IPR001279Metallo-beta-lactamase
Gene3DG3DSA:3.60.15.101.6E-312156IPR001279Metallo-beta-lactamase
PfamPF075211.0E-8262310IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.397597661IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.601.0E-5598661IPR009057Homeodomain-like
SMARTSM007170.0079601663IPR001005SANT/Myb domain
CDDcd122031.40E-16603668No hitNo description
PfamPF138374.7E-15603686No 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: 697 aa     Download sequence    Send to blast
MELIKKRLKE HGIFLTSRLK IFRTKNKFVA GPFEIEPIRV THSIPDCCGL VLRCSDGTIL  60
HTGDWKIDET PLDGKVFDRE ALEELSKEGV TLMMSDSTNV LSPGRTTSES VVADSLLRHI  120
SESKGRVITT QFASNLHRIG SVKAAADLTG RKLVFVGMSL RTYLEAAWKD GKAPFDPSTL  180
VKAEDIDAYA PKDLLIVTTG SQAEPRAALN LASYGSSHAF KLTKEDIVLY SAKVIPGNEN  240
RVMEMMNRIS EIGSTIVMGS NKFLHTSGHA YRGELEEVLR IVKPQHFLPV HGEYLFLKEH  300
ESLGKSTGIH HTAVIKNGEM LGVSHLRNRK VLSNGFISLG KENLQLKYSD GDKAFGTSSE  360
LCIDERLRIA LDGIIVISME ISRPKNLESL AENTLKGKIR ITTRCLWLDK GKLLDALHKA  420
AHAALSSCPV KSPLAHMERT VSEVLRKMVR KYSGKRPEVI AIATENPGAV FADEINKKLS  480
GKSHVGPGVP TLRKKVNERR KENQSTKLQT RDDDIDIEGL LPKKDTTTSR AEGDLPDSED  540
SVEFWKQFIA SSVEKSNKAN NGYVSRKEYK SNVKKDDSEA IDEAKSEEMS NAEPESSKSV  600
KKNKWKAEEV KKLIDLRSDL RDRFKVVKGR MALWEEISQS LLADGISRSP AQCKSLWTSL  660
VLKYEDIKNG KDTRKNWQYL EDMEKILSSD EEPATN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A9e-581465112560RIBONUCLEASE J
5a0t_B9e-581465112560RIBONUCLEASE J
5a0v_A9e-581465112560RIBONUCLEASE J
5a0v_B9e-581465112560RIBONUCLEASE 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
PlantRegMapTp57577_TGAC_v2_mRNA27049
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
GenBankAC1267821e-154AC126782.23 Medicago truncatula clone mth2-14p11, complete sequence.
GenBankCU0120421e-154CU012042.6 M.truncatula DNA sequence from clone MTH2-25G4 on chromosome 3, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_024635632.10.0uncharacterized protein LOC11427815 isoform X2
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A2Z6NXX50.0A0A2Z6NXX5_TRISU; Uncharacterized protein
STRINGXP_004500652.10.0(Cicer arietinum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF50993450
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]