PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID mrna06360.1-v1.0-hybrid
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria
Family Trihelix
Protein Properties Length: 1029aa    MW: 112715 Da    PI: 8.54
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
mrna06360.1-v1.0-hybridgenomeGDRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix64.42.5e-20859939186
                 trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                              +W+ +ev++ i++r ++++r++  k +++lWee+s+++ ++g++rsp qCk+ w +l ++y++ k g++++     +++py+++++
  mrna06360.1-v1.0-hybrid 859 KWKPEEVKKFIKMRGKLHSRFQVVKGRMALWEEISRNLLAEGVNRSPGQCKSLWASLVQKYEESKSGKRSQ-----KSWPYYEEMD 939
                              7******************************************************************9984.....56*******7 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.105.3E-67153403IPR001279Metallo-beta-lactamase
SuperFamilySSF562815.59E-71154568IPR001279Metallo-beta-lactamase
SMARTSM008498.7E-25166363IPR001279Metallo-beta-lactamase
PfamPF127061.3E-10177313IPR001279Metallo-beta-lactamase
PfamPF075218.8E-6509540IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.026852916IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.605.0E-5856917IPR009057Homeodomain-like
PfamPF138378.5E-18857939No hitNo description
CDDcd122036.91E-22858923No 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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009001anatomyfruit
PO:0007010developmental stagewhole plant fruit ripening stage
PO:0007027developmental stagewhole plant fruit formation stage 70% to final size
Sequence ? help Back to Top
Protein Sequence    Length: 1029 aa     Download sequence    Send to blast
MVMGELEQRP EGCEAERDGE KFSHSFFSTS LSISRSSSSS SKSQPHAFSG ASKLMQLGVL  60
GGLSLYHSIY SPAVPAQMAA LGALSPCPYT LLSRLKSSHR SVSCSLGSST APSTGTRGSG  120
YKRSGRVEGP RKSMEDSVQR KMEQFYEGRD GPPLRVLPIG GLGEIGMNCM LVGNYDRYIL  180
IDAGIMFPDF DELGVQKIIP DTTFIRKWKH KIEAIVITHG HEDHIGALPW VIPALDPSTP  240
IFASSFTMEL IRKRLKEHGI FVPSRLKMFK TKRKFMAGPF EIEPVRVTHS IPDCCGLVLR  300
CADGTILHTG DWKIDESPLD GQGFDREGLE ELSKEGVTLM MSDSTNVLSP GRTTSESSVA  360
DALMRHISAA QGRVITTQFA SNIHRLGSVK AAADATGRKL VFVGMSLRTY LDAAWRDGKA  420
PIDPSTLVKV EDIDSYAPKD LLIVTTGSQA EPRAALNLAS FGGSHSVKLT KEDIILYSAK  480
VIPGNESRVM KMLNRISDMG STIVMGKNEG LHTSGHGYRG ELEEVLRIVK PQHFLPIHGE  540
LLFLKEHELL GRSTGIHHTT VIKNGEMLGV SHLRNRRVLS NGFTLLGKEN LQLKYSDGDK  600
AFGTSSELCV DERLKIALDG IIVVSMEILR PQNVNGLAES SIKGKIRITT RCLWLDKGKL  660
YDALYKAAHA ALSSCPINCP LPHMERTVSE VLRKLVRKYS GKRPDVIAIA MENPTAVLAD  720
EVSTRLSGKS HVGYERSALR KVNDGNSNKS RSTRTESDEA KDNIELQSST TEKDFEDDGV  780
EVKAPLPVEV STSSNVNPEN VSSDTEEPND IWNAMVKLSA GDKLAEDKND LVLQEENLKK  840
DDPESTERTS PSKPVKRNKW KPEEVKKFIK MRGKLHSRFQ VVKGRMALWE EISRNLLAEG  900
VNRSPGQCKS LWASLVQKYE ESKSGKRSQK SWPYYEEMDG ALSDSEAMAT KPPTQLSTYA  960
DAVTTSNAAL SSATSSTVAG NQRRSSTSSF SEPPHPTPAA DPKCCAARQT SSPSQQSPSK  1020
LCLVDLRL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A9e-8815471219560RIBONUCLEASE J
5a0t_B9e-8815471219560RIBONUCLEASE J
5a0v_A9e-8815471219560RIBONUCLEASE J
5a0v_B9e-8815471219560RIBONUCLEASE 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
PlantRegMapmrna06360.1-v1.0-hybrid
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_004297533.10.0PREDICTED: uncharacterized protein LOC101299666
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A2P6P4Z10.0A0A2P6P4Z1_ROSCH; Putative beta-lactamase transcription factor MYB family
STRINGXP_004297533.10.0(Fragaria vesca)
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]