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 676739362
Organism
Sisymbrium irio
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Sisymbrieae; Sisymbrium
Family Trihelix
Protein Properties Length: 880aa    MW: 97068.6 Da    PI: 8.0883
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
676739362genomeVEGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix65.21.4e-20788868186
   trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                +W+ +ev++ i++r e+++r++  k +++lWee+s++++++gf+rsp qCk+ w +l ++y+++k+ e+++     +++++f++++
  676739362 788 KWKPEEVKKVIRMRGELHSRFQVVKGRMALWEEISSNLSAEGFNRSPGQCKSLWASLIQKYEECKADERSK-----TSWSHFEDMN 868
                7********************************************************************95.....35******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.106.4E-6879329IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.06E-7180494IPR001279Metallo-beta-lactamase
SMARTSM008495.7E-2592289IPR001279Metallo-beta-lactamase
PfamPF127067.4E-11104239IPR001279Metallo-beta-lactamase
PfamPF075215.9E-7434466IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
Gene3DG3DSA:1.10.10.607.1E-6781847IPR009057Homeodomain-like
PROSITE profilePS500908.165781845IPR017877Myb-like domain
PfamPF138372.9E-17786869No hitNo description
CDDcd122031.30E-22787852No 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: 880 aa     Download sequence    Send to blast
MAAFSALSLC PYTFTFRHSS RIRSTVSCSV TSPPAASGTS SSSKTPRRRS GRLEGAGKSM  60
EDSVKRKMEQ FYEGTDGPPL RVLPIGGLGE IGMNCMLVGN YDRYILIDAG VMFPDYDEPG  120
VQKIMPDTGF IRRWKHKIEA VVITHGHEDH IGALPWVIPA LDSNTPIFAS SFTMELIKKR  180
LKEHGIFVQS RLKTFNTRRR FMAGPFEIEP ITVTHSIPDC SGLVLRCADG NILHTGDWKI  240
DEAPLDGKVF DREALEELSK EGVTLMMSDS TNVLSPGRTT SEKVVADALV RNVMAAKGRV  300
ITTQFASNIH RLGSIKAAAD LTGRKLVFVG MSLRTYLEAA WRDGKAPIDP SSLVKVEDIE  360
AYAPKDLLIV TTGSQAEPRA ALNLASYGSS HAFKLTKEDI ILYSAKVIPG NESRVMKMMN  420
RIADIGPNIV MGKNEMLHTS GHAYRGELEE VLKIVKPQHF LPIHGELLFL KEHELLGKST  480
GIRHTTVIKN GEMLGVSHLR NRRVLSNGFS SLGRENLQLM YSDGDKAFGT SSELCIDERL  540
RIASDGIIVL SMEIMRPGVS ENALKGKIRI TTRCMWLDKG RLLDALHKAA HAALSSCPVN  600
CPLSHMERTV SEVLRKIVRK YSGKRPEVIA IATENPMAVR ADEVSARLSG DPSLGSGVAA  660
LRKVVEGNNK RNRPKKAPSQ EDSPKEEAGD IIDSAGLLAE EDSASSTYTE AAEDVPVRSS  720
AEESDDFWKS FINPSSSPSP GETKNVNKVT DAEPKTEDSE SSREDEDDPS DATDSQTKSS  780
SKRVKRNKWK PEEVKKVIRM RGELHSRFQV VKGRMALWEE ISSNLSAEGF NRSPGQCKSL  840
WASLIQKYEE CKADERSKTS WSHFEDMNNI LSELDTPAPK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A3e-878063419560RIBONUCLEASE J
5a0t_B3e-878063419560RIBONUCLEASE J
5a0v_A3e-878063419560RIBONUCLEASE J
5a0v_B3e-878063419560RIBONUCLEASE 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
PlantRegMap676739362
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
GenBankAK2212720.0AK221272.1 Arabidopsis thaliana mRNA for putative protein, complete cds, clone: RAFL24-15-P14.
GenBankBT0042100.0BT004210.1 Arabidopsis thaliana clone RAFL16-01-C03 (R50172) unknown protein (At5g63420) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006394279.10.0uncharacterized protein LOC18013384
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLV4K1180.0V4K118_EUTSA; Uncharacterized protein
STRINGXP_006394279.10.0(Eutrema salsugineum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95392634
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]