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 SMil_00013349-RA_Salv
Organism
Salvia miltiorrhiza
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Mentheae; Salvia
Family Trihelix
Protein Properties Length: 874aa    MW: 97330.2 Da    PI: 8.9592
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
SMil_00013349-RA_SalvgenomeNDCTCMView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix63.64.5e-20782862186
               trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                            +W  +ev+++i++r e+++r++  k +++lWee+s+++ + g++rsp qCk+ w +l ++y++ k  ++k+     s++pyf++l+
  SMil_00013349-RA_Salv 782 KWRPEEVKKMIKVRGELHNRFQVLKGRMALWEEISANLLADGISRSPGQCKSLWTSLVQKYEESKSDKQKQ-----SSWPYFEDLD 862
                            7***************************************************************9999984.....57******98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.103.5E-6777327IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.05E-7378492IPR001279Metallo-beta-lactamase
SMARTSM008491.5E-2590287IPR001279Metallo-beta-lactamase
PfamPF127065.9E-10102237IPR001279Metallo-beta-lactamase
PfamPF075211.1E-6433464IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.677775839IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.601.4E-4778841IPR009057Homeodomain-like
PfamPF138375.1E-18780864No hitNo description
CDDcd122032.27E-19781846No 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: 874 aa     Download sequence    Send to blast
MAALSTISLC PHKLFWCQPK PRRRFISCCV SVPSVKGIRG SKVPNRRFGR REGAGKSMED  60
SVKRKMEQFY EGSDGPPLRI LPIGGLGEIG MNCMLVGNYD RYILIDAGIM FPDYDDLGIQ  120
KIIPDTTFIK KWSHKIEAVV ITHGHEDHIG ALPWVIPALD SHTPIFASSF TMELIKKRLK  180
EFGIFLPSRL KVFNTRRRFV AGPFEVEPIR VTHSIPDCCG LVFRCADGTI LHTGDWKIDE  240
SPLDGNVFDR EALEELSKEG VTLMMSDSTN VLSPGRTLSE TVVADSLLRH ISAAKGRVVT  300
TQFASNIHRL GSVKAAADLT GRKLVFVGMS LRTYLDAAWK DGKAPIDPST LVKVEDIDAY  360
APKDLLIVTT GSQAEPRAAL NLASHGSSHS LKLNKEDLIL YSAKVIPGNE TRVMKMMNRL  420
AEIGPQIVMG KNELLHTSGH AHREELDEVL KIVKPQHFLP IHGELLFLKE HELLGRSTGV  480
RHTTVIKNGE MLGVSHLRNR RVLSNGFISL GKENLQLMYS DGDKAFGTAT ELCIDERMRI  540
ASDGIIVVSM EIMRPDGSVE KTLKGKIRIT TRCLWLDKGK LLDALHKAAH AALSSCPVTC  600
PLAHMERIVS EVLRKMVRKY SSKRPEVIAI AIENPAGVLA DEINEKLSGK SHISSEFSAL  660
RKAVDRHEKR KQPIARLEED VNGLALERST SAQELEDQDF DEVQGEMAAS TSGLPDRALK  720
TNEPDVFWKS FVSSSEPIQS EHNVELLPAA EHKEKGKEEG SKVDPGLPNP RVKSSKIAKR  780
NKWRPEEVKK MIKVRGELHN RFQVLKGRMA LWEEISANLL ADGISRSPGQ CKSLWTSLVQ  840
KYEESKSDKQ KQSSWPYFED LDKILSSLES SSSK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A3e-867863319560RIBONUCLEASE J
5a0t_B3e-867863319560RIBONUCLEASE J
5a0v_A3e-867863319560RIBONUCLEASE J
5a0v_B3e-867863319560RIBONUCLEASE 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}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. {ECO:0000269|PubMed:25871650}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_011073024.10.0uncharacterized protein LOC105158090 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A4D8YXA30.0A0A4D8YXA3_SALSN; Ribonuclease J
STRINGMigut.I00512.1.p0.0(Erythranthe guttata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA58742331
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]