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 Vradi0043s00060.1
Organism
Vigna radiata
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
Family Trihelix
Protein Properties Length: 874aa    MW: 96842.8 Da    PI: 8.5886
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Vradi0043s00060.1genomeSNUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix61.32.3e-19781861186
           trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                        +W+ +ev++Li +r+e+++r++  k +++lWee+s+k+ + g++rsp qCk+ w +l  +y+ ik+ + ++     +++py +++e
  Vradi0043s00060.1 781 KWKTDEVKKLIGMREELNDRFQVVKGRMALWEEISQKLLADGISRSPGQCKSLWTSLVLKYEGIKNEKDSK-----KSWPYIEDME 861
                        7****************************************************************999984.....56*******8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.106.5E-6398360IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.25E-6699515IPR001279Metallo-beta-lactamase
SMARTSM008498.2E-22111309IPR001279Metallo-beta-lactamase
PfamPF007533.2E-9112256IPR001279Metallo-beta-lactamase
PfamPF075219.1E-7466497IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.42774838IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.603.7E-4775838IPR009057Homeodomain-like
PfamPF138379.7E-16779863No hitNo description
CDDcd122031.39E-18780845No 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
LTSLSLSLRP LSLRRKPTTA TSATLSSLPG TSAPNQSMPF SHSRLWHFTH VLFSGRTHGS  60
TTKAPRRRAR RIEGPRKSME DSVQRKMEQF YEGSDGPPLR VLPIGGLGEI GMNCMLVGNH  120
DRYILIDAGV MFPDYDELGV QKIIPDTTFI RKWSHKIEAL VITHGHEDHI GALPWVIPAL  180
DSNTPIFSSS FTKELINKRL KEHGIFVPSR LKVFRMRKKF VAGPFEIEPI RVTHSIPDCC  240
GLVLRCSDGT ILHTGDWKID ETPLDGNVFD REALEELSKE GVTLIEPMFA PDITLQMMSD  300
STNVLSPGRT ISESVVADAL LRHISASNGR VITTQFASNL HRLGSVKAAA DLTGRKLVFV  360
GMSLRTYLDA AWKDGKAPID PSTLVKAEDI DAYAPKDLLI VTTGSQAEPR AALNLASYGS  420
SHAFKLTKED LVLYSAKVIP GNESRVMKML NRISEIGSTI VMGKNEGLHT SGHAYRGELE  480
EVLRIVKPQH FLPIHGELLF LKEHELLGKS TGIRHTALKY SDGDRAFGTS SELFIDERLR  540
IALDGIIVTS MEIFRPKFLA SLAPNTLKGK IRITTRCLWL DKGKLMDALY KSAHAALSSC  600
PVNSPLAHIE RTVSEVLRKM VRKYSGKRPE VIAIAIENPA STITDEVNTK LSGKTHAGLG  660
ISTAKRAVDR HEKGNQPTSL QITDDSIPNA SGPEDYLSDE DNTASGAEGD LSESEDSDEF  720
WKPFIATLPV EKPLGANNAY DSQKEHESNR KKDDSKIIDE AKSEEISTSE PKSSKSVKRN  780
KWKTDEVKKL IGMREELNDR FQVVKGRMAL WEEISQKLLA DGISRSPGQC KSLWTSLVLK  840
YEGIKNEKDS KKSWPYIEDM ERIMSDKEAP ATK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A8e-819955219435RIBONUCLEASE J
5a0t_B8e-819955219435RIBONUCLEASE J
5a0v_A8e-819955219435RIBONUCLEASE J
5a0v_B8e-819955219435RIBONUCLEASE 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
PlantRegMapVradi0043s00060.1
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
GenBankAP0150350.0AP015035.1 Vigna angularis var. angularis DNA, chromosome 2, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_022632934.10.0uncharacterized protein LOC106752779 isoform X3
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A3Q0ER760.0A0A3Q0ER76_VIGRR; uncharacterized protein LOC106752779 isoform X3
STRINGXP_007137930.10.0(Phaseolus vulgaris)
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]