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 AHYPO_004678-RA
Organism
Amaranthus hypochondriacus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Amaranthaceae; Amaranthus
Family Trihelix
Protein Properties Length: 872aa    MW: 96092.2 Da    PI: 8.1047
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AHYPO_004678-RAgenomeBYUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix67.42.9e-21779859186
         trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                      +W+ +ev++Li +r e++er++ ++ +++lWee+s+ + + g++r+p qCk+ w +l ++y++ k  ek++     +++pyf++++
  AHYPO_004678-RA 779 KWKPEEVKKLIMLRGELHERFQVARGRMALWEEISSSLLADGYTRTPGQCKSLWASLVQKYEESKSDEKNK-----KSWPYFQEMN 859
                      7********************************************************************84.....56*******7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.102.8E-6673323IPR001279Metallo-beta-lactamase
SuperFamilySSF562813.42E-7174488IPR001279Metallo-beta-lactamase
SMARTSM008492.7E-2386283IPR001279Metallo-beta-lactamase
PfamPF127061.9E-1197233IPR001279Metallo-beta-lactamase
PfamPF075212.9E-5428460IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.095772836IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.601.2E-5772838IPR009057Homeodomain-like
PfamPF138377.8E-19777861No hitNo description
CDDcd122039.82E-22778843No 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: 872 aa     Download sequence    Send to blast
MAAFTALSIC PCIRPSLVKH YISCSVAPVC SLGTNATKVP RKRYGRLEGA SKSMEDSVKR  60
KMEQFYEGST GPPLRVLPIG GLGEIGMNCM LVGNYDRYIL IDAGIMFPDF DEFGAQKIVP  120
DTTFIKRWSH KIEAVIITHG HEDHIGALPW VIPALDPSTP IFASSFTMEL IKKRLKEFGI  180
FVPSRLKMFK TRRKFKAGPF EIEPIRVTHS IPDCCGLVMR CSDGTIFHTG DWKIDETPVD  240
GKVFDRVALE ELAKEGVTLM MSDSTNIMSP GRTISESVVA DSLLRHISEA KGRVITTQFA  300
SNIHRLGSVK AAADATGRKL VFVGMSLRTY LDAAWKDGTA PIDPSTLVKV EDIDAYAPKD  360
LLIVTTGSQA EPRAALNLAS YGSSHSLKLS KDDVILYSAK VIPGNETRCM KMFNRIAELG  420
SSLVMGRNEL LHTSGHGHRE ELAEALKIVK PQHFLPIHGE LLFLKEHELL GKSTGVRHTT  480
VIKNGEMLGV SHLRNRRVLS NGFISLGKEN LQLMYNDGDK AFGTSAELCI DERMKIATDG  540
IIVISMEILR PHEVEGSTEN CLKGKIRITT RCLWLDQGKL LDALYKAARA ALSSCPVNSP  600
LSHMERTVSE VLRKVVRKYS GKRPEVIAIA TENPAAVISE EVNGRLSGKL NTGFGISGLR  660
KGFDGHLQRK KARKVQDEED DAQLSINNTP APLSEDDTEI NRLLVENDAS ASASASDIEA  720
SSDSESGDSE DILKLFADFS TLATGKLDKA GMGEDISQEE FANTTNRSSK PSKSTKRNKW  780
KPEEVKKLIM LRGELHERFQ VARGRMALWE EISSSLLADG YTRTPGQCKS LWASLVQKYE  840
ESKSDEKNKK SWPYFQEMNA ILSSLGETVN S*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A5e-847463219560RIBONUCLEASE J
5a0t_B5e-847463219560RIBONUCLEASE J
5a0v_A5e-847463219560RIBONUCLEASE J
5a0v_B5e-847463219560RIBONUCLEASE 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}.
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_021847608.10.0uncharacterized protein LOC110787304 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A0K9QP060.0A0A0K9QP06_SPIOL; Uncharacterized protein
STRINGXP_010677898.10.0(Beta vulgaris)
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]