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 Cotton_A_16240_BGI-A2_v1.0
Organism
Gossypium arboreum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family Trihelix
Protein Properties Length: 846aa    MW: 93833.4 Da    PI: 8.2906
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cotton_A_16240_BGI-A2_v1.0genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix67.42.9e-21754834186
                    trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfd 83 
                                 +W+ +ev++Li++r ++++r++  k +++lWee+s  + e g++rsp qCk+ w +l ++y++ k+ ++++     +++pyf+
  Cotton_A_16240_BGI-A2_v1.0 754 KWKPEEVKKLIKMRGDLHSRFQVVKGRMALWEEISTSLLEDGITRSPAQCKSLWASLVQKYEESKNEKRSH-----KSWPYFE 831
                                 7****************************************************************999996.....57***** PP

                    trihelix  84 qle 86 
                                 +++
  Cotton_A_16240_BGI-A2_v1.0 832 DMN 834
                                 *97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.104.9E-6976326IPR001279Metallo-beta-lactamase
SuperFamilySSF562817.69E-7277491IPR001279Metallo-beta-lactamase
SMARTSM008494.5E-2689286IPR001279Metallo-beta-lactamase
PfamPF127062.6E-11101236IPR001279Metallo-beta-lactamase
PfamPF075211.5E-5432463IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.909747811IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.601.2E-4750813IPR009057Homeodomain-like
PfamPF138377.3E-18752835No hitNo description
CDDcd122032.58E-22753818No 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: 846 aa     Download sequence    Send to blast
MAASTSLSLY PYILCCKTSP RNRYISCAVG SPTPIGTRRT KVPRKSSGRL DGARKSMEDS  60
VQRKMEQFYE GTAGPPLRVL PIGGLGEIGM NCMLVGHYDR YILIDAGVMF PDYDELGVQK  120
IIPDTTFIKK WSHKIEAVVI THGHEDHIGA LPWVIPALDS HTPIYASSFT MELIKKRLKE  180
NGILVPSRLK VFKIRRRFKA GPFEIEPLRV THSIPDCCGL VLRCADGTIL HTGDWKIDES  240
PLDGKTFDRQ FLEELSKEGV TLMMSDSTNV LSPGRTVSES AVADALSRHI SGAKGRIITT  300
QFASNIHRLG SIKAAADVTG RKLVFIGMSL RTYLDAAWKD GKAPIDPSTL VKAEDIDAYA  360
PKDLIIVTTG SQAEPRAALN LASYGSSHSF KLNKEDVILY SAKVIPGNES RVMKMLNRIS  420
EIGSTIVMGK NEGLHTSGHG YRGELEEVLQ IVKPQHFLPI HGELLFLKEH ELLGKSTGIR  480
HTTVIKNGEM LGVSHLRNRR VLSNGFSSLG KENLQLMYSD GDKAFGTSTE LCVDERLRIA  540
SDGIIVVSME ILRPQKIDGM VENTLKGKIK ITTRCLWLDK GKLLDTLHKA AHATLSSCPV  600
NCPLAHMERT VSEVLRKTVR KYSGKRPEVI AIALENPAGV LSDELNEKLS GNYNAGFALP  660
TLRKVVDGHP RRGPPNKMKA EDDDDDAEPE RFLPVEDSSI SSPDYTERLT PNTDDSDELE  720
EHEPEVRSDG TASNGDDSEV TGSQPKSSKP KRNKWKPEEV KKLIKMRGDL HSRFQVVKGR  780
MALWEEISTS LLEDGITRSP AQCKSLWASL VQKYEESKNE KRSHKSWPYF EDMNKVLSDF  840
EATATT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A3e-867763519560RIBONUCLEASE J
5a0t_B3e-867763519560RIBONUCLEASE J
5a0v_A3e-867763519560RIBONUCLEASE J
5a0v_B3e-867763519560RIBONUCLEASE 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_017616142.10.0PREDICTED: ribonuclease J-like isoform X2
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A2P5VX060.0A0A2P5VX06_GOSBA; Uncharacterized protein
STRINGGorai.003G119600.10.0(Gossypium raimondii)
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]