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 Gorai.001G059600.1
Common NameB456_001G059600, LOC105786301
Organism
Gossypium raimondii
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: 885aa    MW: 98329.7 Da    PI: 8.6752
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.001G059600.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix70.33.5e-22792872186
            trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                         +Wt +ev++Li++r e+++r++  k +++lWee+s+ + + g++rsp+qCk++w +l ++y++i+  +k++     + +pyf++++
  Gorai.001G059600.1 792 KWTSEEVKKLIKMRGELHSRFQVLKGRMALWEEISASLLADGISRSPVQCKSRWASLVQKYEEIRSEKKSH-----KDWPYFEEMN 872
                         7*****************************************************************99996.....68*******7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.107.7E-6876326IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.06E-7277491IPR001279Metallo-beta-lactamase
SMARTSM008492.7E-2889286IPR001279Metallo-beta-lactamase
PfamPF127061.6E-11100236IPR001279Metallo-beta-lactamase
PfamPF075215.2E-6430463IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500909.117785849IPR017877Myb-like domain
SuperFamilySSF466896.52E-6788851IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.602.9E-7788851IPR009057Homeodomain-like
SMARTSM007171.8E-5789851IPR001005SANT/Myb domain
PfamPF138376.6E-20790874No hitNo description
CDDcd122035.02E-22791856No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 885 aa     Download sequence    Send to blast
MAASTALSLC PYILSRRPTP RKRLFSCFVG STTPIGTRRT NVPRRSSGRL DGARKSMEDS  60
VQRKMEQFYE GTAGPPLRVL PIGGLGEIGM NCMLVGNYDR YILIDAGVMF PDYDELGVQK  120
ITPDTTFIKK WSHKIEAVVI THGHEDHIGA LPWVIPALDP HTPIYASSFT MELIKKRLKE  180
NGIFVPSRLK VFKMRKRFTA GPFEIEPLRV THSIPDCCGL VLRCADGTIL HTGDWKIDES  240
PLDGNIFDRQ FLEDLSKEGV TLMMSDSTNV LSPGRTTSER VVADALLRHI SNAKGRIITT  300
QFASNIHRLG SVKAAADLTG RKLVFVGMSL RTYLDAAWKD GKAPIDPSTL VKAEDIDAYA  360
PKDLIIVTTG SQAEPRAALN LASYGSSHSF KLNKEDVILY SAKVIPGNES RVMKMLNRIS  420
EIGSTIVMGR NEGLHTSGHG YRGELEEVLK IVKPQHFLPI HGELVFLKEH ELLGKSTGVR  480
HTTVIKNGEM LGVSHLRNRK VLSNGFSSLG KENLQLMYSD GDKAFGTSTE LCIDERLRIA  540
SDGIIVVSME ILRPQKIDGI IENSLKGKIR ITTRCLWLDK GKLLDALHKA AHAALSSCPV  600
NCPLAHMERT VSEVLRKMVR KYSGKRPEVI AIALENPAGV LSDELNEKLS GNSNVGFGIP  660
AVRKVMDGHP KRREPNKIKA ENDSNLHIEN TSEQNLIVGN DVETFLPEEV TTSSSPDHAE  720
RHTRSTEDSD EFWKPFIKSS SPIDNLENDN NGFIPIEEHK SELKSDDATS SGDVSELLSS  780
QLKSSKPAKR NKWTSEEVKK LIKMRGELHS RFQVLKGRMA LWEEISASLL ADGISRSPVQ  840
CKSRWASLVQ KYEEIRSEKK SHKDWPYFEE MNKILSDDFE AAAT*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A2e-877763519560RIBONUCLEASE J
5a0t_B2e-877763519560RIBONUCLEASE J
5a0v_A2e-877763519560RIBONUCLEASE J
5a0v_B2e-877763519560RIBONUCLEASE J
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During the early stages of embryo development, first observed at the transition stage. In the heart and torpedo stages, predominantly present in the upper part of embryos. In seedlings, strongly expressed in shoot meristems, hypocotyls, in the vascular bundles of cotyledons, and in the veins of mature leaves. In reproductive organs, detected in inflorescences, especially in sepals, filaments, and stigmas, as well as in mature siliques and seeds. {ECO:0000269|PubMed:25871650}.
UniprotTISSUE SPECIFICITY: Moslty expressed in inflorescences, seedlings, leaves, flowers and flower buds, and, to a lower extent, in stems, siliques and roots. {ECO:0000269|PubMed:25871650}.
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_012468135.10.0PREDICTED: uncharacterized protein LOC105786301
RefseqXP_012468148.10.0PREDICTED: uncharacterized protein LOC105786301
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A0D2N6480.0A0A0D2N648_GOSRA; Uncharacterized protein
STRINGGorai.001G059600.10.0(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. Paterson AH, et al.
    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Nature, 2012. 492(7429): p. 423-7
    [PMID:23257886]
  3. 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]