PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID GRMZM2G155662_P01
Common Namegpm491, WHY1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea
Family Whirly
Protein Properties Length: 266aa    MW: 29438.7 Da    PI: 9.7599
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GRMZM2G155662_P01genomeMaizeSequenceView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly195.47.9e-61912291139
             Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrk 92 
                        s+yk+kaal+ +++ p f+ ldsg+ k+ ++G++ll++a+a+a+r+ydW +kq+f+ls+ e+++l+ l++ +sceffhdp+++ s+eGkvrk
  GRMZM2G155662_P01  91 SIYKGKAALSFDPRPPLFVPLDSGAYKVAKEGFVLLQFAPAVATRQYDWTRKQVFSLSVWEIGTLLTLGPTDSCEFFHDPFKGRSEEGKVRK 182
                        7******************************************************************************************* PP

             Whirly  93 alkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                        +lk+eP pdG G f+nlsv+n l++++es+++P++k+efav+ s ++
  GRMZM2G155662_P01 183 VLKIEPTPDGNGRFFNLSVQNRLINVDESIYIPITKGEFAVIVSTFN 229
                        ******************************************99875 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.107.9E-7978251IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544475.81E-7484266IPR009044ssDNA-binding transcriptional regulator
PfamPF085364.9E-5892226IPR013742Plant transcription factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006281Biological ProcessDNA repair
GO:0032211Biological Processnegative regulation of telomere maintenance via telomerase
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0045910Biological Processnegative regulation of DNA recombination
GO:0005634Cellular Componentnucleus
GO:0009508Cellular Componentplastid chromosome
GO:0009570Cellular Componentchloroplast stroma
GO:0003677Molecular FunctionDNA binding
GO:0003697Molecular Functionsingle-stranded DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0003723Molecular FunctionRNA binding
GO:0042162Molecular Functiontelomeric DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0006310anatomytassel floret
PO:0006339anatomyjuvenile vascular leaf
PO:0006340anatomyadult vascular leaf
PO:0006341anatomyprimary shoot system
PO:0006354anatomyear floret
PO:0006505anatomycentral spike of ear inflorescence
PO:0008018anatomytransition vascular leaf
PO:0009001anatomyfruit
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009054anatomyinflorescence bract
PO:0009066anatomyanther
PO:0009074anatomystyle
PO:0009084anatomypericarp
PO:0009089anatomyendosperm
PO:0020040anatomyleaf base
PO:0020104anatomyleaf sheath
PO:0020126anatomytassel inflorescence
PO:0020127anatomyprimary root
PO:0020136anatomyear inflorescence
PO:0020142anatomystem internode
PO:0020148anatomyshoot apical meristem
PO:0025142anatomyleaf tip
PO:0025287anatomyseedling coleoptile
PO:0001007developmental stagepollen development stage
PO:0001009developmental stageD pollen mother cell meiosis stage
PO:0001052developmental stagevascular leaf expansion stage
PO:0001053developmental stagevascular leaf post-expansion stage
PO:0001083developmental stageinflorescence development stage
PO:0001094developmental stageplant embryo coleoptilar stage
PO:0001095developmental stageplant embryo true leaf formation stage
PO:0001180developmental stageplant proembryo stage
PO:0007001developmental stageearly whole plant fruit ripening stage
PO:0007003developmental stageIL.03 full inflorescence length reached stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
PO:0007015developmental stageradicle emergence stage
PO:0007016developmental stagewhole plant flowering stage
PO:0007022developmental stageseed imbibition stage
PO:0007026developmental stageFL.00 first flower(s) open stage
PO:0007031developmental stagemid whole plant fruit ripening stage
PO:0007032developmental stagewhole plant fruit formation stage up to 10%
PO:0007045developmental stagecoleoptile emergence stage
PO:0007063developmental stageLP.07 seven leaves visible stage
PO:0007065developmental stageLP.05 five leaves visible stage
PO:0007072developmental stageLP.18 eighteen leaves visible stage
PO:0007094developmental stageLP.01 one leaf visible stage
PO:0007101developmental stageLP.09 nine leaves visible stage
PO:0007104developmental stageLP.15 fifteen leaves visible stage
PO:0007106developmental stageLP.03 three leaves visible stage
PO:0007112developmental stage1 main shoot growth stage
PO:0007116developmental stageLP.11 eleven leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007633developmental stageendosperm development stage
PO:0021004developmental stageinflorescence initiation stage
Sequence ? help Back to Top
Protein Sequence    Length: 266 aa     Download sequence    Send to blast
MPPPAPLFLS LASTPPPALM PVHHPRAPQS LTLVPPVASS RKAAAVPACP VASPRHSDYF  60
DPRAPPPPRG DGGYGRPPNG AQDGRVFTSY SIYKGKAALS FDPRPPLFVP LDSGAYKVAK  120
EGFVLLQFAP AVATRQYDWT RKQVFSLSVW EIGTLLTLGP TDSCEFFHDP FKGRSEEGKV  180
RKVLKIEPTP DGNGRFFNLS VQNRLINVDE SIYIPITKGE FAVIVSTFNY IIPHLMGWST  240
FVSSIKPEES RPYSRPQSTS EYEWRR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A2e-898026532219p24: plant transcriptional regulator PBF-2
1l3a_B2e-898026532219p24: plant transcriptional regulator PBF-2
1l3a_C2e-898026532219p24: plant transcriptional regulator PBF-2
1l3a_D2e-898026532219p24: plant transcriptional regulator PBF-2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Zm.886810.0cell culture| ear| meristem| ovary| pedicel| shoot
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasGRMZM2G155662
Functional Description ? help Back to Top
Source Description
UniProtSingle-stranded DNA and RNA binding protein that maintains plastid genome stability by preventing break-induced and short homology-dependent illegitimate recombinations. Functions in RNA metabolism and is involved in the maturation of the atpF and 23S ribosomal RNAs. {ECO:0000269|PubMed:18676978, ECO:0000269|PubMed:19666500}.
Function -- GeneRIF ? help Back to Top
  1. Genome-wide coimmunoprecipitation assays showed that ZmWHY1 in chloroplast extract is associated with DNA from throughout the plastid genome and with a subset of plastid RNAs that includes atpF transcripts.
    [PMID: 18676978]
  2. The requirement of WHY1 function for maize embryogenesis is dependent on the genetic background.
    [PMID: 23840682]
Cis-element ? help Back to Top
SourceLink
PlantRegMapGRMZM2G155662_P01
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Albino seedlings lacking plastid ribosomes. {ECO:0000269|PubMed:18676978, ECO:0000269|PubMed:19666500}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0433600.0BT043360.1 Zea mays full-length cDNA clone ZM_BFc0169P08 mRNA, complete cds.
GenBankEU5956640.0EU595664.1 Zea mays Whirly family nucleic acid binding protein (WHY1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001123589.10.0single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotB2LXS70.0WHY1_MAIZE; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A1Q1AUG70.0A0A1Q1AUG7_MAIZE; Whirly1
TrEMBLK4JBV10.0K4JBV1_MAIZE; WHIRLY-type transcription factor (Fragment)
STRINGGRMZM2G155662_P010.0(Zea mays)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP30123885
Representative plantOGRP23161635
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02740.22e-94ssDNA-binding transcriptional regulator
Publications ? help Back to Top
  1. Desveaux D,Maréchal A,Brisson N
    Whirly transcription factors: defense gene regulation and beyond.
    Trends Plant Sci., 2005. 10(2): p. 95-102
    [PMID:15708347]
  2. Prikryl J,Watkins KP,Friso G,van Wijk KJ,Barkan A
    A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis.
    Nucleic Acids Res., 2008. 36(16): p. 5152-65
    [PMID:18676978]
  3. Alexandrov NN, et al.
    Insights into corn genes derived from large-scale cDNA sequencing.
    Plant Mol. Biol., 2009. 69(1-2): p. 179-94
    [PMID:18937034]
  4. Maréchal A, et al.
    Whirly proteins maintain plastid genome stability in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2009. 106(34): p. 14693-8
    [PMID:19666500]
  5. Soderlund C, et al.
    Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.
    PLoS Genet., 2009. 5(11): p. e1000740
    [PMID:19936069]
  6. Zhang YF,Hou MM,Tan BC
    The requirement of WHIRLY1 for embryogenesis is dependent on genetic background in maize.
    PLoS ONE, 2013. 8(6): p. e67369
    [PMID:23840682]