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 AT1G23420.1
Common NameF26F24.29, F28C11.6, INO, YAB4
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family YABBY
Protein Properties Length: 231aa    MW: 25957.3 Da    PI: 6.3395
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G23420.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1YABBY259.64.6e-80131822169
        YABBY   2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakas....qllaaeshldeslkeelleelkveeenlksnvekeesasts 95 
                  ++f+ ++q+C+vqC+fC+til+vsvP+tsl++vvtvrCGhCtsllsvnl+kas    +lla+ shlde++kee++++++veee++k+n+eke+s++t 
  AT1G23420.1  13 HLFDLPGQICHVQCGFCTTILLVSVPFTSLSMVVTVRCGHCTSLLSVNLMKASfiplHLLASLSHLDETGKEEVAATDGVEEEAWKVNQEKENSPTTL 110
                  78999**********************************************9999999**************************************** PP

        YABBY  96 vsseklsenedeevprvpp.virPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfg 169
                  vss   s+nede+v+rv++ v++PPekrqr+Psayn+fikeei+r+ka+nP+++h+eafs+aaknWahfP++h++
  AT1G23420.1 111 VSS---SDNEDEDVSRVYQvVNKPPEKRQRAPSAYNCFIKEEIRRLKAQNPSMAHKEAFSLAAKNWAHFPPAHNK 182
                  **9...99***********899***************************************************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046901.6E-6018181IPR006780YABBY protein
SuperFamilySSF470953.93E-9123179IPR009071High mobility group box domain
Gene3DG3DSA:1.10.30.106.1E-6129179IPR009071High mobility group box domain
CDDcd000840.00306137173No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0048481Biological Processplant ovule development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000018anatomyovule primordium
PO:0009009anatomyplant embryo
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009052anatomyflower pedicel
PO:0025022anatomycollective leaf structure
PO:0001185developmental stageplant embryo globular stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 231 aa     Download sequence    Send to blast
MTKLPNMTTT LNHLFDLPGQ ICHVQCGFCT TILLVSVPFT SLSMVVTVRC GHCTSLLSVN  60
LMKASFIPLH LLASLSHLDE TGKEEVAATD GVEEEAWKVN QEKENSPTTL VSSSDNEDED  120
VSRVYQVVNK PPEKRQRAPS AYNCFIKEEI RRLKAQNPSM AHKEAFSLAA KNWAHFPPAH  180
NKRAASDQCF CEEDNNAILP CNVFEDHEES NNGFRERKAQ RHSIWGKSPF E
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.118850.0flower
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO66848150.0
Genevisible262989_at0.0
Expression AtlasAT1G23420-
AtGenExpressAT1G23420-
ATTED-IIAT1G23420-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First detected in a group of around 15 epidermal cells on the abaxial half of each ovule primordium (chalaza, outer integument initiation sites). Later present in the outer cell layer of the outer integument on the abaxial side of the ovule primordium. Confined to the chalazal end of the integument and disappears after anthesis. Also present in embryos at the globular stage. {ECO:0000269|PubMed:10601041, ECO:0000269|PubMed:12183380, ECO:0000269|PubMed:12183381}.
Functional Description ? help Back to Top
Source Description
TAIREssential for formation and asymmetric growth of the ovule outer integument. Member of the YABBY protein family of putative transcription factors that contain apparent Cys(2)-Cys(2) zinc-finger domains and regions of similarity to the high mobility group (HMG) transcription factors. INO may be required for polarity determination in the central part of the ovule.
UniProtEssential for the formation and the abaxial-adaxial asymmetric growth of the ovule outer integument. {ECO:0000269|PubMed:10601041, ECO:0000269|PubMed:12183380, ECO:0000269|PubMed:9093862, ECO:0000269|PubMed:9118807}.
Function -- GeneRIF ? help Back to Top
  1. Promotion of growth of the outer integument of the ovule required a coordination of features along the entire length of the INO protein.
    [PMID: 18326791]
  2. At least two independent regions of the INO promoter contain sufficient regulatory information to direct the specific pattern but not the level of INO gene expression.
    [PMID: 23148487]
  3. we find that INO can directly interact with ADA2b/PROPORZ1 (PRZ1), a transcriptional coactivator that is known to interact with the histone acetyltransferase GENERAL CONTROL NONREPRESSIBLE PROTEIN 5 (GCN5, also known as HAG1).
    [PMID: 28971961]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G23420.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Autoinduction down-regulated by SUP in adaxial region of the ovule outer integument. Negatively and spatially regulated by HLL, ANT, BELL1, NZZ/SPL and SUP. {ECO:0000269|PubMed:10601041, ECO:0000269|PubMed:12183380, ECO:0000269|PubMed:12183381}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G23420 (A), AT3G23130 (R), AT4G27330 (R), AT4G37750 (A), AT5G41410 (A), AT5G42630 (R)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G23420(A), AT4G27330(A), AT4G37750(A)
Interaction ? help Back to Top
Source Intact With
IntActSearch Q9LDT3
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G23420
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1950470.0AF195047.1 Arabidopsis thaliana INNER NO OUTER (INO) mRNA, complete cds.
GenBankBT0264100.0BT026410.1 Arabidopsis thaliana At1g23420 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001320962.11e-174Plant-specific transcription factor YABBY family protein
SwissprotQ9LDT31e-175YAB4_ARATH; Axial regulator YABBY 4
TrEMBLA0A1P8APE21e-173A0A1P8APE2_ARATH; Plant-specific transcription factor YABBY family protein
STRINGAT1G23420.11e-173(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM80442740
Representative plantOGRP9612712
Publications ? help Back to Top
  1. Villanueva JM, et al.
    INNER NO OUTER regulates abaxial- adaxial patterning in Arabidopsis ovules.
    Genes Dev., 1999. 13(23): p. 3160-9
    [PMID:10601041]
  2. Bowman JL
    The YABBY gene family and abaxial cell fate.
    Curr. Opin. Plant Biol., 2000. 3(1): p. 17-22
    [PMID:10679447]
  3. Balasubramanian S,Schneitz K
    NOZZLE regulates proximal-distal pattern formation, cell proliferation and early sporogenesis during ovule development in Arabidopsis thaliana.
    Development, 2000. 127(19): p. 4227-38
    [PMID:10976054]
  4. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  5. Meister RJ,Kotow LM,Gasser CS
    SUPERMAN attenuates positive INNER NO OUTER autoregulation to maintain polar development of Arabidopsis ovule outer integuments.
    Development, 2002. 129(18): p. 4281-9
    [PMID:12183380]
  6. Balasubramanian S,Schneitz K
    NOZZLE links proximal-distal and adaxial-abaxial pattern formation during ovule development in Arabidopsis thaliana.
    Development, 2002. 129(18): p. 4291-300
    [PMID:12183381]
  7. Yamada T,Ito M,Kato M
    Expression pattern of INNER NO OUTER homologue in Nymphaea (water lily family, Nymphaeaceae).
    Dev. Genes Evol., 2003. 213(10): p. 510-3
    [PMID:12928899]
  8. Meister RJ, et al.
    Definition and interactions of a positive regulatory element of the Arabidopsis INNER NO OUTER promoter.
    Plant J., 2004. 37(3): p. 426-38
    [PMID:14731261]
  9. Park SO,Hwang S,Hauser BA
    The phenotype of Arabidopsis ovule mutants mimics the morphology of primitive seed plants.
    Proc. Biol. Sci., 2004. 271(1536): p. 311-6
    [PMID:15058443]
  10. Skinner DJ,Hill TA,Gasser CS
    Regulation of ovule development.
    Plant Cell, 2004. 16 Suppl: p. S32-45
    [PMID:15131247]
  11. Sieber P,Petrascheck M,Barberis A,Schneitz K
    Organ polarity in Arabidopsis. NOZZLE physically interacts with members of the YABBY family.
    Plant Physiol., 2004. 135(4): p. 2172-85
    [PMID:15299139]
  12. Sieber P, et al.
    Pattern formation during early ovule development in Arabidopsis thaliana.
    Dev. Biol., 2004. 273(2): p. 321-34
    [PMID:15328016]
  13. Meister RJ,Oldenhof H,Bowman JL,Gasser CS
    Multiple protein regions contribute to differential activities of YABBY proteins in reproductive development.
    Plant Physiol., 2005. 137(2): p. 651-62
    [PMID:15665244]
  14. McAbee JM,Kuzoff RK,Gasser CS
    Mechanisms of derived unitegmy among Impatiens species.
    Plant Cell, 2005. 17(6): p. 1674-84
    [PMID:15849275]
  15. McAbee JM, et al.
    ABERRANT TESTA SHAPE encodes a KANADI family member, linking polarity determination to separation and growth of Arabidopsis ovule integuments.
    Plant J., 2006. 46(3): p. 522-31
    [PMID:16623911]
  16. Wijeratne AJ, et al.
    Differential gene expression in Arabidopsis wild-type and mutant anthers: insights into anther cell differentiation and regulatory networks.
    Plant J., 2007. 52(1): p. 14-29
    [PMID:17666023]
  17. Brambilla V, et al.
    Genetic and molecular interactions between BELL1 and MADS box factors support ovule development in Arabidopsis.
    Plant Cell, 2007. 19(8): p. 2544-56
    [PMID:17693535]
  18. Gallagher TL,Gasser CS
    Independence and interaction of regions of the INNER NO OUTER protein in growth control during ovule development.
    Plant Physiol., 2008. 147(1): p. 306-15
    [PMID:18326791]
  19. Kelley DR,Skinner DJ,Gasser CS
    Roles of polarity determinants in ovule development.
    Plant J., 2009. 57(6): p. 1054-64
    [PMID:19054366]
  20. Skinner DJ,Gasser CS
    Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants.
    BMC Plant Biol., 2009. 9: p. 29
    [PMID:19291320]
  21. Lora J,Hormaza JI,Herrero M,Gasser CS
    Seedless fruits and the disruption of a conserved genetic pathway in angiosperm ovule development.
    Proc. Natl. Acad. Sci. U.S.A., 2011. 108(13): p. 5461-5
    [PMID:21402944]
  22. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  23. Bartholmes C,Hidalgo O,Gleissberg S
    Evolution of the YABBY gene family with emphasis on the basal eudicot Eschscholzia californica (Papaveraceae).
    Plant Biol (Stuttg), 2012. 14(1): p. 11-23
    [PMID:21974722]
  24. Simon MK,Williams LA,Brady-Passerini K,Brown RH,Gasser CS
    Positive- and negative-acting regulatory elements contribute to the tissue-specific expression of INNER NO OUTER, a YABBY-type transcription factor gene in Arabidopsis.
    BMC Plant Biol., 2012. 12: p. 214
    [PMID:23148487]
  25. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  26. Lora J,Hormaza JI,Herrero M
    Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT).
    New Phytol., 2015. 208(2): p. 584-95
    [PMID:25991552]
  27. Skinner DJ,Brown RH,Kuzoff RK,Gasser CS
    Conservation of the role of INNER NO OUTER in development of unitegmic ovules of the Solanaceae despite a divergence in protein function.
    BMC Plant Biol., 2016. 16(1): p. 143
    [PMID:27350128]
  28. Simon MK,Skinner DJ,Gallagher TL,Gasser CS
    Integument Development in Arabidopsis Depends on Interaction of YABBY Protein INNER NO OUTER with Coactivators and Corepressors.
    Genetics, 2017. 207(4): p. 1489-1500
    [PMID:28971961]
  29. Baker SC,Robinson-Beers K,Villanueva JM,Gaiser JC,Gasser CS
    Interactions among genes regulating ovule development in Arabidopsis thaliana.
    Genetics, 1997. 145(4): p. 1109-24
    [PMID:9093862]
  30. Schneitz K,H
    Dissection of sexual organ ontogenesis: a genetic analysis of ovule development in Arabidopsis thaliana.
    Development, 1997. 124(7): p. 1367-76
    [PMID:9118807]