PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT1G23420.1

Common Name

F26F24.29, F28C11.6, INO, YAB4

Organism

Arabidopsis thaliana

Taxonomic ID

3702

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
AT1G23420.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	259.6	4.6e-80	13	182	2	169
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

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	1.6E-60	18	181	IPR006780	YABBY protein
SuperFamily	SSF47095	3.93E-9	123	179	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	6.1E-6	129	179	IPR009071	High mobility group box domain
CDD	cd00084	0.00306	137	173	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009944	Biological Process	polarity specification of adaxial/abaxial axis
GO:0048481	Biological Process	plant ovule development
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0046872	Molecular Function	metal ion binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000018	anatomy	ovule primordium
PO:0009009	anatomy	plant embryo
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009052	anatomy	flower pedicel
PO:0025022	anatomy	collective leaf structure
PO:0001185	developmental stage	plant embryo globular stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering 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.11885	0.0	flower

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	6684815	0.0
Genevisible	262989_at	0.0
Expression Atlas	AT1G23420	-
AtGenExpress	AT1G23420	-
ATTED-II	AT1G23420	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL 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
TAIR	Essential 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.
UniProt	Essential 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
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] 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] 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
Source	Link
PlantRegMap	AT1G23420.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: 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
PlantRegMap	Retrieve	Retrieve

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
IntAct	Search Q9LDT3

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G23420

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF195047	0.0	AF195047.1 Arabidopsis thaliana INNER NO OUTER (INO) mRNA, complete cds.
GenBank	BT026410	0.0	BT026410.1 Arabidopsis thaliana At1g23420 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001320962.1	1e-174	Plant-specific transcription factor YABBY family protein
Swissprot	Q9LDT3	1e-175	YAB4_ARATH; Axial regulator YABBY 4
TrEMBL	A0A1P8APE2	1e-173	A0A1P8APE2_ARATH; Plant-specific transcription factor YABBY family protein
STRING	AT1G23420.1	1e-173	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM8044	27	40
Representative plant	OGRP9612	7	12

Link Out ? help Back to Top
Phytozome	AT1G23420.1
Entrez Gene	838950
iHOP	AT1G23420
wikigenes	AT1G23420

Publications ? help Back to Top
Villanueva JM, et al. INNER NO OUTER regulates abaxial- adaxial patterning in Arabidopsis ovules. Genes Dev., 1999. 13(23): p. 3160-9 [PMID:10601041] Bowman JL The YABBY gene family and abaxial cell fate. Curr. Opin. Plant Biol., 2000. 3(1): p. 17-22 [PMID:10679447] 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] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] 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] 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] 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] 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] 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] Skinner DJ,Hill TA,Gasser CS Regulation of ovule development. Plant Cell, 2004. 16 Suppl: p. S32-45 [PMID:15131247] 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] Sieber P, et al. Pattern formation during early ovule development in Arabidopsis thaliana. Dev. Biol., 2004. 273(2): p. 321-34 [PMID:15328016] 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] McAbee JM,Kuzoff RK,Gasser CS Mechanisms of derived unitegmy among Impatiens species. Plant Cell, 2005. 17(6): p. 1674-84 [PMID:15849275] 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] 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] 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] 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] Kelley DR,Skinner DJ,Gasser CS Roles of polarity determinants in ovule development. Plant J., 2009. 57(6): p. 1054-64 [PMID:19054366] 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] 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] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] 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] 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] 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] 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] 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] 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] 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] 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]