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

LOC_Os07g06620.4

Common Name

FIL1, LOC4342449, Os07g0160100, YAB1

Organism

Oryza sativa subsp. japonica

Taxonomic ID

39947

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa

Family

YABBY

Protein Properties

Length: 168aa MW: 18661 Da PI: 9.0587

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os07g06620.4	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	244.7	1.9e-75	1	155	1	170
YABBY 1 advfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkeelleelkveeenlksnvekeesas 93 ++v+++se+vCyv+Cn+Cntil+v+vP+++++++vtvrCGhCt++ls++la ++q++++++h ++++++++n+ s+++++++++ LOC_Os07g06620.4 1 MSVQFTSEHVCYVNCNYCNTILVVNVPNNCSYNIVTVRCGHCTMVLSMDLAPFHQARTVQDH----------QNRGFQGNNFGSYDIASRNQR 83 57999******************************************************8..........99*************** PP YABBY 94 tsvsseklsenedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170 ts++++ +++++++ +p irPPekrqrvPsaynrfikeeiqrik+snP+ishreafsaaaknWah+P++hfgl LOC_Os07g06620.4 84 TSTAMYPMPTSQQQVSP-----IRPPEKRQRVPSAYNRFIKEEIQRIKTSNPEISHREAFSAAAKNWAHLPRLHFGL 155 *********9999.....9**************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	1.6E-63	6	155	IPR006780	YABBY protein
SuperFamily	SSF47095	4.58E-9	89	149	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	8.0E-6	103	149	IPR009071	High mobility group box domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0007275	Biological Process	multicellular organism development

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009037	anatomy	lemma
PO:0001047	developmental stage	lemma development stage
PO:0007130	developmental stage	sporophyte reproductive stage

Sequence ? help Back to Top
Protein Sequence Length: 168 aa Download sequence Send to blast
MSVQFTSEHV CYVNCNYCNT ILVVNVPNNC SYNIVTVRCG HCTMVLSMDL APFHQARTVQ 60 DHQNRGFQGN NFGSYDIASR NQRTSTAMYP MPTSQQQVSP IRPPEKRQRV PSAYNRFIKE 120 EIQRIKTSNP EISHREAFSA AAKNWAHLPR LHFGLSVADG GGGGGSN*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Os.74707	1e-32	flower\| panicle\| seed\| stem

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	37990575	1e-32
Expression Atlas	Q7XIM7	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Detected throughout panicle development with the strongest expression in immature panicles, and weakest in mature panicles. Abundantly found in the stamen and carpel primordia of young spikelets. {ECO:0000269\|PubMed:15604733, ECO:0000269\|PubMed:17216490}.
Uniprot	TISSUE SPECIFICITY: Preferentially expressed in flowers. Expressed in leaf blades and leaf sheaths. Does not show polar expression pattern. {ECO:0000269\|PubMed:15604733}.

Functional Description ? help Back to Top
Source	Description
UniProt	May play a role in floral meristem development and maintenance of stamens, rather than in determining polarity in floral organs. {ECO:0000269\|PubMed:15604733, ECO:0000269\|PubMed:17369428}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	LOC_Os07g06620.4

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os07g06620

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB274013	0.0	AB274013.1 Oryza sativa Japonica Group OsYABBY1 mRNA for OsYABBY1 protein, complete cds.
GenBank	AK070045	0.0	AK070045.1 Oryza sativa Japonica Group cDNA clone:J023038F18, full insert sequence.
GenBank	CT828681	0.0	CT828681.1 Oryza sativa (indica cultivar-group) cDNA clone:OSIGCFA230C13, full insert sequence.
GenBank	CT828682	0.0	CT828682.1 Oryza sativa (indica cultivar-group) cDNA clone:OSIGCFA240F12, full insert sequence.
GenBank	CT828683	0.0	CT828683.1 Oryza sativa (indica cultivar-group) cDNA clone:OSIGCFA249C03, full insert sequence.
GenBank	CT832577	0.0	CT832577.1 Oryza sativa (indica cultivar-group) cDNA clone:OSIGCFA333Z37, full insert sequence.
GenBank	FJ750932	0.0	FJ750932.1 Oryza sativa clone KCS005G02 MADS-box transcription factor mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015647415.1	1e-124	protein YABBY 1 isoform X2
Swissprot	Q7XIM7	1e-117	YAB1_ORYSJ; Protein YABBY 1
TrEMBL	A0A0E0LHD2	1e-118	A0A0E0LHD2_ORYPU; Uncharacterized protein
STRING	OMERI07G02380.1	1e-116	(Oryza meridionalis)
STRING	ORUFI07G03450.1	1e-116	(Oryza rufipogon)
STRING	OS07T0160100-02	1e-116	(Oryza sativa)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G08465.1	2e-56	YABBY family protein

Link Out ? help Back to Top
Phytozome	LOC_Os07g06620.4
Entrez Gene	4342449

Publications ? help Back to Top
Sawa S, et al. FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains. Genes Dev., 1999. 13(9): p. 1079-88 [PMID:10323860] Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Jang S, et al. Ectopic expression of OsYAB1 causes extra stamens and carpels in rice. Plant Mol. Biol., 2004. 56(1): p. 133-43 [PMID:15604733] Toriba T, et al. Molecular characterization the YABBY gene family in Oryza sativa and expression analysis of OsYABBY1. Mol. Genet. Genomics, 2007. 277(5): p. 457-68 [PMID:17216490] Dai M, et al. The rice YABBY1 gene is involved in the feedback regulation of gibberellin metabolism. Plant Physiol., 2007. 144(1): p. 121-33 [PMID:17369428] Ohmori Y,Abiko M,Horibata A,Hirano HY A transposon, Ping, is integrated into intron 4 of the DROOPING LEAF gene of rice, weakly reducing its expression and causing a mild drooping leaf phenotype. Plant Cell Physiol., 2008. 49(8): p. 1176-84 [PMID:18593744] Ohmori Y,Toriba T,Nakamura H,Ichikawa H,Hirano HY Temporal and spatial regulation of DROOPING LEAF gene expression that promotes midrib formation in rice. Plant J., 2011. 65(1): p. 77-86 [PMID:21175891] Li H, et al. Rice MADS6 interacts with the floral homeotic genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in specifying floral organ identities and meristem fate. Plant Cell, 2011. 23(7): p. 2536-52 [PMID:21784949] Tanaka W, et al. The YABBY gene TONGARI-BOUSHI1 is involved in lateral organ development and maintenance of meristem organization in the rice spikelet. Plant Cell, 2012. 24(1): p. 80-95 [PMID:22286138] Yang C,Ma Y,Li J The rice YABBY4 gene regulates plant growth and development through modulating the gibberellin pathway. J. Exp. Bot., 2016. 67(18): p. 5545-5556 [PMID:27578842]