Plant Transcription factor database - Universität Potsdam
version: 3.0

Oryza sativa subsp. japonica ARF Family

Description

Guilfoyle et al. 1998: Auxin response factors or ARFs are a recently discovered family of transcription factors that bind with specificity to auxin response elements (AuxREs) in promoters of primary or early auxin-responsive genes. ARFs have an amino-terminal DNA-binding domain related to the carboxyl-terminal DNA-binding domain in the maize transactivator VIVIPAROUS1. All but one ARF identified to date contain a carboxyl-terminal protein-protein interaction domain that forms a putative amphipathic alpha-helix. A similar carboxyl-terminal protein-protein interaction domain is found in the Aux/IAA class of auxin-inducible proteins. Some ARFs contain transcriptional activation domains, while others contain repression domains. ARFs appear to play a pivotal role in auxin-regulated gene expression of primary response genes.

Members of this family
  SHOULD possess Auxin_resp domain

Domain alignments

Benchmark against A. thaliana

The Sensitivity and Positive Predictive Value (PPV) were assessed for this family. The data reported by Remington et al. 2004 for A. thaliana were taken as gold standard.

The gold standard reported 23 members for this family, 21 of which are present in ArabTFDB, giving a PPV of 0.95. Two additional members not present in ArabTFDB might be false negatives, giving a Sensitivity of 0.91.

This family is also present in:

References

There are 46 gene models in this family



Gene modelDescriptionDomains
LOC_Os01g13520.1 auxin response factor 1, putative, expressed Auxin_resp B3
LOC_Os01g13520.2 auxin response factor 1, putative, expressed Auxin_resp B3
LOC_Os01g48060.1 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os01g48060.2 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os01g48060.3 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os01g54990.1 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os01g70270.1 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os01g70270.2 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os01g70270.3 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os01g70270.4 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os02g04810.1 auxin response factor 5, putative, expressed Auxin_resp B3
LOC_Os02g06910.1 auxin response factor 6, putative, expressed Auxin_resp B3
LOC_Os02g35140.1 auxin response factor 7, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os02g41800.1 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os02g41800.2 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os04g36054.1 auxin response factor 9, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os04g43910.1 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os04g56850.1 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os04g56850.2 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os04g57610.1 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os04g57610.3 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os04g59430.1 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os05g43920.1 auxin response factor 14, putative, expressed Auxin_resp B3
LOC_Os05g48870.1 auxin response factor 15, putative, expressed Auxin_resp B3
LOC_Os06g09660.1 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os06g46410.1 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os06g46410.2 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os06g47150.1 auxin response factor 18, putative, expressed Auxin_resp B3
LOC_Os06g47150.2 auxin response factor 18, putative, expressed Auxin_resp B3
LOC_Os06g47150.3 auxin response factor 18, putative, expressed Auxin_resp B3
LOC_Os06g47150.4 auxin response factor 18, putative, expressed Auxin_resp B3
LOC_Os06g48950.1 auxin response factor 19, putative, expressed Auxin_resp B3 Involucrin
LOC_Os07g08520.1 auxin response factor, putative Auxin_resp B3
LOC_Os08g40900.1 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os08g40900.2 auxin response factor, putative, expressed Auxin_resp B3
LOC_Os10g33940.1 auxin response factor 18, putative, expressed Auxin_resp B3
LOC_Os11g32110.1 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os11g32110.2 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os11g32110.3 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os11g32110.4 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os12g29520.1 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os12g29520.2 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os12g29520.3 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os12g29520.4 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os12g29520.5 auxin response factor, putative, expressed AUX_IAA Auxin_resp B3
LOC_Os12g41950.1 auxin response factor, putative, expressed Auxin_resp B3

General references

Guilfoyle, TJ; Ulmasov, T; Hagen, G. 1998. The ARF family of transcription factors and their role in plant hormone-responsive transcription. Cell. Mol. Life Sci. 54(7):619-27 PUBMEDID:9711229
Ulmasov, T; Hagen, G; Guilfoyle, TJ. 1997. ARF1, a transcription factor that binds to auxin response elements. Science 276(5320):1865-8 PUBMEDID:9188533

Specific references

Sato, Y; Nishimura, A; Ito, M; Ashikari, M; Hirano, HY; Matsuoka, M. 2001. Auxin response factor family in rice. Genes Genet. Syst. 76(6):373-80 PUBMEDID:11922106