AthaMap provides a genome-wide map of potential transcription factor and small RNA binding
sites (TFBS) in Arabidopsis thaliana.
Data in AthaMap is based on published transcription factor (TF) binding specificities available as
alignment matrices or experimentally determined single binding sites. Matrix- and pattern-based
screenings were performed to identify potential transcription factor binding sites
in the genome of Arabidopsis thaliana (TAIR release 8). The complete list of
the 142 transcription factors included in AthaMap and the corresponding references and screening results are displayed on the
By using the Search function, the sequence of a specific genomic
position or gene can be displayed in a sequence window including the potential transcription
factor binding sites. A Colocalization function allows the
search for user-defined potential combinatorial elements. A set of pre-calculated known
combinatorial elements is already incorporated in AthaMap. The
Gene Analysis tool enables identification of common transcription
factor binding sites and small RNA target sites in a set of user-submitted genes. The Gene Identification tool allows the search
for genes harbouring specific transcription factor binding sites. All genes targeted by smallRNAs and miRNAs are identified in AthaMap when the
web-tools Colocalization, Gene-Analysis, and Gene Identification are used. Putatively small RNA targeted genes are shown in italics, putatively miRNA regulated genes
are shown in bold. The MicroRNA Targets function permits the identifcation of target genes for miRNAs.
190 screening sequences corresponding
to the 243 miRNA genes and the number of genomic hits can be found on the the Documentation page.
The Small RNA Targets function enables identification of small RNA targets
from different small RNA libraries given on the Documentation page.