Table S1 - Identification of Nuclear and Cytoplasmic mRNA Targets for the Shuttling Protein SF2/ASF

A complete list of binding site annotation using the Ensembl, UCSC Known Gene and Rfam databases. The Excel file can be filtered in order to find binding sites identified by CLIP using nuclear, cytoplasmic or polysomal extracts. Headers for the table are as follows: Chromosome: Defines the specific chromosome from the human genome to which the seq-block mapped. Strand: CLIP preserves the orientation of the captured RNA marker, so that it is possible to determine the strandedness of the locus. Id: Generic description given to each binding site during our annotation work flow. Region start/end: The precise chromosomal coordinates defining the unique or overlapping sequence blocks. Regions are define by at least 2 partially overlapping binding sites mapping to the locus. # of fragments in the Cytoplasm/Nucleus/Polysome indicates if the binding site was identified in each compartment. The number specifies whether a sequence block was absent, present in a single assay or multiple assays. # of sample targets is useful for finding binding sites that are in 1, 2 or all three cellular fractions. Gene Annotation: This column describes the relationship of the seq block to annotated protein coding genes based on the UCSC Known Gene Database. Exon Style: This column describes the relationship of the seq block to annotated parts of protein coding genes (exon, intron etc). The strategy is presented in Supplementary Figure 2. USCS Known Gene database ID: This column refers to the name of a specific gene cluster by the UCSC Known Gene database. Gene Symbol: This column contains information pertaining to the approved HUGO Gene Nomenclature Committee symbol for each protein coding gene. Exon Position: This column describes the position of the exon within the protein coding gene. First/Last exon columns: Designation of ��1�� in either column indicates 5�� or 3�� terminal exon. ��1�� in both columns denotes that the sequence block is in a single exon gene. Upstream/Downstream Exon Position: These columns are useful for determining the position of introns within a protein coding gene. ncRNA Annotation: Describes the relationship of a sequence block to annotated non coding RNA (ncRNA). Annotation is based on the Rfam database. ncRNA Name: This column describes the gene symbol for each ncRNA containing a sequence block. UTR type: Describes the relationship between sequence blocks and untranslated regions of protein coding genes. Splicing Event: Gives alternative splicing annotation for exonic binding sites based upon AceVIEW, ALT Events and Fast-db, databases. (0.13 MB XLS)