Help

Search Interface

Splicing Factor	The user can search information about a specific splicing factor by entering its protein name, e.g "SC35".
Gene	The user can search information about a specific splicing factor by entering its encoding-gene name, e.g "SFRS2". In order to retrieve its binding/no-binding sites click on splicing factor name in result table. Search for "Splicing Factor" or its encoding "Gene" is mutually exclusive.
Binding site length	The user can use the length of binding (and not binding) sites to filter the query. The default values are the minimum and the maximum lengths among all SpliceAid-F sequences.
SF binding sites in	The user can search information, by selecting a specific organism/genome where a human splicing factor binding or activity has been assessed. For example, besides human, user can search for binding/no-binding sites in mouse, rat, rabbit, HIV-1 and so on.
Target chromosome	The user can retrieve all binding/no-binding sites lying in a selected target chromosome. It is possible to enter, for example, both the terms "chr4" or only "4" to retrieve all binding sites (and not binding sites) lying in chromosome 4.
Target Gene/Element	The user can retrieve all binding/no-binding sites lying in a selected target gene, element or synthetic sequences. In case of genes with the same name across species, e.g CSF2 is referred both to Human and Mouse, results for all possible species will be reported in the result table.
Activity	The user can retrieve the binding sites where the binding of a splicing factor induce a specific splicing activity. "Exon definition" and "Intron definition" imply that the splicing factor activity is addressed to the pre-mRNA tract where the binding site lies, whereas other activities as, for example, "Intron definition of upstream and downstream sequences" mean that splicing factor activity concern other pre-mRNA tracts.
Localization	The user can search information by selecting a specific genetic localization of the assessed binding site of a splicing factor, e.g in an exon or intron, near to an Exon/Intron boundary (near a 3'ss or a 5'ss), or in the 3'UTR or 5'UTR. The term "Intron/Exon" means that the binding/no-binding site lies in a tract straddling on an exon/intron boundary.

Result Page

In the Result Page, the number of splicing factors, binding sites and not-binding sites are reported.
Moreover, user can download the obtained results, exporting them in tab-delimited format.
To refine the results, it is possible to use again the Search form.

Splicing Factor Table

Splicing Factor The name of the splicing factor. By clicking on it, user can retrieve all experimentally assessed sites with and without binding activity and experimental information.

Gene The official name of the encoding gene, linked to NCBI EntrezGene.

Aliases Full name and synonymous of the encoding gene.

GeneID The GeneID (NCBI) of the official gene name. By clicking on it, user can retrieve relative information.

HomoloGene By clicking on the link, user can retrieve all known homologous genes and proteins at HomoloGene database.

UniProt The UniProt ID. By clicking on it, user can retrieve relative information stored in UniProt database.

Binding Domain(s) Type of RNA-binding domain(s).

MIM Disease associated to the splicing factor dysfunction or alteration (provided by OMIM database and cross-linked to it).

Protein Interactors List of proteins that are known to interact with the splicing factor. Data are collected from IntAct, STRING, DIP, MINT, HPRD and BioGRID databases.

Chemical Interactors List of proteins that are known to interact with the splicing factor. Data are collected from IntAct, STITCH and ProtChemSI databases.

Expression List of available links to: Cancer Genome Anatomy Project (CGAP), Human Protein Atlas (HPA), Human Protein Reference Database (HPRD), Human Proteinpedia (HPP).

CLIP Data Link to CLIP (Crosslinking and ImmunoPrecipitation) data and related bibliography.

Splicing Factor	The name of the splicing factor. By clicking on it, user can retrieve all experimentally assessed sites with and without binding activity and experimental information.
Gene	The official name of the encoding gene, linked to NCBI EntrezGene.
Aliases	Full name and synonymous of the encoding gene.
GeneID	The GeneID (NCBI) of the official gene name. By clicking on it, user can retrieve relative information.
HomoloGene	By clicking on the link, user can retrieve all known homologous genes and proteins at HomoloGene database.
UniProt	The UniProt ID. By clicking on it, user can retrieve relative information stored in UniProt database.
Binding Domain(s)	Type of RNA-binding domain(s).
MIM	Disease associated to the splicing factor dysfunction or alteration (provided by OMIM database and cross-linked to it).
Protein Interactors	List of proteins that are known to interact with the splicing factor. Data are collected from IntAct, STRING, DIP, MINT, HPRD and BioGRID databases.
Chemical Interactors	List of proteins that are known to interact with the splicing factor. Data are collected from IntAct, STITCH and ProtChemSI databases.
Expression	List of available links to: Cancer Genome Anatomy Project (CGAP), Human Protein Atlas (HPA), Human Protein Reference Database (HPRD), Human Proteinpedia (HPP).
CLIP Data	Link to CLIP (Crosslinking and ImmunoPrecipitation) data and related bibliography.

Binding Sites / No binding evidences Tables

Shaded rows are related to sites without binding activity in a specific context or type of assay that contain a binding site for the same splicing factor.

Sequence Oligo Sequence of the site with or without binding activity for the selected splicing factor.
Score A positive score (+1...+10) was assigned to the target sequences that facilitate exon definition that is ESE (exonic splicing enhancer) and ISS (intronic splicing silencer) motifs. According to the same criteria we assigned a negative score (-1...-10) to the target sequences that facilitate intron definition that is ESS (exonic splicing silencer) and ISE (intronic splicing enhancer) motifs. The binding site score is related to the binding affinity deduced from the related reference.
Target Gene/Element Gene name or element where the binding site lies. A link to NCBI is provided.

Status If the gene is mutated, it is reported.

Target Organism The specific organism where the human splicing factor binding or activity has been assessed.

Cell line Cell line or tissue type where the human splicing factor binding or activity has been assessed.

Splicing Assay Type of splicing assay used in the related article.

Binding Assay Type of binding assay used in the related article.

Coordinates Coordinates of the binding site according to Human hg18 assembly, that is NCBI Build 36.1 (March 2006). Moreover, we used for mouse NCBI37/mm9, for rat Baylor 3.4/rn4, for rabbit Broad/oryCun2, ICGSC Gallus_gallus-4.0/galGal4, for D. melanogaster BDGP R5/dm3 and for S. cerevisiae SacCer_Apr2011/sacCer3 assemblies.

Activity The specific assessed splicing activity of the splicing factor.

Localization The genetic localization of the assessed binding site of the splicing factor.

Disease correlation Disease associated to the binding site alteration (provided by OMIM database and cross-linked to it).

Reference PubMed ID (PMID) and the year of publication. By clicking on it, user can come back to the reference experimentally supporting the binding and download the article from PubMed database at NCBI.

ASPicDB Link to ASPicDB results page, reporting the whole set of information available for the gene in such database. ASPicDB is a database designed to provide access to reliable annotations of the alternative splicing pattern of genes, obtained by ASPic algorithm (Castrignano' et al. 2006), and to the functional annotation of predicted isoforms.

Sequence Oligo	Sequence of the site with or without binding activity for the selected splicing factor.
Score	A positive score (+1...+10) was assigned to the target sequences that facilitate exon definition that is ESE (exonic splicing enhancer) and ISS (intronic splicing silencer) motifs. According to the same criteria we assigned a negative score (-1...-10) to the target sequences that facilitate intron definition that is ESS (exonic splicing silencer) and ISE (intronic splicing enhancer) motifs. The binding site score is related to the binding affinity deduced from the related reference.
Target Gene/Element	Gene name or element where the binding site lies. A link to NCBI is provided.
Status	If the gene is mutated, it is reported.
Target Organism	The specific organism where the human splicing factor binding or activity has been assessed.
Cell line	Cell line or tissue type where the human splicing factor binding or activity has been assessed.
Splicing Assay	Type of splicing assay used in the related article.
Binding Assay	Type of binding assay used in the related article.
Coordinates	Coordinates of the binding site according to Human hg18 assembly, that is NCBI Build 36.1 (March 2006). Moreover, we used for mouse NCBI37/mm9, for rat Baylor 3.4/rn4, for rabbit Broad/oryCun2, ICGSC Gallus_gallus-4.0/galGal4, for D. melanogaster BDGP R5/dm3 and for S. cerevisiae SacCer_Apr2011/sacCer3 assemblies.
Activity	The specific assessed splicing activity of the splicing factor.
Localization	The genetic localization of the assessed binding site of the splicing factor.
Disease correlation	Disease associated to the binding site alteration (provided by OMIM database and cross-linked to it).
Reference	PubMed ID (PMID) and the year of publication. By clicking on it, user can come back to the reference experimentally supporting the binding and download the article from PubMed database at NCBI.
ASPicDB	Link to ASPicDB results page, reporting the whole set of information available for the gene in such database. ASPicDB is a database designed to provide access to reliable annotations of the alternative splicing pattern of genes, obtained by ASPic algorithm (Castrignano' et al. 2006), and to the functional annotation of predicted isoforms.

If you have any scientific or technical questions please contact us.