Frequently Asked Questions:

What is IGD?

What is an intronless gene?

Why intronless genes are interesting?

What is the source of data in IGD?

What is the difference between Xpro, SEGE and IGD?

How to search in IGD?

How to limit a search to a subset of IGD?

What is the difference between search query strategy and IG viewer strategy?

How to browse IGD?

How to download IGD?

How to compare a query DNA /protein sequence against IGD?

How do I contact the IGD team?

Is IGD frequently updated?

What is the best browser to use?

Availability of IGD


What is IGD?

IGD is an annotated and curated database of Intronless Genes in human genome established in 2009 and maintained by the Bioinformatics and Functional Genomics Group (BFGG) of the Centre of Biotechnology of Sfax (CBS). The IGD assembles data on human intronless genes identified on 24 chromosomes (23 autosomes, X and Y chromosomes). Each IGD entry contains textual data on one gene, including: IGD Identifier, gene Name, Gene accession number, official Full Name, other Aliases, organism, chromosome and RefSeq Status. In addition to this textual data, IGD provides one image showing the location of the gene on the chromosome. Moreover DNA, protein and coding sequences of each gene are available. Cross-references are provided to GENE, OMIM, PubMed, SNP, UniGene, Conserved Domains and UniSTS databases which offer many links to other molecular databases (Books, CCDS, EST, GEO Profiles,Genome, HomoloGene, Map Viewer, Nucleotide, Protein, RefSeq, Ensembl, UCSC, MGC etc).

What is an intronless gene?

An intronless gene is a single exon gene which do not contain introns from its beginning (TSS: Transcription Start Site) until its end (Terminal Transcription Site TTS), neither in its CDS region nor in its UTR regions (see figure below).


Why intronless genes are interesting?

Intronless genes fraction varies between 2.7 to 97.7% in eukaryotic genomes (estimated 12 % in human genome)(Sakharkar and Sakharkar, 2007). In addition to that, intronless eukaryotic genes are very difficult to predict because of their special structure (short sequence, absence of splicing signals...). It is very interesting to study this class of genes in order to discover new features that will help to improve intronless gene prediction and to understand: what is the advantage for a gene to be intronless? In fact, there are some gene classes that are in their major part intronless such as GPCRs and histones (Gentles and Karlin, 1999 - Bryson-Richardson et al., 2004 - Doenecke and Albig, 2005 - Alem et al., 2009). There is a need to understand why this feature is important for such genes (rapid expression and turnover? fast evolution and silencing...).

What is the source of data in IGD?

The IGD assembles data on human intronless genes from curated public databases. In fact the structure of intronless genes were checked in Entrez Gene database while, nucleotide, protein and CDS sequences were collected respectively from Entrez nucleotide, Entrez protein, CCDS databases through links in Entrez Gene database entries.

What is the difference between Xpro, SEGE and IGD?

Several databases such as the Xpro contain a division of intronless coding sequences but there is only one database, called SEGE, entirely devoted to intronless genes. However, all these databases seem to consider intronless coding sequences (CDS) i.e. genes having their coding sequences contained in a single exon, rather than genuine intronless genes. In fact, genes with intronless CDS might have one, two or more non-coding exons (see figure below). This means that a variable number of the entries of Xpro and SEGE databases may be multi-exonic. IGD is more specific and uses a narrow definition of intronless genes (see what is an intronless gene?)


How to search in IGD?

Through the site of the bioinfo-cbs.org server (see http://bioinfo-cbs.org/.), you can search IGD by search query. Search query is based on search term. It provides capabilities for searching in several ways:
* by IGD accession number (e.g. IG11.34, IG2.5),
* by Gene accession number (e.g. GeneID: 10881, GeneID: 83935),
* by Gene official full name (as it is described in Gene database),
* by Gene name (symbol),
* by Gene aliases (symbol).
In order to facilitate search, query terms can be entered in their entirety or truncated by using "*" as a wildcard. (For more details see help.)

How to limit a search to a subset of IGD?

To refine search results, limit options are offered. Different subsets are available: OMIM entries intronless genes and RefSeq status subsets. In limit page you should check the subset name to limit your search to specified division. For example, to retrieve reviewed or validated intronless genes by RefSeq database and involved in diseases, user should cross-check Reviewed, Validated and OMIM boxes in "Limits" page

What is the difference between search query strategy and IG viewer strategy?

The query search strategy provides an easy way to query the IGD. It is based on search term providing several ways of seeking (see "How to search in IGD?" ). The IG viewer strategy provides a list of intronless genes classified by chromosome. The access to each entry gene is provided by clicking on Details button.

How to browse IGD?

You can browse IGD by IG viewer strategy. It provides special browsing capabilities for chromosomes in IGD. IG Viewer allows you to view and search all IGD intronless genes by clicking on each chromosome in caryotype page.


How to download IGD?

The Content of IGD database is available for download in FASTA format. You can download all IGD sequences by selecting "ALL" in the drop-down menu or specifying one chromosome by selecting its number in the drop-down menu. By clicking on download button, sequences in format FASTA of the set you want to download were displayed. You can then copying and save them any where.

How to compare a query DNA /protein sequence against IGD?

DNA /protein sequence can be compared against IGD using BLAST program. Through IGD web site, The BLAST tab leads to the BLAST page. This page provides links to BLAST forms of two BLAST programs that allow DNA/protein sequence comparison against IGD. See help.

How do I contact the IGD team?

The administrator of IGD can be contacted by Email at: contact.IGD@bioinfo-cbs.org

Is IGD frequently updated?

IGD is updated yearly. Furthermore links to Gene and OMIM databases are available in each IGD entry, what provides access to the latest update of two databases.

What is the best browser to use?

From our experience and user feedback you will get better performance with Mozilla Firefox browser.

Availability of IGD

IGD database is freely available for online access and for download as FASTA formatted flat files on URL http://www.bioinfo-cbs.org/igd.



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