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This depends on what information you are starting with.
1. Starting with cDNA/EST/protein sequences
Assuming you have a certain cDNA sequence and want to find the corresponding gene in the EnsEMBL database at http://www.ensembl.org/Danio_rerio you have several options. Firstly, you can use BLAST or SSAHA at http://www.ensembl.org/Multi/blastview?species=Danio_rerio to align the cDNA sequence to the assembly. It is recommended to use BLAST for non-zebrafish sequences, whereas SSAHA should be the tool of choice for zebrafish-zebrafish searches for reasons of accuracy and speed.
An even better place to look for your gene of choice is the Vega database that hosts finished clones that are undergoing manual annotation at http://vega.sanger.ac.uk/Danio_rerio/. You can use the Vega BLAST server at http://vega.sanger.ac.uk/Multi/blastview?species=Danio_rerio.
The third option is to perform a BLAST search against all finished and unfinished clones, not only the ones currently in Vega, at http://www.sanger.ac.uk/cgi-bin/blast/submitblast/d_rerio.
2. Starting with the gene name
Your second option is to use the general text search in either EnsEMBL (http://www.ensembl.org/Multi/textview) or Vega (http://vega.sanger.ac.uk/Multi/textview?species=Danio_rerio) and to find a zebrafish gene with an appropriate name. You can also start at ZFIN and use the link provided.
3. Starting with a homolog
In EnsEMBL, yet another way to get to a result is to identify a gene in a different organism and then go to the zebrafish homologue if listed under 'Homology Matches' on the GeneView page (example: http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139445).
4. Starting with marker or genomic position (clone)
In EnsEMBL or Vega, use the text search to find the marker or clone (accession number). You can then browse 'ContigView' to get information about the region.
We also offer the mapsearch service that makes it easy to retrieve this information from the EnsEMBL database (http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/mapsearch). Mapsearch contains the positions of STS markers, ESTs listed by ZFIN with map information and BAC end sequences on the latest release of the genome assembly. You can either look for a specified type of marker on a given assembly contig or for contigs that contains a specific marker. The results page allows you to access the available marker information and also to check the corresponding assembly contigs in EnsEMBL.
If you cannot find an appropriate gene, this might be due to the corresponding part of the genome sequence being absent from the current assembly or chromosomal tiling path. This will improve over time.
A reason for the absence of a certain gene in EnsEMBL might be that neither the cDNA/protein sequence from the gene you are looking for, nor any homologous sequence from another species with high enough similarity, was available at the time the gene build was performed. In this case it may appear in subsequent releases and in the meantime you can use the other displayed features in ContigView (BLAST matches, Genscan predictions) to get an idea of what the gene might look like.