315 refseq_zebrafish Zebrafish cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Zebrafish RefSeq cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
316 augustus Ab initio prediction of protein coding genes by Augustus, a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model. Stanke et al., Nucleic Acids Res., 34: W435-W439 (2006). Augustus prediction 1
317 RepeatMasker Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org/">RepeatMasker</a> using ab initio repeat profiles specific to the species. Repeats (Recon) 1
318 polyA_signal PolyA signals identified during manual annotation PolyA Signal 1
319 pseudo_polyA Poly A like structures associated with pseudogenes Pseudo PolyA 1
320 RSS The IG and T-cell recombination signal sequences motifs are canonically considered to be nonamers and heptamers seperated by spacers of 12 or 23 nucleotides and are found at the 3' end of the V elements, the 5' end of the J elements, and on both sides of the D elements [ V(D)J recombination mechanism]. RSS Motif. 1
321 otter_eucomm Virtual mouse genes, produced for the <a rel="external" href="http://www.eucomm.org">/EUCOMM</a> project, representing the gene structure produced after knockout of exons critical to gene function. KO gene (EUCOMM) 1 {'colour_key' => '[gene.logic_name]_[gene.biotype]'}
322 otter_komp Virtual mouse genes, produced for the <a rel="external" href="http://www.nih.gov/science/models/mouse/knockout/">/KOMP</a> project, representing the gene structure produced after knockout of exons critical to gene function. KO gene (KOMP) 1 {'colour_key' => '[gene.logic_name]_[gene.biotype]'}
323 EUCOMM This mouse track is linked to the mouse Knockout gene track. It shows the locations of exons identified by Havana as being critical for correct translation of the longest transcript at a specific loci. Knockout Deletion 1
318 polyA_signal PolyA signals identified during manual annotation PolyA Signal 1 {'strand'=>'b','transcript_associated'=>1}
319 pseudo_polyA Poly A like structures associated with pseudogenes Pseudo PolyA 1 {'strand'=>'b','transcript_associated'=>1}
320 RSS The IG and T-cell recombination signal sequences motifs are canonically considered to be nonamers and heptamers seperated by spacers of 12 or 23 nucleotides and are found at the 3' end of the V elements, the 5' end of the J elements, and on both sides of the D elements [ V(D)J recombination mechanism]. RSS Motif. 1 {'strand'=>'b','transcript_associated'=>1}
321 otter_eucomm Virtual mouse genes (produced for the <a rel="external" href="http://www.eucomm.org">EUCOMM</a> project) representing the gene structure produced after knockout of exons critical to gene function. KO gene (EUCOMM) 1 {'colour_key' => '[gene.logic_name]_[gene.biotype]'}
322 otter_komp Virtual mouse genes (produced for the <a rel="external" href="http://www.nih.gov/science/models/mouse/knockout/">KOMP</a> project) representing the gene structure produced after knockout of exons critical to gene function. KO gene (KOMP) 1 {'colour_key' => '[gene.logic_name]_[gene.biotype]'}
323 EUCOMM This mouse track is linked to the mouse Knockout gene track. It shows the locations of exons identified by Havana as being critical for correct translation of the longest transcript at a specific loci. Knockout Deletion 1 {'strand'=>'b','transcript_associated'=>1}
324 est2genome_fish Alignment of mouse ESTs (expressed sequence tags) to the genome using the program <a rel="external" href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/est2genome.html">Est2genome</a>. ESTs are from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> Zebrafish EST (EST2genome) 1 {'type'=>'est'}
325 PCodDensity Density of Vega protein coding genes Genes (density) 1
326 PTransDensity Density of Vega processed transcripts Genes (density) 1
