8275	Annotation produced by the Ensembl <a href="http://www.ensembl.org/info/docs/genebuild/genome_annotation.html" class="cp-external">genebuild</a>.	Ensembl genes	1	{'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Genes (Merged Ensembl/Havana) (GENCODE)','name' => 'Merged Ensembl and Havana genes (GENCODE)','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl'}
8276	Sequences from various databases are matched to Ensembl transcripts using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. These are external references, or 'Xrefs'.	DNA match	0	\N
8277	Homo Sapiens cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate cdna2genome model</a>.	Human cDNAs (cdna2genome)	0	{'type' => 'cdna'}
8278	match	Protein	0	\N
8279	Xref mapping based on checksum equivalency	Xref checksum	0	\N
8280	Non-coding RNAs (ncRNAs) predicted using sequences from <a href="http://rfam.sanger.ac.uk">RFAM</a> and <a href="http://microrna.sanger.ac.uk/sequences/index.shtml">miRBase</a>. See <a href="http://www.ensembl.org/info/docs/genebuild/ncrna.html" class="cp-external">article</a>.	ncRNAs	1	{'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Genes (Merged Ensembl/Havana) (GENCODE)','name' => 'Merged Ensembl and Havana genes (GENCODE)','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl'}
8281	<a href="http://www.ensembl.org/info/docs/genebuild/ncrna.html" class="cp-external">Positions</a> of ncRNAs (non-coding RNAs) from the <a rel="external" href="http://rfam.sanger.ac.uk/">Rfam </a> database are shown. Initial BLASTN hits of genomic sequence to RFAM ncRNAs are clustered and filtered by E value. These hits are supporting evidence for ncRNA genes.	RFAM ncRNAs	0	\N
8282	Annotation for this gene includes both automatic annotation from Ensembl and <a rel="external" href="http://vega.sanger.ac.uk/index.html">Havana</a> manual curation, see <a href="http://www.ensembl.org/info/docs/genebuild/genome_annotation.html" class="cp-external">article</a>.	Ensembl/Havana merge genes	1	{'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Genes (Merged Ensembl/Havana) (GENCODE)','name' => 'Merged Ensembl and Havana genes (GENCODE)','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl'}
8283	Transcript where the Ensembl genebuild transcript and the <a rel="external" href="http://vega.sanger.ac.uk/index.html">Vega</a> manual annotation have the same sequence, for every base pair. See <a href="http://www.ensembl.org/info/docs/genebuild/genome_annotation.html" class="cp-external">article</a>.	Ensembl/Havana merge	1	{'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Genes (Merged Ensembl/Havana) (GENCODE)','name' => 'Merged Ensembl and Havana genes (GENCODE)','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl'}
8284	Positions of vertebrate mRNAs along the genome. mRNAs are from the <a rel="external" href="http://www.ebi.ac.uk/embl/">European Nucleotide Archive</a> database. Initial alignments are performed using TBLASTN of Genscan-predicted peptides against the European Nucleotide Archive mRNAs.	Vertebrate cDNAs (ENA)	0	{'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
8285	Proteins from the <a rel="external" href="http://uniprot.org">UniProtKB Swiss-Prot</a> database, aligned to the genome by Havana.	UniProt proteins	0	\N
8286	Proteins from the <a rel="external" href="http://uniprot.org">UniProtKB TrEMBL</a> database, aligned to the genome by Havana.	TrEMBL proteins	0	\N
8287	Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D138?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Bateman&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;resourcetype=HWCIT">Pfam</a> database.	Pfam domain	1	{'type' => 'domain'}
8288	Protein domains and motifs in the <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6WK7-457CXWM-3D&amp;_user=776054&amp;_coverDate=11%2F02%2F2001&amp;_rdoc=17&amp;_fmt=high&amp;_orig=browse&amp;_srch=doc-info(%23toc%236899%232001%23996869995%23286382%23FLA%23display%23Volume)&amp;_cdi=6899&amp;_sort=d&amp;_docanchor=&amp;_ct=17&amp;_acct=C000042238&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;md5=a921e84cd71c59f75644aa28f3224b58">SUPERFAMILY</a> database.	Superfamily domains	1	{'type' => 'domain'}
8289	Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D257?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=letunic&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;fdate=1/1/2006&amp;tdate=12/31/2006&amp;resourcetype=HWCIT">SMART</a> database.	SMART domains	1	{'type' => 'domain'}
8290	Identification of peptide low complexity sequences by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6TFV-44PXMF3-45&amp;_user=776054&amp;_coverDate=06%2F30%2F1993&amp;_rdoc=6&amp;_fmt=high&amp;_orig=browse&amp;_srch=doc-info(%23toc%235236%231993%23999829997%23279143%23FLP%23display%23Volume)&amp;_cdi=5236&amp;_sort=d&amp;_docanchor=&amp;_ct=13&amp;_acct=C000042238&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;md5=ac6f98882f2c6626643118367fb28cad">Seg</a>.	Low complexity (Seg)	1	\N
8291	Protein domains and motifs from the <a rel="external" href="http://www.ebi.ac.uk/ppsearch/">PROSITE</a> profiles database are aligned to the genome.	PROSITE profiles	1	{'type' => 'domain'}
8292	Protein fingerprints (groups of conserved motifs) are aligned to the genome. These motifs come from the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/abstract/31/1/400?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Attwood&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;resourcetype=HWCIT">PRINTS</a> database.	Prints domain	1	{'type' => 'domain'}
8293	Protein coding sequences agreed upon by the Consensus Coding Sequence project, or <a href="http://www.ensembl.org/info/docs/genebuild/ccds.html" class="cp-external">CCDS</a>.	CCDS set	1	{'dna_align_feature' => {'do_not_display' => '1'},'type' => 'cdna','default' => {'contigviewbottom' => 'normal'}}
8294	Manual annotation (determined on a case-by-case basis) from the <a rel="external" href="http://www.sanger.ac.uk/HGP/havana/havana.shtml">Havana</a> project.	Havana	1	{'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Genes (Merged Ensembl/Havana) (GENCODE)','name' => 'Merged Ensembl and Havana genes (GENCODE)','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl'}
8295	Alignment of human 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>	Human EST (EST2genome)	0	{'type' => 'est'}
8296	Alignment of ESTs (expressed sequence tags) from another species 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>	Other EST (EST2genome)	0	{'type' => 'est'}
8297	Human cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">ENA</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.	Human cDNAs	0	{'type' => 'cdna'}
8298	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>	Mouse EST (EST2genome)	0	{'type' => 'est'}
8299	Human protein sequences from <a rel="external" href="http://uniprot.org">UniProtKB</a> and <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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;resourcetype=HWCIT">GeneWise</a> or <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.	Human proteins	1	\N
8300	Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/31/1/371?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Haft&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;fdate=1/1/2003&amp;tdate=12/31/2003&amp;resourcetype=HWCIT">TIGRFAM</a> database.	TIGRFAM domain	1	{'type' => 'domain'}
8301	Homo sapiens 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.	Human ESTs	0	{'type' => 'est'}
8302	Prediction of coiled-coil regions in proteins is by <a rel="external" href="http://www.sciencemag.org/cgi/reprint/252/5009/1162">Ncoils</a>.	Coiled-coils (Ncoils)	1	\N
8303	Annotation produced by aligning human cDNA sequences to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate's</a> cdna2genome model, which utilises annotation identifying the coding regions of the cDNA sequences, along with protein evidence from <a rel="external" href="http://uniprot.org">UniProtKB</a>, from various species, aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;resourcetype=HWCIT">GeneWise</a>. This annotation is used where there is no manual annotation and annotation could not be projected from the <a rel="external" href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml">primary assembly</a>.	Ensembl assembly patch	1	{'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Genes (Merged Ensembl/Havana) (GENCODE)','name' => 'Merged Ensembl and Havana genes (GENCODE)','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl'}
8304	First Exon Finder (<a rel="external" href="http://www.nature.com/ng/journal/v29/n4/full/ng780.html">First EF</a>) predicts positions of the first exons of transcripts, both coding and non-coding, using the sequence to identify features such as CpG islands and promoter regions.	First EF	1	\N
8305	CpG islands are regions of nucleic acid sequence containing a high number of adjacent cytosine guanine pairs (along one strand). Usually unmethylated, they are associated with promoters and regulatory regions. They are determined from the genomic sequence using a program written by G. Miklem, similar to <a rel="external" href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/newcpgreport.html">newcpgreport</a> in the EMBOSS package.	CpG islands	1	\N
8306	Transcription start sites predicted by <a rel="external" href="http://www.sanger.ac.uk/Users/td2/eponine/">Eponine-TSS</a>.	TSS (Eponine)	1	\N
