8160	Transcripts were annotated by the Ensembl <a href="http://www.ensembl.org/info/docs/genebuild/genome_annotation.html" class="cp-external">genebuild</a>.	Ensembl gene	1	{'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Ensembl/Havana gene','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'}
8161	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
8162	match	Protein	0	\N
8163	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'}
8164	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 domain	1	{'type' => 'domain'}
8165	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
8166	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 domain	1	{'type' => 'domain'}
8167	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'}
8168	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'}
8169	Manually annotated transcripts (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 gene	1	{'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Ensembl/Havana gene','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'}
8170	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'}
8171	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.	ENA vertebrate cDNA (Havana)	0	{'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
8172	Proteins from the <a rel="external" href="http://uniprot.org">UniProtKB Swiss-Prot</a> database, aligned to the genome by Havana.	UniProt prot.	0	\N
8173	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/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.	Human RefSeq/EMBL cDNA	0	{'type' => 'cdna'}
8174	Human proteins 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>.	Human prot.	1	\N
8175	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'}}
8176	Gene containing both Ensembl genebuild transcripts 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 gene	1	{'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Ensembl/Havana gene','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'}
8177	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 transcript	1	{'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Ensembl/Havana gene','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'}
8178	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
8179	Prediction of transmembrane helices in proteins by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6WK7-457D7V9-K&amp;_user=776054&amp;_rdoc=1&amp;_fmt=&amp;_orig=search&amp;_sort=d&amp;view=c&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;md5=a113464457fa5206c6699b9d464cbfee">TMHMM</a>.	Transmembrane helices	1	\N
8180	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 patterns	1	{'type' => 'domain'}
8181	Non-coding RNA (ncRNA) is 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>.	ncRNA gene	1	{'colour_key' => 'rna','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label','cytoview' => 'gene_label'}}
8182	Positions of miRNAs along the genome are shown. A BLASTN of genomic sequence regions against <a rel="external" href="http://microrna.sanger.ac.uk">miRBase</a> sequences is performed, and hits are clustered and filtered by E value. Aligned genomic sequence is then checked for possible secondary structure using RNAFold. If evidence is found that the genomic sequence could form a stable hairpin structure the locus is used to create a miRNA gene model. The resulting BLAST hit is used as supporting evidence for the miRNA gene. See <a href="http://www.ensembl.org/info/docs/genebuild/ncrna.html" class="cp-external">article</a>.	miRBase miRNA	1	{'type' => 'rna'}
8183	Prediction of signal peptide cleavage sites by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6WK7-4CKBS0M-3&amp;_user=776054&amp;_coverDate=07%2F16%2F2004&amp;_alid=772330061&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_cdi=6899&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_ct=1&amp;_acct=C000042238&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;md5=9f42be939814b7711268fd414604c9dd">SignalP</a>.	Cleavage site (Signalp)	1	\N
8184	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.	ENA vertebrate cDNA	1	{'type' => 'cdna'}
8185	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'}
8186	Proteins from the <a rel="external" href="http://uniprot.org">UniProtKB TrEMBL</a> database, aligned to the genome by Havana.	TrEMBL prot.	0	\N
8187	Large intergenic non-coding RNA genes (lincRNAs) were annotated by the <a href="/info/docs/genebuild/ncrna.html" class="cp-external">Ensembl lincRNA annotation pipeline</a>.	Ensembl lincRNA gene	1	{'multi_name' => 'Merged Ensembl and Havana lincRNA genes','colour_key' => 'lincrna','caption' => 'Ensembl/Havana merge lincRNA gene','name' => 'Merged Ensembl and Havana lincRNA genes','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'lincrna_gene'}
8188	The latest set of cDNAs for this species from the European Nucleotide Archive and NCBI RefSeq were aligned to the current genome using <a rel="external" href="http://www.ebi.ac.uk/~guy/exonerate/">Exonerate</a>.	cDNA update	0	{'multi_name' => 'Mouse/Human specific cDNA','name' => 'Species specific RefSeq/ENA cDNA','label_key' => '[text_label] [display_label]','gene' => {'do_not_display' => 1},'type' => 'cdna','default' => {'contigviewbottom' => 'stack'},'key' => 'species_specific_cdna'}
8189	Protein domains and motifs from the <a rel="external" href="http://pir.georgetown.edu/pirwww/index.shtml">PIR (Protein Information Resource)</a> Superfamily database.	PIRSF domain	1	{'type' => 'domain'}
8190	<a href="http://www.ensembl.org/info/docs/genebuild/ncrna.html" class="cp-external">Positions</a>Positions 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 ncRNA gene	1	{'type' => 'rna'}
8191	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'}
8192	Seleno protein cDNAs aligned using <a rel="external" href="http://www.ebi.ac.uk/~guy/exonerate/">Exonerate</a> with selenocysteines added based on EMBL annotation.	EMBL seleno protein cDNA	1	\N
