8405	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	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'}
8406	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
8407	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'}
8408	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'}
8409	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'}}
8410	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'}
8411	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'}
8412	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
8413	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
8414	Proteins from the <a rel="external" href="http://uniprot.org">UniProtKB TrEMBL</a> database, aligned to the genome by Havana.	TrEMBL proteins	0	\N
8415	match	Protein	0	\N
8416	Xref mapping based on checksum equivalency	Xref checksum	0	\N
8417	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'}
8418	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'}
8419	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'}
8420	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
8421	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'}
8422	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'}
8423	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
8424	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'}}
8425	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'}
8426	Annotation produced by the Ensembl <a href="http://www.ensembl.org/info/docs/genebuild/genome_annotation.html" class="cp-external">genebuild</a>.	Ensembl	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'}
8427	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'}
8428	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'}
8429	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
8430	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'}
8431	<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
8432	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'}
8433	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>. These were projected to the <a rel="external" href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml">alternate locus</a> via a mapping from the <a rel="external" href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml">primary assembly</a>.	Projected ncRNA	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'}
8434	Transcript that was projected from the primary assembly, aligned to the alternate locus version as supporting evidence.	Projected transcript	0	{'type':'cdna'}
8435	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, projected to the <a rel="external" href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml">alternate locus</a> via a mapping from the <a rel="external" href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml">primary assembly</a>.	Projected 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'}
8436	Data from LRG database	LRG	0	{'multi_name':'LRG genes','colour_key':'rna_[status]','caption':'LRG gene','name':'LRG Genes','label_key':'[text_label] [display_label]','default':{'MultiTop':'gene_label','contigviewbottom':'transcript_label','MultiBottom':'collapsed_label','contigviewtop':'gene_label','cytoview':'gene_label','alignsliceviewbottom':'as_collapsed_label'}}
8437	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
8438	Transcription start sites predicted by <a rel="external" href="http://www.sanger.ac.uk/resources/software/eponine/">Eponine-TSS</a>.	TSS (Eponine)	1	\N
8439	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
8440	Ab initio prediction of protein coding genes by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6WK7-45VGF7T-9&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=aa15a5f8122912c172ddb9dd15b237dc">Genscan</a>. The splice site models used are described in more detail in C. Burge, Modelling dependencies in pre-mRNA splicing signals. 1998 In Salzberg, S., Searls, D. and Kasif, S., eds. Computational Methods in Molecular Biology, Elsevier Science, Amsterdam, 127-163.	Genscan predictions	1	\N
8441	Short non-coding gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Production/Pipeline/Production/NonCodingDensity.pm?root=ensembl&view=markup">ShortNonCodingDensity.pm</a>.	Short non-coding genes (density)	1	\N
8442	Coding gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Pipeline/Production/CodingDensity.pm?root=ensembl&view=markup">gene_density_calc.pl</a>.	Coding genes (density)	1	\N
8443	Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.)	Repeats (percent)	1	\N
8444	Percentage of G/C bases in the sequence.	GC content	1	\N
8445	Pseudogene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Pipeline/Production/PseudogeneDensity.pm?root=ensembl&view=markup">PseudogeneDensity</a>.	Pseudogenes (density)	1	\N
8446	Long non-coding gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Production/Pipeline/Production/NonCodingDensity.pm?root=ensembl&view=markup">LongNonCodingDensity.pm</a>.	Long non-coding genes (density)	1	\N
8447	Markers, or sequence tagged sites (STS), from <a rel="external" href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists">UniSTS</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/full/7/5/541">Electronic PCR (e-PCR)</a>.	Marker	1	\N
