| Source ID |
Type |
Tax ID |
Position |
| ENSG00000160917-ENSG00000241468 |
CGP |
9606 |
7:99438922-99466331  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0004TM_0001 [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_0004TM_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000106246' => 'pentatricopeptide repeat domain 1',
'ENSG00000160917' => 'cleavage and polyadenylation specific factor 4, 30kDa',
'ENSG00000228335' => null,
'ENSG00000241468' => 'ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2',
'ENSG00000248919' => 'ATP5J2-PTCD1 readthrough',
'ENSMUSG00000029625' => 'cleavage and polyadenylation specific factor 4',
'ENSMUSG00000038690' => 'ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F2'
),
'gene_name_arr' => array(
'ENSG00000106246' => 'PTCD1',
'ENSG00000160917' => 'CPSF4',
'ENSG00000228335' => 'AC073063.10',
'ENSG00000241468' => 'ATP5J2',
'ENSG00000248919' => 'ATP5J2-PTCD1',
'ENSMUSG00000029625' => 'Cpsf4',
'ENSMUSG00000038690' => 'Atp5j2'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 15 => 'Brain',
(int) 23 => 'Breast',
(int) 29 => 'Colon',
(int) 36 => 'Heart',
(int) 44 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 64 => 'Muscle',
(int) 72 => 'Ovary',
(int) 79 => 'Placenta',
(int) 86 => 'Testis'
),
'column_titles' => array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
),
'geneviewer' => array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
),
'transcript_count' => (int) 45,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000292478' => array(
'start' => '99416739',
'end' => '99438916',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-001'
),
'ENST00000419981' => array(
'start' => '99434925',
'end' => '99438755',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-002'
),
'ENST00000430029' => array(
'start' => '99434810',
'end' => '99438647',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-004'
),
'ENST00000430982' => array(
'start' => '99433380',
'end' => '99466163',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-007'
),
'ENST00000485746' => array(
'start' => '99429098',
'end' => '99435019',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTCD1-005'
),
'ENST00000292476' => array(
'start' => '99439073',
'end' => '99457371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-003'
),
'ENST00000412686' => array(
'start' => '99439425',
'end' => '99450795',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-010'
),
'ENST00000430038' => array(
'start' => '99439113',
'end' => '99450795',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPSF4-005'
),
'ENST00000436336' => array(
'start' => '99438922',
'end' => '99457342',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-001'
),
'ENST00000440514' => array(
'start' => '99450325',
'end' => '99456578',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-011'
),
'ENST00000441580' => array(
'start' => '99439376',
'end' => '99456589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-004'
),
'ENST00000451876' => array(
'start' => '99438946',
'end' => '99457371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-002'
),
'ENST00000452047' => array(
'start' => '99444785',
'end' => '99456645',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-007'
),
'ENST00000465132' => array(
'start' => '99450766',
'end' => '99453264',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-009'
),
'ENST00000469897' => array(
'start' => '99453687',
'end' => '99456670',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-012'
),
'ENST00000471455' => array(
'start' => '99444810',
'end' => '99454023',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPSF4-008'
),
'ENST00000482251' => array(
'start' => '99450464',
'end' => '99452609',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-013'
),
'ENST00000484112' => array(
'start' => '99439450',
'end' => '99451079',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-006'
),
'ENST00000434352' => array(
'start' => '99442890',
'end' => '99443496',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC073063.10-001'
),
'ENST00000292475' => array(
'start' => '99458195',
'end' => '99466331',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-001'
),
'ENST00000359832' => array(
'start' => '99458195',
'end' => '99466164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-009'
),
'ENST00000394186' => array(
'start' => '99458309',
'end' => '99466161',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-013'
),
'ENST00000414062' => array(
'start' => '99448956',
'end' => '99466165',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP5J2-010'
),
'ENST00000449683' => array(
'start' => '99458190',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-006'
),
'ENST00000466753' => array(
'start' => '99448475',
'end' => '99466165',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5J2-011'
),
'ENST00000481899' => array(
'start' => '99458940',
'end' => '99460499',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-007'
),
'ENST00000485011' => array(
'start' => '99459655',
'end' => '99466186',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-005'
),
'ENST00000488775' => array(
'start' => '99458197',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-012'
),
'ENST00000491560' => array(
'start' => '99458195',
'end' => '99460465',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-008'
),
'ENST00000523680' => array(
'start' => '99459237',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-015'
),
'ENST00000524321' => array(
'start' => '99459664',
'end' => '99466164',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-014'
),
'ENST00000413834' => array(
'start' => '99419749',
'end' => '99466164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-PTCD1-001'
),
'ENST00000437572' => array(
'start' => '99435031',
'end' => '99466197',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5J2-PTCD1-003'
),
'ENST00000451138' => array(
'start' => '99435178',
'end' => '99466162',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP5J2-PTCD1-002'
),
'ENSMUST00000070487' => array(
'start' => '145167224',
'end' => '145182041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-001'
),
'ENSMUST00000160422' => array(
'start' => '145167247',
'end' => '145182040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-005'
),
'ENSMUST00000160437' => array(
'start' => '145170543',
'end' => '145182041',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpsf4-006'
),
'ENSMUST00000160574' => array(
'start' => '145167268',
'end' => '145181232',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Cpsf4-004'
),
'ENSMUST00000160629' => array(
'start' => '145167213',
'end' => '145182041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-002'
),
'ENSMUST00000160762' => array(
'start' => '145167455',
'end' => '145181353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-007'
),
'ENSMUST00000162244' => array(
'start' => '145167254',
'end' => '145181753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-003'
),
'ENSMUST00000037056' => array(
'start' => '145183709',
'end' => '145191592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-003'
),
'ENSMUST00000161741' => array(
'start' => '145183698',
'end' => '145192062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-001'
),
'ENSMUST00000161845' => array(
'start' => '145184386',
'end' => '145191511',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-004'
),
'ENSMUST00000162360' => array(
'start' => '145183706',
'end' => '145191592',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Atp5j2-002'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0004TM_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0004TM_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000038690' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Ovary',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Adrenal',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Liver',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Adipose',
(int) 44 => 'Bladder',
(int) 45 => 'Breast',
(int) 46 => 'Colon',
(int) 47 => 'Heart',
(int) 48 => 'Kidney',
(int) 49 => 'Liver',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Placenta',
(int) 54 => 'Testis',
(int) 55 => 'Adipose',
(int) 56 => 'Adrenal',
(int) 57 => 'Bladder',
(int) 58 => 'Brain',
(int) 59 => 'Breast',
(int) 60 => 'Colon',
(int) 61 => 'Heart',
(int) 62 => 'Kidney',
(int) 63 => 'Liver',
(int) 64 => 'Lung',
(int) 65 => 'Muscle',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis',
(int) 69 => 'Adipose',
(int) 70 => 'Adrenal',
(int) 71 => 'Bladder',
(int) 72 => 'Brain',
(int) 73 => 'Breast',
(int) 74 => 'Colon',
(int) 75 => 'Heart',
(int) 76 => 'Kidney',
(int) 77 => 'Liver',
(int) 78 => 'Lung',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Placenta',
(int) 82 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000106246' => 'pentatricopeptide repeat domain 1',
'ENSG00000160917' => 'cleavage and polyadenylation specific factor 4, 30kDa',
'ENSG00000228335' => null,
'ENSG00000241468' => 'ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2',
'ENSG00000248919' => 'ATP5J2-PTCD1 readthrough',
'ENSMUSG00000029625' => 'cleavage and polyadenylation specific factor 4',
'ENSMUSG00000038690' => 'ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F2'
)
$gene_name_arr = array(
'ENSG00000106246' => 'PTCD1',
'ENSG00000160917' => 'CPSF4',
'ENSG00000228335' => 'AC073063.10',
'ENSG00000241468' => 'ATP5J2',
'ENSG00000248919' => 'ATP5J2-PTCD1',
'ENSMUSG00000029625' => 'Cpsf4',
'ENSMUSG00000038690' => 'Atp5j2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004TM_0001',
'tax_id' => '9606',
'chromosome' => '7',
'seq_start' => '99438922',
'seq_end' => '99466331',
'region_length' => '27409',
'region_type' => 'CGP',
'el_id' => 'ENSG00000160917-ENSG00000241468'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004TM_0002',
'tax_id' => '10090',
'chromosome' => '5',
'seq_start' => '145167213',
'seq_end' => '145192062',
'region_length' => '24849',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000029625-ENSMUSG00000038690'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 15 => 'Brain',
(int) 23 => 'Breast',
(int) 29 => 'Colon',
(int) 36 => 'Heart',
(int) 44 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 64 => 'Muscle',
(int) 72 => 'Ovary',
(int) 79 => 'Placenta',
(int) 86 => 'Testis'
)
$column_titles = array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
)
$geneviewer = array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
)
$transcript_count = (int) 45
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000292478' => array(
'start' => '99416739',
'end' => '99438916',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-001'
),
'ENST00000419981' => array(
'start' => '99434925',
'end' => '99438755',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-002'
),
'ENST00000430029' => array(
'start' => '99434810',
'end' => '99438647',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-004'
),
'ENST00000430982' => array(
'start' => '99433380',
'end' => '99466163',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-007'
),
'ENST00000485746' => array(
'start' => '99429098',
'end' => '99435019',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTCD1-005'
),
'ENST00000292476' => array(
'start' => '99439073',
'end' => '99457371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-003'
),
'ENST00000412686' => array(
'start' => '99439425',
'end' => '99450795',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-010'
),
'ENST00000430038' => array(
'start' => '99439113',
'end' => '99450795',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPSF4-005'
),
'ENST00000436336' => array(
'start' => '99438922',
'end' => '99457342',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-001'
),
'ENST00000440514' => array(
'start' => '99450325',
'end' => '99456578',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-011'
),
'ENST00000441580' => array(
'start' => '99439376',
'end' => '99456589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-004'
),
'ENST00000451876' => array(
'start' => '99438946',
'end' => '99457371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-002'
),
'ENST00000452047' => array(
'start' => '99444785',
'end' => '99456645',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-007'
),
'ENST00000465132' => array(
'start' => '99450766',
'end' => '99453264',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-009'
),
'ENST00000469897' => array(
'start' => '99453687',
'end' => '99456670',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-012'
),
'ENST00000471455' => array(
'start' => '99444810',
'end' => '99454023',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPSF4-008'
),
'ENST00000482251' => array(
'start' => '99450464',
'end' => '99452609',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-013'
),
'ENST00000484112' => array(
'start' => '99439450',
'end' => '99451079',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-006'
),
'ENST00000434352' => array(
'start' => '99442890',
'end' => '99443496',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC073063.10-001'
),
'ENST00000292475' => array(
'start' => '99458195',
'end' => '99466331',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-001'
),
'ENST00000359832' => array(
'start' => '99458195',
'end' => '99466164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-009'
),
'ENST00000394186' => array(
'start' => '99458309',
'end' => '99466161',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-013'
),
'ENST00000414062' => array(
'start' => '99448956',
'end' => '99466165',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP5J2-010'
),
'ENST00000449683' => array(
'start' => '99458190',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-006'
),
'ENST00000466753' => array(
'start' => '99448475',
'end' => '99466165',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5J2-011'
),
'ENST00000481899' => array(
'start' => '99458940',
'end' => '99460499',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-007'
),
'ENST00000485011' => array(
'start' => '99459655',
'end' => '99466186',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-005'
),
'ENST00000488775' => array(
'start' => '99458197',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-012'
),
'ENST00000491560' => array(
'start' => '99458195',
'end' => '99460465',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-008'
),
'ENST00000523680' => array(
'start' => '99459237',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-015'
),
'ENST00000524321' => array(
'start' => '99459664',
'end' => '99466164',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-014'
),
'ENST00000413834' => array(
'start' => '99419749',
'end' => '99466164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-PTCD1-001'
),
'ENST00000437572' => array(
'start' => '99435031',
'end' => '99466197',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5J2-PTCD1-003'
),
'ENST00000451138' => array(
'start' => '99435178',
'end' => '99466162',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP5J2-PTCD1-002'
),
'ENSMUST00000070487' => array(
'start' => '145167224',
'end' => '145182041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-001'
),
'ENSMUST00000160422' => array(
'start' => '145167247',
'end' => '145182040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-005'
),
'ENSMUST00000160437' => array(
'start' => '145170543',
'end' => '145182041',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpsf4-006'
),
'ENSMUST00000160574' => array(
'start' => '145167268',
'end' => '145181232',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Cpsf4-004'
),
'ENSMUST00000160629' => array(
'start' => '145167213',
'end' => '145182041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-002'
),
'ENSMUST00000160762' => array(
'start' => '145167455',
'end' => '145181353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-007'
),
'ENSMUST00000162244' => array(
'start' => '145167254',
'end' => '145181753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-003'
),
'ENSMUST00000037056' => array(
'start' => '145183709',
'end' => '145191592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-003'
),
'ENSMUST00000161741' => array(
'start' => '145183698',
'end' => '145192062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-001'
),
'ENSMUST00000161845' => array(
'start' => '145184386',
'end' => '145191511',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-004'
),
'ENSMUST00000162360' => array(
'start' => '145183706',
'end' => '145191592',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Atp5j2-002'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0004TM_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000038690' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Ovary',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Adrenal',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Liver',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Adipose',
(int) 44 => 'Bladder',
(int) 45 => 'Breast',
(int) 46 => 'Colon',
(int) 47 => 'Heart',
(int) 48 => 'Kidney',
(int) 49 => 'Liver',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Placenta',
(int) 54 => 'Testis',
(int) 55 => 'Adipose',
(int) 56 => 'Adrenal',
(int) 57 => 'Bladder',
(int) 58 => 'Brain',
(int) 59 => 'Breast',
(int) 60 => 'Colon',
(int) 61 => 'Heart',
(int) 62 => 'Kidney',
(int) 63 => 'Liver',
(int) 64 => 'Lung',
(int) 65 => 'Muscle',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis',
(int) 69 => 'Adipose',
(int) 70 => 'Adrenal',
(int) 71 => 'Bladder',
(int) 72 => 'Brain',
(int) 73 => 'Breast',
(int) 74 => 'Colon',
(int) 75 => 'Heart',
(int) 76 => 'Kidney',
(int) 77 => 'Liver',
(int) 78 => 'Lung',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Placenta',
(int) 82 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0004TM_0001',
'tax_id' => '9606',
'chromosome' => '7',
'seq_start' => '99438922',
'seq_end' => '99466331',
'region_length' => '27409',
'region_type' => 'CGP',
'el_id' => 'ENSG00000160917-ENSG00000241468'
)
)
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_0004TM_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000106246' => 'pentatricopeptide repeat domain 1',
'ENSG00000160917' => 'cleavage and polyadenylation specific factor 4, 30kDa',
'ENSG00000228335' => null,
'ENSG00000241468' => 'ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2',
'ENSG00000248919' => 'ATP5J2-PTCD1 readthrough',
'ENSMUSG00000029625' => 'cleavage and polyadenylation specific factor 4',
'ENSMUSG00000038690' => 'ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F2'
),
'gene_name_arr' => array(
'ENSG00000106246' => 'PTCD1',
'ENSG00000160917' => 'CPSF4',
'ENSG00000228335' => 'AC073063.10',
'ENSG00000241468' => 'ATP5J2',
'ENSG00000248919' => 'ATP5J2-PTCD1',
'ENSMUSG00000029625' => 'Cpsf4',
'ENSMUSG00000038690' => 'Atp5j2'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 15 => 'Brain',
(int) 23 => 'Breast',
(int) 29 => 'Colon',
(int) 36 => 'Heart',
(int) 44 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 64 => 'Muscle',
(int) 72 => 'Ovary',
(int) 79 => 'Placenta',
(int) 86 => 'Testis'
),
'column_titles' => array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
),
'geneviewer' => array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
),
'transcript_count' => (int) 45,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000292478' => array(
'start' => '99416739',
'end' => '99438916',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-001'
),
'ENST00000419981' => array(
'start' => '99434925',
'end' => '99438755',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-002'
),
'ENST00000430029' => array(
'start' => '99434810',
'end' => '99438647',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-004'
),
'ENST00000430982' => array(
'start' => '99433380',
'end' => '99466163',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-007'
),
'ENST00000485746' => array(
'start' => '99429098',
'end' => '99435019',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTCD1-005'
),
'ENST00000292476' => array(
'start' => '99439073',
'end' => '99457371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-003'
),
'ENST00000412686' => array(
'start' => '99439425',
'end' => '99450795',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-010'
),
'ENST00000430038' => array(
'start' => '99439113',
'end' => '99450795',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPSF4-005'
),
'ENST00000436336' => array(
'start' => '99438922',
'end' => '99457342',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-001'
),
'ENST00000440514' => array(
'start' => '99450325',
'end' => '99456578',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-011'
),
'ENST00000441580' => array(
'start' => '99439376',
'end' => '99456589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-004'
),
'ENST00000451876' => array(
'start' => '99438946',
'end' => '99457371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-002'
),
'ENST00000452047' => array(
'start' => '99444785',
'end' => '99456645',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-007'
),
'ENST00000465132' => array(
'start' => '99450766',
'end' => '99453264',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-009'
),
'ENST00000469897' => array(
'start' => '99453687',
'end' => '99456670',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-012'
),
'ENST00000471455' => array(
'start' => '99444810',
'end' => '99454023',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPSF4-008'
),
'ENST00000482251' => array(
'start' => '99450464',
'end' => '99452609',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-013'
),
'ENST00000484112' => array(
'start' => '99439450',
'end' => '99451079',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-006'
),
'ENST00000434352' => array(
'start' => '99442890',
'end' => '99443496',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC073063.10-001'
),
'ENST00000292475' => array(
'start' => '99458195',
'end' => '99466331',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-001'
),
'ENST00000359832' => array(
'start' => '99458195',
'end' => '99466164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-009'
),
'ENST00000394186' => array(
'start' => '99458309',
'end' => '99466161',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-013'
),
'ENST00000414062' => array(
'start' => '99448956',
'end' => '99466165',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP5J2-010'
),
'ENST00000449683' => array(
'start' => '99458190',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-006'
),
'ENST00000466753' => array(
'start' => '99448475',
'end' => '99466165',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5J2-011'
),
'ENST00000481899' => array(
'start' => '99458940',
'end' => '99460499',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-007'
),
'ENST00000485011' => array(
'start' => '99459655',
'end' => '99466186',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-005'
),
'ENST00000488775' => array(
'start' => '99458197',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-012'
),
'ENST00000491560' => array(
'start' => '99458195',
'end' => '99460465',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-008'
),
'ENST00000523680' => array(
'start' => '99459237',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-015'
),
'ENST00000524321' => array(
'start' => '99459664',
'end' => '99466164',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-014'
),
'ENST00000413834' => array(
'start' => '99419749',
'end' => '99466164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-PTCD1-001'
),
'ENST00000437572' => array(
'start' => '99435031',
'end' => '99466197',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5J2-PTCD1-003'
),
'ENST00000451138' => array(
'start' => '99435178',
'end' => '99466162',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP5J2-PTCD1-002'
),
'ENSMUST00000070487' => array(
'start' => '145167224',
'end' => '145182041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-001'
),
'ENSMUST00000160422' => array(
'start' => '145167247',
'end' => '145182040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-005'
),
'ENSMUST00000160437' => array(
'start' => '145170543',
'end' => '145182041',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpsf4-006'
),
'ENSMUST00000160574' => array(
'start' => '145167268',
'end' => '145181232',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Cpsf4-004'
),
'ENSMUST00000160629' => array(
'start' => '145167213',
'end' => '145182041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-002'
),
'ENSMUST00000160762' => array(
'start' => '145167455',
'end' => '145181353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-007'
),
'ENSMUST00000162244' => array(
'start' => '145167254',
'end' => '145181753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-003'
),
'ENSMUST00000037056' => array(
'start' => '145183709',
'end' => '145191592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-003'
),
'ENSMUST00000161741' => array(
'start' => '145183698',
'end' => '145192062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-001'
),
'ENSMUST00000161845' => array(
'start' => '145184386',
'end' => '145191511',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-004'
),
'ENSMUST00000162360' => array(
'start' => '145183706',
'end' => '145191592',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Atp5j2-002'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0004TM_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0004TM_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000038690' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Ovary',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Adrenal',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Liver',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Adipose',
(int) 44 => 'Bladder',
(int) 45 => 'Breast',
(int) 46 => 'Colon',
(int) 47 => 'Heart',
(int) 48 => 'Kidney',
(int) 49 => 'Liver',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Placenta',
(int) 54 => 'Testis',
(int) 55 => 'Adipose',
(int) 56 => 'Adrenal',
(int) 57 => 'Bladder',
(int) 58 => 'Brain',
(int) 59 => 'Breast',
(int) 60 => 'Colon',
(int) 61 => 'Heart',
(int) 62 => 'Kidney',
(int) 63 => 'Liver',
(int) 64 => 'Lung',
(int) 65 => 'Muscle',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis',
(int) 69 => 'Adipose',
(int) 70 => 'Adrenal',
(int) 71 => 'Bladder',
(int) 72 => 'Brain',
(int) 73 => 'Breast',
(int) 74 => 'Colon',
(int) 75 => 'Heart',
(int) 76 => 'Kidney',
(int) 77 => 'Liver',
(int) 78 => 'Lung',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Placenta',
(int) 82 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000106246' => 'pentatricopeptide repeat domain 1',
'ENSG00000160917' => 'cleavage and polyadenylation specific factor 4, 30kDa',
'ENSG00000228335' => null,
'ENSG00000241468' => 'ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2',
'ENSG00000248919' => 'ATP5J2-PTCD1 readthrough',
'ENSMUSG00000029625' => 'cleavage and polyadenylation specific factor 4',
'ENSMUSG00000038690' => 'ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F2'
)
$gene_name_arr = array(
'ENSG00000106246' => 'PTCD1',
'ENSG00000160917' => 'CPSF4',
'ENSG00000228335' => 'AC073063.10',
'ENSG00000241468' => 'ATP5J2',
'ENSG00000248919' => 'ATP5J2-PTCD1',
'ENSMUSG00000029625' => 'Cpsf4',
'ENSMUSG00000038690' => 'Atp5j2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004TM_0001',
'tax_id' => '9606',
'chromosome' => '7',
'seq_start' => '99438922',
'seq_end' => '99466331',
'region_length' => '27409',
'region_type' => 'CGP',
'el_id' => 'ENSG00000160917-ENSG00000241468'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004TM_0002',
'tax_id' => '10090',
'chromosome' => '5',
'seq_start' => '145167213',
'seq_end' => '145192062',
'region_length' => '24849',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000029625-ENSMUSG00000038690'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 15 => 'Brain',
(int) 23 => 'Breast',
(int) 29 => 'Colon',
(int) 36 => 'Heart',
(int) 44 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 64 => 'Muscle',
(int) 72 => 'Ovary',
(int) 79 => 'Placenta',
(int) 86 => 'Testis'
)
$column_titles = array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
)
$geneviewer = array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
)
$transcript_count = (int) 45
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000292478' => array(
'start' => '99416739',
'end' => '99438916',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-001'
),
'ENST00000419981' => array(
'start' => '99434925',
'end' => '99438755',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-002'
),
'ENST00000430029' => array(
'start' => '99434810',
'end' => '99438647',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-004'
),
'ENST00000430982' => array(
'start' => '99433380',
'end' => '99466163',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTCD1-007'
),
'ENST00000485746' => array(
'start' => '99429098',
'end' => '99435019',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTCD1-005'
),
'ENST00000292476' => array(
'start' => '99439073',
'end' => '99457371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-003'
),
'ENST00000412686' => array(
'start' => '99439425',
'end' => '99450795',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-010'
),
'ENST00000430038' => array(
'start' => '99439113',
'end' => '99450795',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPSF4-005'
),
'ENST00000436336' => array(
'start' => '99438922',
'end' => '99457342',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-001'
),
'ENST00000440514' => array(
'start' => '99450325',
'end' => '99456578',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-011'
),
'ENST00000441580' => array(
'start' => '99439376',
'end' => '99456589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-004'
),
'ENST00000451876' => array(
'start' => '99438946',
'end' => '99457371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-002'
),
'ENST00000452047' => array(
'start' => '99444785',
'end' => '99456645',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPSF4-007'
),
'ENST00000465132' => array(
'start' => '99450766',
'end' => '99453264',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-009'
),
'ENST00000469897' => array(
'start' => '99453687',
'end' => '99456670',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-012'
),
'ENST00000471455' => array(
'start' => '99444810',
'end' => '99454023',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPSF4-008'
),
'ENST00000482251' => array(
'start' => '99450464',
'end' => '99452609',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-013'
),
'ENST00000484112' => array(
'start' => '99439450',
'end' => '99451079',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPSF4-006'
),
'ENST00000434352' => array(
'start' => '99442890',
'end' => '99443496',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC073063.10-001'
),
'ENST00000292475' => array(
'start' => '99458195',
'end' => '99466331',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-001'
),
'ENST00000359832' => array(
'start' => '99458195',
'end' => '99466164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-009'
),
'ENST00000394186' => array(
'start' => '99458309',
'end' => '99466161',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-013'
),
'ENST00000414062' => array(
'start' => '99448956',
'end' => '99466165',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP5J2-010'
),
'ENST00000449683' => array(
'start' => '99458190',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-006'
),
'ENST00000466753' => array(
'start' => '99448475',
'end' => '99466165',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5J2-011'
),
'ENST00000481899' => array(
'start' => '99458940',
'end' => '99460499',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-007'
),
'ENST00000485011' => array(
'start' => '99459655',
'end' => '99466186',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-005'
),
'ENST00000488775' => array(
'start' => '99458197',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-012'
),
'ENST00000491560' => array(
'start' => '99458195',
'end' => '99460465',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-008'
),
'ENST00000523680' => array(
'start' => '99459237',
'end' => '99466167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-015'
),
'ENST00000524321' => array(
'start' => '99459664',
'end' => '99466164',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5J2-014'
),
'ENST00000413834' => array(
'start' => '99419749',
'end' => '99466164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5J2-PTCD1-001'
),
'ENST00000437572' => array(
'start' => '99435031',
'end' => '99466197',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5J2-PTCD1-003'
),
'ENST00000451138' => array(
'start' => '99435178',
'end' => '99466162',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP5J2-PTCD1-002'
),
'ENSMUST00000070487' => array(
'start' => '145167224',
'end' => '145182041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-001'
),
'ENSMUST00000160422' => array(
'start' => '145167247',
'end' => '145182040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-005'
),
'ENSMUST00000160437' => array(
'start' => '145170543',
'end' => '145182041',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpsf4-006'
),
'ENSMUST00000160574' => array(
'start' => '145167268',
'end' => '145181232',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Cpsf4-004'
),
'ENSMUST00000160629' => array(
'start' => '145167213',
'end' => '145182041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-002'
),
'ENSMUST00000160762' => array(
'start' => '145167455',
'end' => '145181353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-007'
),
'ENSMUST00000162244' => array(
'start' => '145167254',
'end' => '145181753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpsf4-003'
),
'ENSMUST00000037056' => array(
'start' => '145183709',
'end' => '145191592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-003'
),
'ENSMUST00000161741' => array(
'start' => '145183698',
'end' => '145192062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-001'
),
'ENSMUST00000161845' => array(
'start' => '145184386',
'end' => '145191511',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5j2-004'
),
'ENSMUST00000162360' => array(
'start' => '145183706',
'end' => '145191592',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Atp5j2-002'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0004TM_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000038690' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Ovary',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Adrenal',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Liver',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Adipose',
(int) 44 => 'Bladder',
(int) 45 => 'Breast',
(int) 46 => 'Colon',
(int) 47 => 'Heart',
(int) 48 => 'Kidney',
(int) 49 => 'Liver',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Placenta',
(int) 54 => 'Testis',
(int) 55 => 'Adipose',
(int) 56 => 'Adrenal',
(int) 57 => 'Bladder',
(int) 58 => 'Brain',
(int) 59 => 'Breast',
(int) 60 => 'Colon',
(int) 61 => 'Heart',
(int) 62 => 'Kidney',
(int) 63 => 'Liver',
(int) 64 => 'Lung',
(int) 65 => 'Muscle',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis',
(int) 69 => 'Adipose',
(int) 70 => 'Adrenal',
(int) 71 => 'Bladder',
(int) 72 => 'Brain',
(int) 73 => 'Breast',
(int) 74 => 'Colon',
(int) 75 => 'Heart',
(int) 76 => 'Kidney',
(int) 77 => 'Liver',
(int) 78 => 'Lung',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Placenta',
(int) 82 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0004TM_0001',
'tax_id' => '9606',
'chromosome' => '7',
'seq_start' => '99438922',
'seq_end' => '99466331',
'region_length' => '27409',
'region_type' => 'CGP',
'el_id' => 'ENSG00000160917-ENSG00000241468'
)
)
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
(Atp5j2)