Query information from Ensembl
Usage
queryEnsemblByGene(gene, species = NULL, assembly = NULL)
queryEnsemblByEvent(event, species = NULL, assembly = NULL, data = NULL)See also
Other functions to retrieve external information:
ensemblToUniprot(),
plotProtein(),
plotTranscripts()
Examples
queryEnsemblByGene("BRCA1", "human", "hg19")
#> $seq_region_name
#> [1] "17"
#>
#> $id
#> [1] "ENSG00000012048"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $version
#> [1] 15
#>
#> $end
#> [1] 41277500
#>
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#>
#> $object_type
#> [1] "Gene"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $start
#> [1] 41196312
#>
#> $species
#> [1] "human"
#>
#> $display_name
#> [1] "BRCA1"
#>
#> $strand
#> [1] -1
#>
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>
#> $db_type
#> [1] "core"
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $Transcript
#> length assembly_name db_type gencode_primary Translation.id
#> 1 7094 GRCh37 core 0 ENSP00000350283
#> 2 3273 GRCh37 core 0 ENSP00000417148
#> 3 781 GRCh37 core 0 ENSP00000465818
#> 4 1282 GRCh37 core 0 ENSP00000467329
#> 5 563 GRCh37 core 0 ENSP00000465347
#> 6 5732 GRCh37 core 0 ENSP00000418775
#> 7 5936 GRCh37 core 0 ENSP00000418960
#> 8 5693 GRCh37 core 0 ENSP00000418548
#> 9 2379 GRCh37 core 0 ENSP00000420705
#> 10 1495 GRCh37 core 0 ENSP00000419481
#> 11 1972 GRCh37 core 0 ENSP00000420412
#> 12 1948 GRCh37 core 0 ENSP00000418819
#> 13 561 GRCh37 core 0 <NA>
#> 14 800 GRCh37 core 0 ENSP00000418212
#> 15 726 GRCh37 core 0 ENSP00000417241
#> 16 4497 GRCh37 core 0 <NA>
#> 17 1312 GRCh37 core 0 ENSP00000397145
#> 18 2108 GRCh37 core 0 ENSP00000419274
#> 19 1980 GRCh37 core 0 ENSP00000419988
#> 20 1584 GRCh37 core 0 ENSP00000420253
#> 21 779 GRCh37 core 0 ENSP00000418986
#> 22 1612 GRCh37 core 0 ENSP00000419103
#> 23 958 GRCh37 core 0 ENSP00000420201
#> 24 769 GRCh37 core 0 ENSP00000417554
#> 25 582 GRCh37 core 0 ENSP00000417988
#> 26 455 GRCh37 core 0 ENSP00000420781
#> 27 6411 GRCh37 core 0 ENSP00000326002
#> 28 3780 GRCh37 core 0 ENSP00000312236
#> 29 6451 GRCh37 core 0 ENSP00000246907
#> 30 3444 GRCh37 core 0 ENSP00000338007
#> 31 7114 GRCh37 core 0 ENSP00000310938
#> Translation.Parent Translation.start Translation.species Translation.end
#> 1 ENST00000357654 41197695 human 41276113
#> 2 ENST00000468300 41197801 human 41276113
#> 3 ENST00000586385 41197695 human 41277202
#> 4 ENST00000591534 41197695 human 41226495
#> 5 ENST00000591849 41197695 human 41202109
#> 6 ENST00000493795 41197695 human 41258543
#> 7 ENST00000471181 41197695 human 41276113
#> 8 ENST00000461221 41256972 human 41276113
#> 9 ENST00000491747 41197695 human 41276113
#> 10 ENST00000484087 41215361 human 41256933
#> 11 ENST00000478531 41215361 human 41276113
#> 12 ENST00000493919 41215377 human 41258543
#> 13 <NA> NA <NA> NA
#> 14 ENST00000487825 41228505 human 41256933
#> 15 ENST00000461574 41228554 human 41243841
#> 16 <NA> NA <NA> NA
#> 17 ENST00000412061 41245587 human 41247883
#> 18 ENST00000470026 41245601 human 41276113
#> 19 ENST00000477152 41245603 human 41276113
#> 20 ENST00000492859 41262552 human 41276113
#> 21 ENST00000497488 41246129 human 41246659
#> 22 ENST00000494123 41246129 human 41276113
#> 23 ENST00000473961 41246187 human 41256908
#> 24 ENST00000476777 41247863 human 41276113
#> 25 ENST00000461798 41256972 human 41276113
#> 26 ENST00000489037 41256206 human 41276113
#> 27 ENST00000354071 41197695 human 41276113
#> 28 ENST00000352993 41197695 human 41276113
#> 29 ENST00000346315 41197695 human 41276113
#> 30 ENST00000351666 41197695 human 41276113
#> 31 ENST00000309486 41197695 human 41246659
#> Translation.length Translation.object_type Translation.version
#> 1 1863 Translation 3
#> 2 699 Translation 1
#> 3 173 Translation 1
#> 4 354 Translation 1
#> 5 96 Translation 1
#> 6 1816 Translation 1
#> 7 1884 Translation 2
#> 8 63 Translation 1
#> 9 759 Translation 2
#> 10 498 Translation 1
#> 11 623 Translation 1
#> 12 572 Translation 1
#> 13 NA <NA> NA
#> 14 266 Translation 1
#> 15 242 Translation 1
#> 16 NA <NA> NA
#> 17 437 Translation 3
#> 18 649 Translation 1
#> 19 622 Translation 1
#> 20 59 Translation 1
#> 21 177 Translation 1
#> 22 473 Translation 1
#> 23 319 Translation 1
#> 24 222 Translation 1
#> 25 63 Translation 1
#> 26 98 Translation 1
#> 27 1598 Translation 6
#> 28 721 Translation 5
#> 29 1624 Translation 4
#> 30 680 Translation 3
#> 31 1567 Translation 4
#> Translation.db_type display_name strand Exon species start
#> 1 core BRCA1-001 -1 c(412772.... human 41196312
#> 2 core BRCA1-007 -1 c(-1, -1.... human 41196822
#> 3 core BRCA1-023 -1 c(-1, -1.... human 41197580
#> 4 core BRCA1-024 -1 c(1, 1, .... human 41197580
#> 5 core BRCA1-025 -1 c("Exon".... human 41197580
#> 6 core BRCA1-006 -1 c("ENSE0.... human 41197646
#> 7 core BRCA1-005 -1 c("17", .... human 41197646
#> 8 core BRCA1-010 -1 c(-1, -1.... human 41197695
#> 9 core BRCA1-014 -1 c("Exon".... human 41197695
#> 10 core BRCA1-015 -1 c(-1, -1.... human 41215361
#> 11 core BRCA1-009 -1 c(1, 1, .... human 41215361
#> 12 core BRCA1-008 -1 c(-1, -1.... human 41215377
#> 13 <NA> BRCA1-021 -1 c("core".... human 41219291
#> 14 core BRCA1-019 -1 c("Exon".... human 41228505
#> 15 core BRCA1-022 -1 c(1, 1, .... human 41228554
#> 16 <NA> BRCA1-012 -1 c(-1, -1.... human 41243115
#> 17 core BRCA1-026 -1 c(-1, -1.... human 41245587
#> 18 core BRCA1-011 -1 c(1, 1, .... human 41245601
#> 19 core BRCA1-004 -1 c(-1, -1.... human 41245603
#> 20 core BRCA1-002 -1 c("core".... human 41246129
#> 21 core BRCA1-003 -1 c(-1, -1.... human 41246129
#> 22 core BRCA1-013 -1 c(1, 1, .... human 41246129
#> 23 core BRCA1-018 -1 c(-1, -1.... human 41246187
#> 24 core BRCA1-017 -1 c(-1, -1.... human 41247863
#> 25 core BRCA1-020 -1 c("17", .... human 41251848
#> 26 core BRCA1-016 -1 c(1, 1, .... human 41256206
#> 27 core BRCA1-205 -1 c(412772.... human 41196313
#> 28 core BRCA1-204 -1 c("core".... human 41196313
#> 29 core BRCA1-202 -1 c(1, 1, .... human 41196313
#> 30 core BRCA1-203 -1 c("17", .... human 41196313
#> 31 core BRCA1-201 -1 c(412772.... human 41196313
#> object_type source end version logic_name
#> 1 Transcript ensembl_havana 41277387 3 ensembl_havana_transcript
#> 2 Transcript ensembl_havana 41277468 1 ensembl_havana_transcript
#> 3 Transcript havana 41277346 1 havana_homo_sapiens_37
#> 4 Transcript havana 41277346 1 havana_homo_sapiens_37
#> 5 Transcript havana 41277346 1 havana_homo_sapiens_37
#> 6 Transcript ensembl_havana 41277419 1 ensembl_havana_transcript
#> 7 Transcript ensembl_havana 41277500 2 ensembl_havana_transcript
#> 8 Transcript havana 41277305 1 havana_homo_sapiens_37
#> 9 Transcript havana 41277373 2 havana_homo_sapiens_37
#> 10 Transcript havana 41256933 1 havana_homo_sapiens_37
#> 11 Transcript havana 41277376 1 havana_homo_sapiens_37
#> 12 Transcript havana 41277419 1 havana_homo_sapiens_37
#> 13 Transcript havana 41223083 1 havana_homo_sapiens_37
#> 14 Transcript havana 41256933 1 havana_homo_sapiens_37
#> 15 Transcript havana 41243841 1 havana_homo_sapiens_37
#> 16 Transcript havana 41277332 1 havana_homo_sapiens_37
#> 17 Transcript havana 41247883 3 havana_homo_sapiens_37
#> 18 Transcript havana 41277340 1 havana_homo_sapiens_37
#> 19 Transcript havana 41277381 1 havana_homo_sapiens_37
#> 20 Transcript havana 41277317 1 havana_homo_sapiens_37
#> 21 Transcript havana 41277317 1 havana_homo_sapiens_37
#> 22 Transcript havana 41277467 1 havana_homo_sapiens_37
#> 23 Transcript havana 41256908 1 havana_homo_sapiens_37
#> 24 Transcript havana 41277370 1 havana_homo_sapiens_37
#> 25 Transcript havana 41277387 1 havana_homo_sapiens_37
#> 26 Transcript havana 41277338 1 havana_homo_sapiens_37
#> 27 Transcript ensembl 41277500 3 ensembl_homo_sapiens_37
#> 28 Transcript ensembl 41277500 3 ensembl_homo_sapiens_37
#> 29 Transcript ensembl 41277468 3 ensembl_homo_sapiens_37
#> 30 Transcript ensembl 41276132 3 ensembl_homo_sapiens_37
#> 31 Transcript ensembl 41277468 4 ensembl_homo_sapiens_37
#> biotype is_canonical seq_region_name Parent
#> 1 protein_coding 0 17 ENSG00000012048
#> 2 protein_coding 0 17 ENSG00000012048
#> 3 protein_coding 0 17 ENSG00000012048
#> 4 protein_coding 0 17 ENSG00000012048
#> 5 protein_coding 0 17 ENSG00000012048
#> 6 protein_coding 0 17 ENSG00000012048
#> 7 protein_coding 1 17 ENSG00000012048
#> 8 nonsense_mediated_decay 0 17 ENSG00000012048
#> 9 protein_coding 0 17 ENSG00000012048
#> 10 protein_coding 0 17 ENSG00000012048
#> 11 protein_coding 0 17 ENSG00000012048
#> 12 protein_coding 0 17 ENSG00000012048
#> 13 retained_intron 0 17 ENSG00000012048
#> 14 protein_coding 0 17 ENSG00000012048
#> 15 protein_coding 0 17 ENSG00000012048
#> 16 retained_intron 0 17 ENSG00000012048
#> 17 non_stop_decay 0 17 ENSG00000012048
#> 18 protein_coding 0 17 ENSG00000012048
#> 19 protein_coding 0 17 ENSG00000012048
#> 20 nonsense_mediated_decay 0 17 ENSG00000012048
#> 21 protein_coding 0 17 ENSG00000012048
#> 22 protein_coding 0 17 ENSG00000012048
#> 23 protein_coding 0 17 ENSG00000012048
#> 24 protein_coding 0 17 ENSG00000012048
#> 25 nonsense_mediated_decay 0 17 ENSG00000012048
#> 26 protein_coding 0 17 ENSG00000012048
#> 27 protein_coding 0 17 ENSG00000012048
#> 28 protein_coding 0 17 ENSG00000012048
#> 29 protein_coding 0 17 ENSG00000012048
#> 30 protein_coding 0 17 ENSG00000012048
#> 31 protein_coding 0 17 ENSG00000012048
#> id
#> 1 ENST00000357654
#> 2 ENST00000468300
#> 3 ENST00000586385
#> 4 ENST00000591534
#> 5 ENST00000591849
#> 6 ENST00000493795
#> 7 ENST00000471181
#> 8 ENST00000461221
#> 9 ENST00000491747
#> 10 ENST00000484087
#> 11 ENST00000478531
#> 12 ENST00000493919
#> 13 ENST00000472490
#> 14 ENST00000487825
#> 15 ENST00000461574
#> 16 ENST00000467274
#> 17 ENST00000412061
#> 18 ENST00000470026
#> 19 ENST00000477152
#> 20 ENST00000492859
#> 21 ENST00000497488
#> 22 ENST00000494123
#> 23 ENST00000473961
#> 24 ENST00000476777
#> 25 ENST00000461798
#> 26 ENST00000489037
#> 27 ENST00000354071
#> 28 ENST00000352993
#> 29 ENST00000346315
#> 30 ENST00000351666
#> 31 ENST00000309486
#>
queryEnsemblByGene("ENSG00000139618")
#> $assembly_name
#> [1] "GRCh37"
#>
#> $Transcript
#> id seq_region_name Parent is_canonical
#> 1 ENST00000380152 13 ENSG00000139618 0
#> 2 ENST00000530893 13 ENSG00000139618 0
#> 3 ENST00000528762 13 ENSG00000139618 0
#> 4 ENST00000470094 13 ENSG00000139618 0
#> 5 ENST00000533776 13 ENSG00000139618 0
#> 6 ENST00000544455 13 ENSG00000139618 1
#> biotype logic_name version end
#> 1 protein_coding ensembl_havana_transcript 3 32973347
#> 2 protein_coding havana_homo_sapiens_37 2 32907428
#> 3 nonsense_mediated_decay havana_homo_sapiens_37 1 32953632
#> 4 nonsense_mediated_decay havana_homo_sapiens_37 1 32972409
#> 5 retained_intron havana_homo_sapiens_37 1 32972585
#> 6 protein_coding ensembl_homo_sapiens_37 1 32973805
#> source object_type start species Exon display_name
#> 1 ensembl_havana Transcript 32889611 homo_sapiens c(328896.... BRCA2-001
#> 2 havana Transcript 32889642 homo_sapiens c("GRCh3.... BRCA2-003
#> 3 havana Transcript 32945108 homo_sapiens c("ENSE0.... BRCA2-005
#> 4 havana Transcript 32953977 homo_sapiens c("Exon".... BRCA2-002
#> 5 havana Transcript 32970946 homo_sapiens c(1, 1),.... BRCA2-006
#> 6 ensembl Transcript 32889617 homo_sapiens c("homo_.... BRCA2-201
#> Translation.start Translation.species Translation.Parent Translation.id
#> 1 32890598 homo_sapiens ENST00000380152 ENSP00000369497
#> 2 32899266 homo_sapiens ENST00000530893 ENSP00000435699
#> 3 32945108 homo_sapiens ENST00000528762 ENSP00000433168
#> 4 32953977 homo_sapiens ENST00000470094 ENSP00000434898
#> 5 NA <NA> <NA> <NA>
#> 6 32890598 homo_sapiens ENST00000544455 ENSP00000439902
#> Translation.db_type Translation.version Translation.length
#> 1 core 3 3418
#> 2 core 2 481
#> 3 core 1 64
#> 4 core 1 186
#> 5 <NA> NA NA
#> 6 core 1 3418
#> Translation.object_type Translation.end strand gencode_primary db_type
#> 1 Translation 32972907 1 0 core
#> 2 Translation 32907428 1 0 core
#> 3 Translation 32950807 1 0 core
#> 4 Translation 32970229 1 0 core
#> 5 <NA> NA 1 0 core
#> 6 Translation 32972907 1 0 core
#> assembly_name length
#> 1 GRCh37 10930
#> 2 GRCh37 2011
#> 3 GRCh37 495
#> 4 GRCh37 842
#> 5 GRCh37 523
#> 6 GRCh37 10984
#>
#> $db_type
#> [1] "core"
#>
#> $display_name
#> [1] "BRCA2"
#>
#> $strand
#> [1] 1
#>
#> $canonical_transcript
#> [1] "ENST00000544455.1"
#>
#> $start
#> [1] 32889611
#>
#> $species
#> [1] "homo_sapiens"
#>
#> $end
#> [1] 32973805
#>
#> $object_type
#> [1] "Gene"
#>
#> $description
#> [1] "breast cancer 2, early onset [Source:HGNC Symbol;Acc:1101]"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $version
#> [1] 10
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $seq_region_name
#> [1] "13"
#>
#> $id
#> [1] "ENSG00000139618"
#>
event <- "SE_17_-_41251792_41249306_41249261_41246877_BRCA1"
queryEnsemblByEvent(event, species="human", assembly="hg19")
#> $source
#> [1] "ensembl_havana"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $version
#> [1] 15
#>
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $display_name
#> [1] "BRCA1"
#>
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#>
#> $db_type
#> [1] "core"
#>
#> $object_type
#> [1] "Gene"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $end
#> [1] 41277500
#>
#> $Transcript
#> Translation.end Translation.id Translation.start Translation.species
#> 1 41276113 ENSP00000350283 41197695 human
#> 2 41276113 ENSP00000417148 41197801 human
#> 3 41277202 ENSP00000465818 41197695 human
#> 4 41226495 ENSP00000467329 41197695 human
#> 5 41202109 ENSP00000465347 41197695 human
#> 6 41258543 ENSP00000418775 41197695 human
#> 7 41276113 ENSP00000418960 41197695 human
#> 8 41276113 ENSP00000418548 41256972 human
#> 9 41276113 ENSP00000420705 41197695 human
#> 10 41256933 ENSP00000419481 41215361 human
#> 11 41276113 ENSP00000420412 41215361 human
#> 12 41258543 ENSP00000418819 41215377 human
#> 13 NA <NA> NA <NA>
#> 14 41256933 ENSP00000418212 41228505 human
#> 15 41243841 ENSP00000417241 41228554 human
#> 16 NA <NA> NA <NA>
#> 17 41247883 ENSP00000397145 41245587 human
#> 18 41276113 ENSP00000419274 41245601 human
#> 19 41276113 ENSP00000419988 41245603 human
#> 20 41276113 ENSP00000420253 41262552 human
#> 21 41246659 ENSP00000418986 41246129 human
#> 22 41276113 ENSP00000419103 41246129 human
#> 23 41256908 ENSP00000420201 41246187 human
#> 24 41276113 ENSP00000417554 41247863 human
#> 25 41276113 ENSP00000417988 41256972 human
#> 26 41276113 ENSP00000420781 41256206 human
#> 27 41276113 ENSP00000326002 41197695 human
#> 28 41276113 ENSP00000312236 41197695 human
#> 29 41276113 ENSP00000246907 41197695 human
#> 30 41276113 ENSP00000338007 41197695 human
#> 31 41246659 ENSP00000310938 41197695 human
#> Translation.db_type Translation.version Translation.Parent
#> 1 core 3 ENST00000357654
#> 2 core 1 ENST00000468300
#> 3 core 1 ENST00000586385
#> 4 core 1 ENST00000591534
#> 5 core 1 ENST00000591849
#> 6 core 1 ENST00000493795
#> 7 core 2 ENST00000471181
#> 8 core 1 ENST00000461221
#> 9 core 2 ENST00000491747
#> 10 core 1 ENST00000484087
#> 11 core 1 ENST00000478531
#> 12 core 1 ENST00000493919
#> 13 <NA> NA <NA>
#> 14 core 1 ENST00000487825
#> 15 core 1 ENST00000461574
#> 16 <NA> NA <NA>
#> 17 core 3 ENST00000412061
#> 18 core 1 ENST00000470026
#> 19 core 1 ENST00000477152
#> 20 core 1 ENST00000492859
#> 21 core 1 ENST00000497488
#> 22 core 1 ENST00000494123
#> 23 core 1 ENST00000473961
#> 24 core 1 ENST00000476777
#> 25 core 1 ENST00000461798
#> 26 core 1 ENST00000489037
#> 27 core 6 ENST00000354071
#> 28 core 5 ENST00000352993
#> 29 core 4 ENST00000346315
#> 30 core 3 ENST00000351666
#> 31 core 4 ENST00000309486
#> Translation.object_type Translation.length version biotype
#> 1 Translation 1863 3 protein_coding
#> 2 Translation 699 1 protein_coding
#> 3 Translation 173 1 protein_coding
#> 4 Translation 354 1 protein_coding
#> 5 Translation 96 1 protein_coding
#> 6 Translation 1816 1 protein_coding
#> 7 Translation 1884 2 protein_coding
#> 8 Translation 63 1 nonsense_mediated_decay
#> 9 Translation 759 2 protein_coding
#> 10 Translation 498 1 protein_coding
#> 11 Translation 623 1 protein_coding
#> 12 Translation 572 1 protein_coding
#> 13 <NA> NA 1 retained_intron
#> 14 Translation 266 1 protein_coding
#> 15 Translation 242 1 protein_coding
#> 16 <NA> NA 1 retained_intron
#> 17 Translation 437 3 non_stop_decay
#> 18 Translation 649 1 protein_coding
#> 19 Translation 622 1 protein_coding
#> 20 Translation 59 1 nonsense_mediated_decay
#> 21 Translation 177 1 protein_coding
#> 22 Translation 473 1 protein_coding
#> 23 Translation 319 1 protein_coding
#> 24 Translation 222 1 protein_coding
#> 25 Translation 63 1 nonsense_mediated_decay
#> 26 Translation 98 1 protein_coding
#> 27 Translation 1598 3 protein_coding
#> 28 Translation 721 3 protein_coding
#> 29 Translation 1624 3 protein_coding
#> 30 Translation 680 3 protein_coding
#> 31 Translation 1567 4 protein_coding
#> source is_canonical display_name assembly_name db_type
#> 1 ensembl_havana 0 BRCA1-001 GRCh37 core
#> 2 ensembl_havana 0 BRCA1-007 GRCh37 core
#> 3 havana 0 BRCA1-023 GRCh37 core
#> 4 havana 0 BRCA1-024 GRCh37 core
#> 5 havana 0 BRCA1-025 GRCh37 core
#> 6 ensembl_havana 0 BRCA1-006 GRCh37 core
#> 7 ensembl_havana 1 BRCA1-005 GRCh37 core
#> 8 havana 0 BRCA1-010 GRCh37 core
#> 9 havana 0 BRCA1-014 GRCh37 core
#> 10 havana 0 BRCA1-015 GRCh37 core
#> 11 havana 0 BRCA1-009 GRCh37 core
#> 12 havana 0 BRCA1-008 GRCh37 core
#> 13 havana 0 BRCA1-021 GRCh37 core
#> 14 havana 0 BRCA1-019 GRCh37 core
#> 15 havana 0 BRCA1-022 GRCh37 core
#> 16 havana 0 BRCA1-012 GRCh37 core
#> 17 havana 0 BRCA1-026 GRCh37 core
#> 18 havana 0 BRCA1-011 GRCh37 core
#> 19 havana 0 BRCA1-004 GRCh37 core
#> 20 havana 0 BRCA1-002 GRCh37 core
#> 21 havana 0 BRCA1-003 GRCh37 core
#> 22 havana 0 BRCA1-013 GRCh37 core
#> 23 havana 0 BRCA1-018 GRCh37 core
#> 24 havana 0 BRCA1-017 GRCh37 core
#> 25 havana 0 BRCA1-020 GRCh37 core
#> 26 havana 0 BRCA1-016 GRCh37 core
#> 27 ensembl 0 BRCA1-205 GRCh37 core
#> 28 ensembl 0 BRCA1-204 GRCh37 core
#> 29 ensembl 0 BRCA1-202 GRCh37 core
#> 30 ensembl 0 BRCA1-203 GRCh37 core
#> 31 ensembl 0 BRCA1-201 GRCh37 core
#> Parent length object_type end gencode_primary
#> 1 ENSG00000012048 7094 Transcript 41277387 0
#> 2 ENSG00000012048 3273 Transcript 41277468 0
#> 3 ENSG00000012048 781 Transcript 41277346 0
#> 4 ENSG00000012048 1282 Transcript 41277346 0
#> 5 ENSG00000012048 563 Transcript 41277346 0
#> 6 ENSG00000012048 5732 Transcript 41277419 0
#> 7 ENSG00000012048 5936 Transcript 41277500 0
#> 8 ENSG00000012048 5693 Transcript 41277305 0
#> 9 ENSG00000012048 2379 Transcript 41277373 0
#> 10 ENSG00000012048 1495 Transcript 41256933 0
#> 11 ENSG00000012048 1972 Transcript 41277376 0
#> 12 ENSG00000012048 1948 Transcript 41277419 0
#> 13 ENSG00000012048 561 Transcript 41223083 0
#> 14 ENSG00000012048 800 Transcript 41256933 0
#> 15 ENSG00000012048 726 Transcript 41243841 0
#> 16 ENSG00000012048 4497 Transcript 41277332 0
#> 17 ENSG00000012048 1312 Transcript 41247883 0
#> 18 ENSG00000012048 2108 Transcript 41277340 0
#> 19 ENSG00000012048 1980 Transcript 41277381 0
#> 20 ENSG00000012048 1584 Transcript 41277317 0
#> 21 ENSG00000012048 779 Transcript 41277317 0
#> 22 ENSG00000012048 1612 Transcript 41277467 0
#> 23 ENSG00000012048 958 Transcript 41256908 0
#> 24 ENSG00000012048 769 Transcript 41277370 0
#> 25 ENSG00000012048 582 Transcript 41277387 0
#> 26 ENSG00000012048 455 Transcript 41277338 0
#> 27 ENSG00000012048 6411 Transcript 41277500 0
#> 28 ENSG00000012048 3780 Transcript 41277500 0
#> 29 ENSG00000012048 6451 Transcript 41277468 0
#> 30 ENSG00000012048 3444 Transcript 41276132 0
#> 31 ENSG00000012048 7114 Transcript 41277468 0
#> logic_name Exon seq_region_name strand
#> 1 ensembl_havana_transcript c("GRCh3.... 17 -1
#> 2 ensembl_havana_transcript c(1, 1, .... 17 -1
#> 3 havana_homo_sapiens_37 c("GRCh3.... 17 -1
#> 4 havana_homo_sapiens_37 c(-1, -1.... 17 -1
#> 5 havana_homo_sapiens_37 c(1, 1, .... 17 -1
#> 6 ensembl_havana_transcript c(412774.... 17 -1
#> 7 ensembl_havana_transcript c(412775.... 17 -1
#> 8 havana_homo_sapiens_37 c(412773.... 17 -1
#> 9 havana_homo_sapiens_37 c("GRCh3.... 17 -1
#> 10 havana_homo_sapiens_37 c(1, 1, .... 17 -1
#> 11 havana_homo_sapiens_37 c(1, 1, .... 17 -1
#> 12 havana_homo_sapiens_37 c("17", .... 17 -1
#> 13 havana_homo_sapiens_37 c(1, 1),.... 17 -1
#> 14 havana_homo_sapiens_37 c("GRCh3.... 17 -1
#> 15 havana_homo_sapiens_37 c(1, 1, .... 17 -1
#> 16 havana_homo_sapiens_37 c("core".... 17 -1
#> 17 havana_homo_sapiens_37 c(1, 1),.... 17 -1
#> 18 havana_homo_sapiens_37 c("17", .... 17 -1
#> 19 havana_homo_sapiens_37 c("GRCh3.... 17 -1
#> 20 havana_homo_sapiens_37 c("GRCh3.... 17 -1
#> 21 havana_homo_sapiens_37 c("ENSE0.... 17 -1
#> 22 havana_homo_sapiens_37 c(1, 1, .... 17 -1
#> 23 havana_homo_sapiens_37 c("Exon".... 17 -1
#> 24 havana_homo_sapiens_37 c(1, 1, .... 17 -1
#> 25 havana_homo_sapiens_37 c(412773.... 17 -1
#> 26 havana_homo_sapiens_37 c("17", .... 17 -1
#> 27 ensembl_homo_sapiens_37 c(412775.... 17 -1
#> 28 ensembl_homo_sapiens_37 c(412775.... 17 -1
#> 29 ensembl_homo_sapiens_37 c("human.... 17 -1
#> 30 ensembl_homo_sapiens_37 c("core".... 17 -1
#> 31 ensembl_homo_sapiens_37 c(412774.... 17 -1
#> id species start
#> 1 ENST00000357654 human 41196312
#> 2 ENST00000468300 human 41196822
#> 3 ENST00000586385 human 41197580
#> 4 ENST00000591534 human 41197580
#> 5 ENST00000591849 human 41197580
#> 6 ENST00000493795 human 41197646
#> 7 ENST00000471181 human 41197646
#> 8 ENST00000461221 human 41197695
#> 9 ENST00000491747 human 41197695
#> 10 ENST00000484087 human 41215361
#> 11 ENST00000478531 human 41215361
#> 12 ENST00000493919 human 41215377
#> 13 ENST00000472490 human 41219291
#> 14 ENST00000487825 human 41228505
#> 15 ENST00000461574 human 41228554
#> 16 ENST00000467274 human 41243115
#> 17 ENST00000412061 human 41245587
#> 18 ENST00000470026 human 41245601
#> 19 ENST00000477152 human 41245603
#> 20 ENST00000492859 human 41246129
#> 21 ENST00000497488 human 41246129
#> 22 ENST00000494123 human 41246129
#> 23 ENST00000473961 human 41246187
#> 24 ENST00000476777 human 41247863
#> 25 ENST00000461798 human 41251848
#> 26 ENST00000489037 human 41256206
#> 27 ENST00000354071 human 41196313
#> 28 ENST00000352993 human 41196313
#> 29 ENST00000346315 human 41196313
#> 30 ENST00000351666 human 41196313
#> 31 ENST00000309486 human 41196313
#>
#> $id
#> [1] "ENSG00000012048"
#>
#> $start
#> [1] 41196312
#>
#> $species
#> [1] "human"
#>
#> $strand
#> [1] -1
#>
#> $seq_region_name
#> [1] "17"
#>