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"
#>
#> $species
#> [1] "human"
#>
#> $start
#> [1] 41196312
#>
#> $display_name
#> [1] "BRCA1"
#>
#> $strand
#> [1] -1
#>
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>
#> $db_type
#> [1] "core"
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $Transcript
#> version logic_name source object_type end
#> 1 3 ensembl_havana_transcript ensembl_havana Transcript 41277387
#> 2 1 ensembl_havana_transcript ensembl_havana Transcript 41277468
#> 3 1 havana_homo_sapiens_37 havana Transcript 41277346
#> 4 1 havana_homo_sapiens_37 havana Transcript 41277346
#> 5 1 havana_homo_sapiens_37 havana Transcript 41277346
#> 6 1 ensembl_havana_transcript ensembl_havana Transcript 41277419
#> 7 2 ensembl_havana_transcript ensembl_havana Transcript 41277500
#> 8 1 havana_homo_sapiens_37 havana Transcript 41277305
#> 9 2 havana_homo_sapiens_37 havana Transcript 41277373
#> 10 1 havana_homo_sapiens_37 havana Transcript 41256933
#> 11 1 havana_homo_sapiens_37 havana Transcript 41277376
#> 12 1 havana_homo_sapiens_37 havana Transcript 41277419
#> 13 1 havana_homo_sapiens_37 havana Transcript 41223083
#> 14 1 havana_homo_sapiens_37 havana Transcript 41256933
#> 15 1 havana_homo_sapiens_37 havana Transcript 41243841
#> 16 1 havana_homo_sapiens_37 havana Transcript 41277332
#> 17 3 havana_homo_sapiens_37 havana Transcript 41247883
#> 18 1 havana_homo_sapiens_37 havana Transcript 41277340
#> 19 1 havana_homo_sapiens_37 havana Transcript 41277381
#> 20 1 havana_homo_sapiens_37 havana Transcript 41277317
#> 21 1 havana_homo_sapiens_37 havana Transcript 41277317
#> 22 1 havana_homo_sapiens_37 havana Transcript 41277467
#> 23 1 havana_homo_sapiens_37 havana Transcript 41256908
#> 24 1 havana_homo_sapiens_37 havana Transcript 41277370
#> 25 1 havana_homo_sapiens_37 havana Transcript 41277387
#> 26 1 havana_homo_sapiens_37 havana Transcript 41277338
#> 27 3 ensembl_homo_sapiens_37 ensembl Transcript 41277500
#> 28 3 ensembl_homo_sapiens_37 ensembl Transcript 41277500
#> 29 3 ensembl_homo_sapiens_37 ensembl Transcript 41277468
#> 30 3 ensembl_homo_sapiens_37 ensembl Transcript 41276132
#> 31 4 ensembl_homo_sapiens_37 ensembl Transcript 41277468
#> is_canonical id seq_region_name Parent
#> 1 0 ENST00000357654 17 ENSG00000012048
#> 2 0 ENST00000468300 17 ENSG00000012048
#> 3 0 ENST00000586385 17 ENSG00000012048
#> 4 0 ENST00000591534 17 ENSG00000012048
#> 5 0 ENST00000591849 17 ENSG00000012048
#> 6 0 ENST00000493795 17 ENSG00000012048
#> 7 1 ENST00000471181 17 ENSG00000012048
#> 8 0 ENST00000461221 17 ENSG00000012048
#> 9 0 ENST00000491747 17 ENSG00000012048
#> 10 0 ENST00000484087 17 ENSG00000012048
#> 11 0 ENST00000478531 17 ENSG00000012048
#> 12 0 ENST00000493919 17 ENSG00000012048
#> 13 0 ENST00000472490 17 ENSG00000012048
#> 14 0 ENST00000487825 17 ENSG00000012048
#> 15 0 ENST00000461574 17 ENSG00000012048
#> 16 0 ENST00000467274 17 ENSG00000012048
#> 17 0 ENST00000412061 17 ENSG00000012048
#> 18 0 ENST00000470026 17 ENSG00000012048
#> 19 0 ENST00000477152 17 ENSG00000012048
#> 20 0 ENST00000492859 17 ENSG00000012048
#> 21 0 ENST00000497488 17 ENSG00000012048
#> 22 0 ENST00000494123 17 ENSG00000012048
#> 23 0 ENST00000473961 17 ENSG00000012048
#> 24 0 ENST00000476777 17 ENSG00000012048
#> 25 0 ENST00000461798 17 ENSG00000012048
#> 26 0 ENST00000489037 17 ENSG00000012048
#> 27 0 ENST00000354071 17 ENSG00000012048
#> 28 0 ENST00000352993 17 ENSG00000012048
#> 29 0 ENST00000346315 17 ENSG00000012048
#> 30 0 ENST00000351666 17 ENSG00000012048
#> 31 0 ENST00000309486 17 ENSG00000012048
#> biotype db_type length assembly_name start species
#> 1 protein_coding core 7094 GRCh37 41196312 human
#> 2 protein_coding core 3273 GRCh37 41196822 human
#> 3 protein_coding core 781 GRCh37 41197580 human
#> 4 protein_coding core 1282 GRCh37 41197580 human
#> 5 protein_coding core 563 GRCh37 41197580 human
#> 6 protein_coding core 5732 GRCh37 41197646 human
#> 7 protein_coding core 5936 GRCh37 41197646 human
#> 8 nonsense_mediated_decay core 5693 GRCh37 41197695 human
#> 9 protein_coding core 2379 GRCh37 41197695 human
#> 10 protein_coding core 1495 GRCh37 41215361 human
#> 11 protein_coding core 1972 GRCh37 41215361 human
#> 12 protein_coding core 1948 GRCh37 41215377 human
#> 13 retained_intron core 561 GRCh37 41219291 human
#> 14 protein_coding core 800 GRCh37 41228505 human
#> 15 protein_coding core 726 GRCh37 41228554 human
#> 16 retained_intron core 4497 GRCh37 41243115 human
#> 17 non_stop_decay core 1312 GRCh37 41245587 human
#> 18 protein_coding core 2108 GRCh37 41245601 human
#> 19 protein_coding core 1980 GRCh37 41245603 human
#> 20 nonsense_mediated_decay core 1584 GRCh37 41246129 human
#> 21 protein_coding core 779 GRCh37 41246129 human
#> 22 protein_coding core 1612 GRCh37 41246129 human
#> 23 protein_coding core 958 GRCh37 41246187 human
#> 24 protein_coding core 769 GRCh37 41247863 human
#> 25 nonsense_mediated_decay core 582 GRCh37 41251848 human
#> 26 protein_coding core 455 GRCh37 41256206 human
#> 27 protein_coding core 6411 GRCh37 41196313 human
#> 28 protein_coding core 3780 GRCh37 41196313 human
#> 29 protein_coding core 6451 GRCh37 41196313 human
#> 30 protein_coding core 3444 GRCh37 41196313 human
#> 31 protein_coding core 7114 GRCh37 41196313 human
#> gencode_primary Exon strand Translation.end Translation.object_type
#> 1 0 c(1, 1, .... -1 41276113 Translation
#> 2 0 c("GRCh3.... -1 41276113 Translation
#> 3 0 c("GRCh3.... -1 41277202 Translation
#> 4 0 c(-1, -1.... -1 41226495 Translation
#> 5 0 c("ENSE0.... -1 41202109 Translation
#> 6 0 c("Exon".... -1 41258543 Translation
#> 7 0 c("GRCh3.... -1 41276113 Translation
#> 8 0 c(412773.... -1 41276113 Translation
#> 9 0 c("GRCh3.... -1 41276113 Translation
#> 10 0 c(1, 1, .... -1 41256933 Translation
#> 11 0 c("human.... -1 41276113 Translation
#> 12 0 c("core".... -1 41258543 Translation
#> 13 0 c("core".... -1 NA <NA>
#> 14 0 c("ENSE0.... -1 41256933 Translation
#> 15 0 c("ENSE0.... -1 41243841 Translation
#> 16 0 c("Exon".... -1 NA <NA>
#> 17 0 c("ENSE0.... -1 41247883 Translation
#> 18 0 c("Exon".... -1 41276113 Translation
#> 19 0 c(-1, -1.... -1 41276113 Translation
#> 20 0 c(-1, -1.... -1 41276113 Translation
#> 21 0 c(-1, -1.... -1 41246659 Translation
#> 22 0 c("GRCh3.... -1 41276113 Translation
#> 23 0 c(412568.... -1 41256908 Translation
#> 24 0 c("core".... -1 41276113 Translation
#> 25 0 c("core".... -1 41276113 Translation
#> 26 0 c(-1, -1.... -1 41276113 Translation
#> 27 0 c("ENSE0.... -1 41276113 Translation
#> 28 0 c("GRCh3.... -1 41276113 Translation
#> 29 0 c("core".... -1 41276113 Translation
#> 30 0 c(412760.... -1 41276113 Translation
#> 31 0 c(412772.... -1 41246659 Translation
#> Translation.length Translation.db_type Translation.version
#> 1 1863 core 3
#> 2 699 core 1
#> 3 173 core 1
#> 4 354 core 1
#> 5 96 core 1
#> 6 1816 core 1
#> 7 1884 core 2
#> 8 63 core 1
#> 9 759 core 2
#> 10 498 core 1
#> 11 623 core 1
#> 12 572 core 1
#> 13 NA <NA> NA
#> 14 266 core 1
#> 15 242 core 1
#> 16 NA <NA> NA
#> 17 437 core 3
#> 18 649 core 1
#> 19 622 core 1
#> 20 59 core 1
#> 21 177 core 1
#> 22 473 core 1
#> 23 319 core 1
#> 24 222 core 1
#> 25 63 core 1
#> 26 98 core 1
#> 27 1598 core 6
#> 28 721 core 5
#> 29 1624 core 4
#> 30 680 core 3
#> 31 1567 core 4
#> Translation.Parent Translation.id Translation.start Translation.species
#> 1 ENST00000357654 ENSP00000350283 41197695 human
#> 2 ENST00000468300 ENSP00000417148 41197801 human
#> 3 ENST00000586385 ENSP00000465818 41197695 human
#> 4 ENST00000591534 ENSP00000467329 41197695 human
#> 5 ENST00000591849 ENSP00000465347 41197695 human
#> 6 ENST00000493795 ENSP00000418775 41197695 human
#> 7 ENST00000471181 ENSP00000418960 41197695 human
#> 8 ENST00000461221 ENSP00000418548 41256972 human
#> 9 ENST00000491747 ENSP00000420705 41197695 human
#> 10 ENST00000484087 ENSP00000419481 41215361 human
#> 11 ENST00000478531 ENSP00000420412 41215361 human
#> 12 ENST00000493919 ENSP00000418819 41215377 human
#> 13 <NA> <NA> NA <NA>
#> 14 ENST00000487825 ENSP00000418212 41228505 human
#> 15 ENST00000461574 ENSP00000417241 41228554 human
#> 16 <NA> <NA> NA <NA>
#> 17 ENST00000412061 ENSP00000397145 41245587 human
#> 18 ENST00000470026 ENSP00000419274 41245601 human
#> 19 ENST00000477152 ENSP00000419988 41245603 human
#> 20 ENST00000492859 ENSP00000420253 41262552 human
#> 21 ENST00000497488 ENSP00000418986 41246129 human
#> 22 ENST00000494123 ENSP00000419103 41246129 human
#> 23 ENST00000473961 ENSP00000420201 41246187 human
#> 24 ENST00000476777 ENSP00000417554 41247863 human
#> 25 ENST00000461798 ENSP00000417988 41256972 human
#> 26 ENST00000489037 ENSP00000420781 41256206 human
#> 27 ENST00000354071 ENSP00000326002 41197695 human
#> 28 ENST00000352993 ENSP00000312236 41197695 human
#> 29 ENST00000346315 ENSP00000246907 41197695 human
#> 30 ENST00000351666 ENSP00000338007 41197695 human
#> 31 ENST00000309486 ENSP00000310938 41197695 human
#> display_name
#> 1 BRCA1-001
#> 2 BRCA1-007
#> 3 BRCA1-023
#> 4 BRCA1-024
#> 5 BRCA1-025
#> 6 BRCA1-006
#> 7 BRCA1-005
#> 8 BRCA1-010
#> 9 BRCA1-014
#> 10 BRCA1-015
#> 11 BRCA1-009
#> 12 BRCA1-008
#> 13 BRCA1-021
#> 14 BRCA1-019
#> 15 BRCA1-022
#> 16 BRCA1-012
#> 17 BRCA1-026
#> 18 BRCA1-011
#> 19 BRCA1-004
#> 20 BRCA1-002
#> 21 BRCA1-003
#> 22 BRCA1-013
#> 23 BRCA1-018
#> 24 BRCA1-017
#> 25 BRCA1-020
#> 26 BRCA1-016
#> 27 BRCA1-205
#> 28 BRCA1-204
#> 29 BRCA1-202
#> 30 BRCA1-203
#> 31 BRCA1-201
#>
queryEnsemblByGene("ENSG00000139618")
#> $assembly_name
#> [1] "GRCh37"
#>
#> $seq_region_name
#> [1] "13"
#>
#> $Transcript
#> seq_region_name is_canonical Exon assembly_name species version
#> 1 13 0 c(328896.... GRCh37 homo_sapiens 3
#> 2 13 0 c("GRCh3.... GRCh37 homo_sapiens 2
#> 3 13 0 c("Exon".... GRCh37 homo_sapiens 1
#> 4 13 0 c("GRCh3.... GRCh37 homo_sapiens 1
#> 5 13 0 c(329711.... GRCh37 homo_sapiens 1
#> 6 13 1 c(1, 1, .... GRCh37 homo_sapiens 1
#> gencode_primary source display_name start Translation.id
#> 1 0 ensembl_havana BRCA2-001 32889611 ENSP00000369497
#> 2 0 havana BRCA2-003 32889642 ENSP00000435699
#> 3 0 havana BRCA2-005 32945108 ENSP00000433168
#> 4 0 havana BRCA2-002 32953977 ENSP00000434898
#> 5 0 havana BRCA2-006 32970946 <NA>
#> 6 0 ensembl BRCA2-201 32889617 ENSP00000439902
#> Translation.Parent Translation.object_type Translation.end Translation.length
#> 1 ENST00000380152 Translation 32972907 3418
#> 2 ENST00000530893 Translation 32907428 481
#> 3 ENST00000528762 Translation 32950807 64
#> 4 ENST00000470094 Translation 32970229 186
#> 5 <NA> <NA> NA NA
#> 6 ENST00000544455 Translation 32972907 3418
#> Translation.species Translation.version Translation.start Translation.db_type
#> 1 homo_sapiens 3 32890598 core
#> 2 homo_sapiens 2 32899266 core
#> 3 homo_sapiens 1 32945108 core
#> 4 homo_sapiens 1 32953977 core
#> 5 <NA> NA NA <NA>
#> 6 homo_sapiens 1 32890598 core
#> id Parent length object_type end
#> 1 ENST00000380152 ENSG00000139618 10930 Transcript 32973347
#> 2 ENST00000530893 ENSG00000139618 2011 Transcript 32907428
#> 3 ENST00000528762 ENSG00000139618 495 Transcript 32953632
#> 4 ENST00000470094 ENSG00000139618 842 Transcript 32972409
#> 5 ENST00000533776 ENSG00000139618 523 Transcript 32972585
#> 6 ENST00000544455 ENSG00000139618 10984 Transcript 32973805
#> biotype db_type logic_name strand
#> 1 protein_coding core ensembl_havana_transcript 1
#> 2 protein_coding core havana_homo_sapiens_37 1
#> 3 nonsense_mediated_decay core havana_homo_sapiens_37 1
#> 4 nonsense_mediated_decay core havana_homo_sapiens_37 1
#> 5 retained_intron core havana_homo_sapiens_37 1
#> 6 protein_coding core ensembl_homo_sapiens_37 1
#>
#> $start
#> [1] 32889611
#>
#> $display_name
#> [1] "BRCA2"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $version
#> [1] 10
#>
#> $species
#> [1] "homo_sapiens"
#>
#> $description
#> [1] "breast cancer 2, early onset [Source:HGNC Symbol;Acc:1101]"
#>
#> $id
#> [1] "ENSG00000139618"
#>
#> $canonical_transcript
#> [1] "ENST00000544455.1"
#>
#> $strand
#> [1] 1
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $db_type
#> [1] "core"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $end
#> [1] 32973805
#>
#> $object_type
#> [1] "Gene"
#>
event <- "SE_17_-_41251792_41249306_41249261_41246877_BRCA1"
queryEnsemblByEvent(event, species="human", assembly="hg19")
#> $species
#> [1] "human"
#>
#> $Transcript
#> id biotype logic_name version
#> 1 ENST00000357654 protein_coding ensembl_havana_transcript 3
#> 2 ENST00000468300 protein_coding ensembl_havana_transcript 1
#> 3 ENST00000586385 protein_coding havana_homo_sapiens_37 1
#> 4 ENST00000591534 protein_coding havana_homo_sapiens_37 1
#> 5 ENST00000591849 protein_coding havana_homo_sapiens_37 1
#> 6 ENST00000493795 protein_coding ensembl_havana_transcript 1
#> 7 ENST00000471181 protein_coding ensembl_havana_transcript 2
#> 8 ENST00000461221 nonsense_mediated_decay havana_homo_sapiens_37 1
#> 9 ENST00000491747 protein_coding havana_homo_sapiens_37 2
#> 10 ENST00000484087 protein_coding havana_homo_sapiens_37 1
#> 11 ENST00000478531 protein_coding havana_homo_sapiens_37 1
#> 12 ENST00000493919 protein_coding havana_homo_sapiens_37 1
#> 13 ENST00000472490 retained_intron havana_homo_sapiens_37 1
#> 14 ENST00000487825 protein_coding havana_homo_sapiens_37 1
#> 15 ENST00000461574 protein_coding havana_homo_sapiens_37 1
#> 16 ENST00000467274 retained_intron havana_homo_sapiens_37 1
#> 17 ENST00000412061 non_stop_decay havana_homo_sapiens_37 3
#> 18 ENST00000470026 protein_coding havana_homo_sapiens_37 1
#> 19 ENST00000477152 protein_coding havana_homo_sapiens_37 1
#> 20 ENST00000492859 nonsense_mediated_decay havana_homo_sapiens_37 1
#> 21 ENST00000497488 protein_coding havana_homo_sapiens_37 1
#> 22 ENST00000494123 protein_coding havana_homo_sapiens_37 1
#> 23 ENST00000473961 protein_coding havana_homo_sapiens_37 1
#> 24 ENST00000476777 protein_coding havana_homo_sapiens_37 1
#> 25 ENST00000461798 nonsense_mediated_decay havana_homo_sapiens_37 1
#> 26 ENST00000489037 protein_coding havana_homo_sapiens_37 1
#> 27 ENST00000354071 protein_coding ensembl_homo_sapiens_37 3
#> 28 ENST00000352993 protein_coding ensembl_homo_sapiens_37 3
#> 29 ENST00000346315 protein_coding ensembl_homo_sapiens_37 3
#> 30 ENST00000351666 protein_coding ensembl_homo_sapiens_37 3
#> 31 ENST00000309486 protein_coding ensembl_homo_sapiens_37 4
#> seq_region_name Translation.object_type Translation.version
#> 1 17 Translation 3
#> 2 17 Translation 1
#> 3 17 Translation 1
#> 4 17 Translation 1
#> 5 17 Translation 1
#> 6 17 Translation 1
#> 7 17 Translation 2
#> 8 17 Translation 1
#> 9 17 Translation 2
#> 10 17 Translation 1
#> 11 17 Translation 1
#> 12 17 Translation 1
#> 13 17 <NA> NA
#> 14 17 Translation 1
#> 15 17 Translation 1
#> 16 17 <NA> NA
#> 17 17 Translation 3
#> 18 17 Translation 1
#> 19 17 Translation 1
#> 20 17 Translation 1
#> 21 17 Translation 1
#> 22 17 Translation 1
#> 23 17 Translation 1
#> 24 17 Translation 1
#> 25 17 Translation 1
#> 26 17 Translation 1
#> 27 17 Translation 6
#> 28 17 Translation 5
#> 29 17 Translation 4
#> 30 17 Translation 3
#> 31 17 Translation 4
#> Translation.start Translation.id Translation.length Translation.species
#> 1 41197695 ENSP00000350283 1863 human
#> 2 41197801 ENSP00000417148 699 human
#> 3 41197695 ENSP00000465818 173 human
#> 4 41197695 ENSP00000467329 354 human
#> 5 41197695 ENSP00000465347 96 human
#> 6 41197695 ENSP00000418775 1816 human
#> 7 41197695 ENSP00000418960 1884 human
#> 8 41256972 ENSP00000418548 63 human
#> 9 41197695 ENSP00000420705 759 human
#> 10 41215361 ENSP00000419481 498 human
#> 11 41215361 ENSP00000420412 623 human
#> 12 41215377 ENSP00000418819 572 human
#> 13 NA <NA> NA <NA>
#> 14 41228505 ENSP00000418212 266 human
#> 15 41228554 ENSP00000417241 242 human
#> 16 NA <NA> NA <NA>
#> 17 41245587 ENSP00000397145 437 human
#> 18 41245601 ENSP00000419274 649 human
#> 19 41245603 ENSP00000419988 622 human
#> 20 41262552 ENSP00000420253 59 human
#> 21 41246129 ENSP00000418986 177 human
#> 22 41246129 ENSP00000419103 473 human
#> 23 41246187 ENSP00000420201 319 human
#> 24 41247863 ENSP00000417554 222 human
#> 25 41256972 ENSP00000417988 63 human
#> 26 41256206 ENSP00000420781 98 human
#> 27 41197695 ENSP00000326002 1598 human
#> 28 41197695 ENSP00000312236 721 human
#> 29 41197695 ENSP00000246907 1624 human
#> 30 41197695 ENSP00000338007 680 human
#> 31 41197695 ENSP00000310938 1567 human
#> Translation.db_type Translation.Parent Translation.end end strand
#> 1 core ENST00000357654 41276113 41277387 -1
#> 2 core ENST00000468300 41276113 41277468 -1
#> 3 core ENST00000586385 41277202 41277346 -1
#> 4 core ENST00000591534 41226495 41277346 -1
#> 5 core ENST00000591849 41202109 41277346 -1
#> 6 core ENST00000493795 41258543 41277419 -1
#> 7 core ENST00000471181 41276113 41277500 -1
#> 8 core ENST00000461221 41276113 41277305 -1
#> 9 core ENST00000491747 41276113 41277373 -1
#> 10 core ENST00000484087 41256933 41256933 -1
#> 11 core ENST00000478531 41276113 41277376 -1
#> 12 core ENST00000493919 41258543 41277419 -1
#> 13 <NA> <NA> NA 41223083 -1
#> 14 core ENST00000487825 41256933 41256933 -1
#> 15 core ENST00000461574 41243841 41243841 -1
#> 16 <NA> <NA> NA 41277332 -1
#> 17 core ENST00000412061 41247883 41247883 -1
#> 18 core ENST00000470026 41276113 41277340 -1
#> 19 core ENST00000477152 41276113 41277381 -1
#> 20 core ENST00000492859 41276113 41277317 -1
#> 21 core ENST00000497488 41246659 41277317 -1
#> 22 core ENST00000494123 41276113 41277467 -1
#> 23 core ENST00000473961 41256908 41256908 -1
#> 24 core ENST00000476777 41276113 41277370 -1
#> 25 core ENST00000461798 41276113 41277387 -1
#> 26 core ENST00000489037 41276113 41277338 -1
#> 27 core ENST00000354071 41276113 41277500 -1
#> 28 core ENST00000352993 41276113 41277500 -1
#> 29 core ENST00000346315 41276113 41277468 -1
#> 30 core ENST00000351666 41276113 41276132 -1
#> 31 core ENST00000309486 41246659 41277468 -1
#> gencode_primary db_type Parent length object_type display_name
#> 1 0 core ENSG00000012048 7094 Transcript BRCA1-001
#> 2 0 core ENSG00000012048 3273 Transcript BRCA1-007
#> 3 0 core ENSG00000012048 781 Transcript BRCA1-023
#> 4 0 core ENSG00000012048 1282 Transcript BRCA1-024
#> 5 0 core ENSG00000012048 563 Transcript BRCA1-025
#> 6 0 core ENSG00000012048 5732 Transcript BRCA1-006
#> 7 0 core ENSG00000012048 5936 Transcript BRCA1-005
#> 8 0 core ENSG00000012048 5693 Transcript BRCA1-010
#> 9 0 core ENSG00000012048 2379 Transcript BRCA1-014
#> 10 0 core ENSG00000012048 1495 Transcript BRCA1-015
#> 11 0 core ENSG00000012048 1972 Transcript BRCA1-009
#> 12 0 core ENSG00000012048 1948 Transcript BRCA1-008
#> 13 0 core ENSG00000012048 561 Transcript BRCA1-021
#> 14 0 core ENSG00000012048 800 Transcript BRCA1-019
#> 15 0 core ENSG00000012048 726 Transcript BRCA1-022
#> 16 0 core ENSG00000012048 4497 Transcript BRCA1-012
#> 17 0 core ENSG00000012048 1312 Transcript BRCA1-026
#> 18 0 core ENSG00000012048 2108 Transcript BRCA1-011
#> 19 0 core ENSG00000012048 1980 Transcript BRCA1-004
#> 20 0 core ENSG00000012048 1584 Transcript BRCA1-002
#> 21 0 core ENSG00000012048 779 Transcript BRCA1-003
#> 22 0 core ENSG00000012048 1612 Transcript BRCA1-013
#> 23 0 core ENSG00000012048 958 Transcript BRCA1-018
#> 24 0 core ENSG00000012048 769 Transcript BRCA1-017
#> 25 0 core ENSG00000012048 582 Transcript BRCA1-020
#> 26 0 core ENSG00000012048 455 Transcript BRCA1-016
#> 27 0 core ENSG00000012048 6411 Transcript BRCA1-205
#> 28 0 core ENSG00000012048 3780 Transcript BRCA1-204
#> 29 0 core ENSG00000012048 6451 Transcript BRCA1-202
#> 30 0 core ENSG00000012048 3444 Transcript BRCA1-203
#> 31 0 core ENSG00000012048 7114 Transcript BRCA1-201
#> start Exon source assembly_name species is_canonical
#> 1 41196312 c("human.... ensembl_havana GRCh37 human 0
#> 2 41196822 c("core".... ensembl_havana GRCh37 human 0
#> 3 41197580 c("ENSE0.... havana GRCh37 human 0
#> 4 41197580 c("core".... havana GRCh37 human 0
#> 5 41197580 c(1, 1, .... havana GRCh37 human 0
#> 6 41197646 c("ENSE0.... ensembl_havana GRCh37 human 0
#> 7 41197646 c("ENSE0.... ensembl_havana GRCh37 human 1
#> 8 41197695 c("GRCh3.... havana GRCh37 human 0
#> 9 41197695 c(412773.... havana GRCh37 human 0
#> 10 41215361 c("GRCh3.... havana GRCh37 human 0
#> 11 41215361 c(412773.... havana GRCh37 human 0
#> 12 41215377 c("Exon".... havana GRCh37 human 0
#> 13 41219291 c("17", .... havana GRCh37 human 0
#> 14 41228505 c("Exon".... havana GRCh37 human 0
#> 15 41228554 c("core".... havana GRCh37 human 0
#> 16 41243115 c("ENSE0.... havana GRCh37 human 0
#> 17 41245587 c("ENSE0.... havana GRCh37 human 0
#> 18 41245601 c("17", .... havana GRCh37 human 0
#> 19 41245603 c("GRCh3.... havana GRCh37 human 0
#> 20 41246129 c("human.... havana GRCh37 human 0
#> 21 41246129 c("human.... havana GRCh37 human 0
#> 22 41246129 c("ENSE0.... havana GRCh37 human 0
#> 23 41246187 c(-1, -1.... havana GRCh37 human 0
#> 24 41247863 c("GRCh3.... havana GRCh37 human 0
#> 25 41251848 c("17", .... havana GRCh37 human 0
#> 26 41256206 c("core".... havana GRCh37 human 0
#> 27 41196313 c("ENSE0.... ensembl GRCh37 human 0
#> 28 41196313 c("GRCh3.... ensembl GRCh37 human 0
#> 29 41196313 c("human.... ensembl GRCh37 human 0
#> 30 41196313 c(412760.... ensembl GRCh37 human 0
#> 31 41196313 c("Exon".... ensembl GRCh37 human 0
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $display_name
#> [1] "BRCA1"
#>
#> $start
#> [1] 41196312
#>
#> $object_type
#> [1] "Gene"
#>
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>
#> $db_type
#> [1] "core"
#>
#> $end
#> [1] 41277500
#>
#> $strand
#> [1] -1
#>
#> $seq_region_name
#> [1] "17"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#>
#> $version
#> [1] 15
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $id
#> [1] "ENSG00000012048"
#>