Query information from Ensembl
Usage
queryEnsemblByGene(gene, species = NULL, assembly = NULL)
queryEnsemblByEvent(event, species = NULL, assembly = NULL, data = NULL)Arguments
- gene
Character: gene
- species
Character: species (may be
NULLfor an Ensembl identifier)- assembly
Character: assembly version (may be NULL for an Ensembl identifier)
- event
Character: alternative splicing event
- data
Matrix or data frame: alternative splicing information
See also
Other functions to retrieve external information:
ensemblToUniprot(),
plotProtein(),
plotTranscripts()
Examples
queryEnsemblByGene("BRCA1", "human", "hg19")
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>
#> $start
#> [1] 41196312
#>
#> $db_type
#> [1] "core"
#>
#> $Transcript
#> species object_type version assembly_name seq_region_name source
#> 1 human Transcript 3 GRCh37 17 ensembl_havana
#> 2 human Transcript 1 GRCh37 17 ensembl_havana
#> 3 human Transcript 1 GRCh37 17 havana
#> 4 human Transcript 1 GRCh37 17 havana
#> 5 human Transcript 1 GRCh37 17 havana
#> 6 human Transcript 1 GRCh37 17 ensembl_havana
#> 7 human Transcript 2 GRCh37 17 ensembl_havana
#> 8 human Transcript 1 GRCh37 17 havana
#> 9 human Transcript 2 GRCh37 17 havana
#> 10 human Transcript 1 GRCh37 17 havana
#> 11 human Transcript 1 GRCh37 17 havana
#> 12 human Transcript 1 GRCh37 17 havana
#> 13 human Transcript 1 GRCh37 17 havana
#> 14 human Transcript 1 GRCh37 17 havana
#> 15 human Transcript 1 GRCh37 17 havana
#> 16 human Transcript 1 GRCh37 17 havana
#> 17 human Transcript 3 GRCh37 17 havana
#> 18 human Transcript 1 GRCh37 17 havana
#> 19 human Transcript 1 GRCh37 17 havana
#> 20 human Transcript 1 GRCh37 17 havana
#> 21 human Transcript 1 GRCh37 17 havana
#> 22 human Transcript 1 GRCh37 17 havana
#> 23 human Transcript 1 GRCh37 17 havana
#> 24 human Transcript 1 GRCh37 17 havana
#> 25 human Transcript 1 GRCh37 17 havana
#> 26 human Transcript 1 GRCh37 17 havana
#> 27 human Transcript 3 GRCh37 17 ensembl
#> 28 human Transcript 3 GRCh37 17 ensembl
#> 29 human Transcript 3 GRCh37 17 ensembl
#> 30 human Transcript 3 GRCh37 17 ensembl
#> 31 human Transcript 4 GRCh37 17 ensembl
#> end strand logic_name display_name db_type start
#> 1 41277387 -1 ensembl_havana_transcript BRCA1-001 core 41196312
#> 2 41277468 -1 ensembl_havana_transcript BRCA1-007 core 41196822
#> 3 41277346 -1 havana_homo_sapiens_37 BRCA1-023 core 41197580
#> 4 41277346 -1 havana_homo_sapiens_37 BRCA1-024 core 41197580
#> 5 41277346 -1 havana_homo_sapiens_37 BRCA1-025 core 41197580
#> 6 41277419 -1 ensembl_havana_transcript BRCA1-006 core 41197646
#> 7 41277500 -1 ensembl_havana_transcript BRCA1-005 core 41197646
#> 8 41277305 -1 havana_homo_sapiens_37 BRCA1-010 core 41197695
#> 9 41277373 -1 havana_homo_sapiens_37 BRCA1-014 core 41197695
#> 10 41256933 -1 havana_homo_sapiens_37 BRCA1-015 core 41215361
#> 11 41277376 -1 havana_homo_sapiens_37 BRCA1-009 core 41215361
#> 12 41277419 -1 havana_homo_sapiens_37 BRCA1-008 core 41215377
#> 13 41223083 -1 havana_homo_sapiens_37 BRCA1-021 core 41219291
#> 14 41256933 -1 havana_homo_sapiens_37 BRCA1-019 core 41228505
#> 15 41243841 -1 havana_homo_sapiens_37 BRCA1-022 core 41228554
#> 16 41277332 -1 havana_homo_sapiens_37 BRCA1-012 core 41243115
#> 17 41247883 -1 havana_homo_sapiens_37 BRCA1-026 core 41245587
#> 18 41277340 -1 havana_homo_sapiens_37 BRCA1-011 core 41245601
#> 19 41277381 -1 havana_homo_sapiens_37 BRCA1-004 core 41245603
#> 20 41277317 -1 havana_homo_sapiens_37 BRCA1-002 core 41246129
#> 21 41277317 -1 havana_homo_sapiens_37 BRCA1-003 core 41246129
#> 22 41277467 -1 havana_homo_sapiens_37 BRCA1-013 core 41246129
#> 23 41256908 -1 havana_homo_sapiens_37 BRCA1-018 core 41246187
#> 24 41277370 -1 havana_homo_sapiens_37 BRCA1-017 core 41247863
#> 25 41277387 -1 havana_homo_sapiens_37 BRCA1-020 core 41251848
#> 26 41277338 -1 havana_homo_sapiens_37 BRCA1-016 core 41256206
#> 27 41277500 -1 ensembl_homo_sapiens_37 BRCA1-205 core 41196313
#> 28 41277500 -1 ensembl_homo_sapiens_37 BRCA1-204 core 41196313
#> 29 41277468 -1 ensembl_homo_sapiens_37 BRCA1-202 core 41196313
#> 30 41276132 -1 ensembl_homo_sapiens_37 BRCA1-203 core 41196313
#> 31 41277468 -1 ensembl_homo_sapiens_37 BRCA1-201 core 41196313
#> id Exon Parent Translation.end
#> 1 ENST00000357654 c(-1, -1.... ENSG00000012048 41276113
#> 2 ENST00000468300 c("human.... ENSG00000012048 41276113
#> 3 ENST00000586385 c("core".... ENSG00000012048 41277202
#> 4 ENST00000591534 c("core".... ENSG00000012048 41226495
#> 5 ENST00000591849 c("ENSE0.... ENSG00000012048 41202109
#> 6 ENST00000493795 c("ENSE0.... ENSG00000012048 41258543
#> 7 ENST00000471181 c("human.... ENSG00000012048 41276113
#> 8 ENST00000461221 c("core".... ENSG00000012048 41276113
#> 9 ENST00000491747 c("Exon".... ENSG00000012048 41276113
#> 10 ENST00000484087 c("human.... ENSG00000012048 41256933
#> 11 ENST00000478531 c("ENSE0.... ENSG00000012048 41276113
#> 12 ENST00000493919 c("GRCh3.... ENSG00000012048 41258543
#> 13 ENST00000472490 c("ENSE0.... ENSG00000012048 NA
#> 14 ENST00000487825 c("17", .... ENSG00000012048 41256933
#> 15 ENST00000461574 c("ENSE0.... ENSG00000012048 41243841
#> 16 ENST00000467274 c("Exon".... ENSG00000012048 NA
#> 17 ENST00000412061 c("ENSE0.... ENSG00000012048 41247883
#> 18 ENST00000470026 c(1, 1, .... ENSG00000012048 41276113
#> 19 ENST00000477152 c(-1, -1.... ENSG00000012048 41276113
#> 20 ENST00000492859 c("GRCh3.... ENSG00000012048 41276113
#> 21 ENST00000497488 c("17", .... ENSG00000012048 41246659
#> 22 ENST00000494123 c("human.... ENSG00000012048 41276113
#> 23 ENST00000473961 c(-1, -1.... ENSG00000012048 41256908
#> 24 ENST00000476777 c(1, 1, .... ENSG00000012048 41276113
#> 25 ENST00000461798 c("human.... ENSG00000012048 41276113
#> 26 ENST00000489037 c(412773.... ENSG00000012048 41276113
#> 27 ENST00000354071 c(412775.... ENSG00000012048 41276113
#> 28 ENST00000352993 c("17", .... ENSG00000012048 41276113
#> 29 ENST00000346315 c("core".... ENSG00000012048 41276113
#> 30 ENST00000351666 c("ENSE0.... ENSG00000012048 41276113
#> 31 ENST00000309486 c("human.... ENSG00000012048 41246659
#> Translation.length Translation.id Translation.Parent Translation.start
#> 1 1863 ENSP00000350283 ENST00000357654 41197695
#> 2 699 ENSP00000417148 ENST00000468300 41197801
#> 3 173 ENSP00000465818 ENST00000586385 41197695
#> 4 354 ENSP00000467329 ENST00000591534 41197695
#> 5 96 ENSP00000465347 ENST00000591849 41197695
#> 6 1816 ENSP00000418775 ENST00000493795 41197695
#> 7 1884 ENSP00000418960 ENST00000471181 41197695
#> 8 63 ENSP00000418548 ENST00000461221 41256972
#> 9 759 ENSP00000420705 ENST00000491747 41197695
#> 10 498 ENSP00000419481 ENST00000484087 41215361
#> 11 623 ENSP00000420412 ENST00000478531 41215361
#> 12 572 ENSP00000418819 ENST00000493919 41215377
#> 13 NA <NA> <NA> NA
#> 14 266 ENSP00000418212 ENST00000487825 41228505
#> 15 242 ENSP00000417241 ENST00000461574 41228554
#> 16 NA <NA> <NA> NA
#> 17 437 ENSP00000397145 ENST00000412061 41245587
#> 18 649 ENSP00000419274 ENST00000470026 41245601
#> 19 622 ENSP00000419988 ENST00000477152 41245603
#> 20 59 ENSP00000420253 ENST00000492859 41262552
#> 21 177 ENSP00000418986 ENST00000497488 41246129
#> 22 473 ENSP00000419103 ENST00000494123 41246129
#> 23 319 ENSP00000420201 ENST00000473961 41246187
#> 24 222 ENSP00000417554 ENST00000476777 41247863
#> 25 63 ENSP00000417988 ENST00000461798 41256972
#> 26 98 ENSP00000420781 ENST00000489037 41256206
#> 27 1598 ENSP00000326002 ENST00000354071 41197695
#> 28 721 ENSP00000312236 ENST00000352993 41197695
#> 29 1624 ENSP00000246907 ENST00000346315 41197695
#> 30 680 ENSP00000338007 ENST00000351666 41197695
#> 31 1567 ENSP00000310938 ENST00000309486 41197695
#> Translation.species Translation.db_type Translation.version
#> 1 human core 3
#> 2 human core 1
#> 3 human core 1
#> 4 human core 1
#> 5 human core 1
#> 6 human core 1
#> 7 human core 2
#> 8 human core 1
#> 9 human core 2
#> 10 human core 1
#> 11 human core 1
#> 12 human core 1
#> 13 <NA> <NA> NA
#> 14 human core 1
#> 15 human core 1
#> 16 <NA> <NA> NA
#> 17 human core 3
#> 18 human core 1
#> 19 human core 1
#> 20 human core 1
#> 21 human core 1
#> 22 human core 1
#> 23 human core 1
#> 24 human core 1
#> 25 human core 1
#> 26 human core 1
#> 27 human core 6
#> 28 human core 5
#> 29 human core 4
#> 30 human core 3
#> 31 human core 4
#> Translation.object_type biotype is_canonical
#> 1 Translation protein_coding 0
#> 2 Translation protein_coding 0
#> 3 Translation protein_coding 0
#> 4 Translation protein_coding 0
#> 5 Translation protein_coding 0
#> 6 Translation protein_coding 0
#> 7 Translation protein_coding 1
#> 8 Translation nonsense_mediated_decay 0
#> 9 Translation protein_coding 0
#> 10 Translation protein_coding 0
#> 11 Translation protein_coding 0
#> 12 Translation protein_coding 0
#> 13 <NA> retained_intron 0
#> 14 Translation protein_coding 0
#> 15 Translation protein_coding 0
#> 16 <NA> retained_intron 0
#> 17 Translation non_stop_decay 0
#> 18 Translation protein_coding 0
#> 19 Translation protein_coding 0
#> 20 Translation nonsense_mediated_decay 0
#> 21 Translation protein_coding 0
#> 22 Translation protein_coding 0
#> 23 Translation protein_coding 0
#> 24 Translation protein_coding 0
#> 25 Translation nonsense_mediated_decay 0
#> 26 Translation protein_coding 0
#> 27 Translation protein_coding 0
#> 28 Translation protein_coding 0
#> 29 Translation protein_coding 0
#> 30 Translation protein_coding 0
#> 31 Translation protein_coding 0
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $id
#> [1] "ENSG00000012048"
#>
#> $seq_region_name
#> [1] "17"
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#>
#> $version
#> [1] 15
#>
#> $object_type
#> [1] "Gene"
#>
#> $species
#> [1] "human"
#>
#> $display_name
#> [1] "BRCA1"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $strand
#> [1] -1
#>
#> $end
#> [1] 41277500
#>
#> $source
#> [1] "ensembl_havana"
#>
queryEnsemblByGene("ENSG00000139618")
#> $assembly_name
#> [1] "GRCh37"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $description
#> [1] "breast cancer 2, early onset [Source:HGNC Symbol;Acc:1101]"
#>
#> $canonical_transcript
#> [1] "ENST00000544455.1"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $Transcript
#> is_canonical start object_type display_name seq_region_name source
#> 1 0 32889611 Transcript BRCA2-001 13 ensembl_havana
#> 2 0 32889642 Transcript BRCA2-003 13 havana
#> 3 0 32945108 Transcript BRCA2-005 13 havana
#> 4 0 32953977 Transcript BRCA2-002 13 havana
#> 5 0 32970946 Transcript BRCA2-006 13 havana
#> 6 1 32889617 Transcript BRCA2-201 13 ensembl
#> db_type Parent end strand version Translation.version
#> 1 core ENSG00000139618 32973347 1 3 3
#> 2 core ENSG00000139618 32907428 1 2 2
#> 3 core ENSG00000139618 32953632 1 1 1
#> 4 core ENSG00000139618 32972409 1 1 1
#> 5 core ENSG00000139618 32972585 1 1 NA
#> 6 core ENSG00000139618 32973805 1 1 1
#> Translation.length Translation.id Translation.species Translation.db_type
#> 1 3418 ENSP00000369497 homo_sapiens core
#> 2 481 ENSP00000435699 homo_sapiens core
#> 3 64 ENSP00000433168 homo_sapiens core
#> 4 186 ENSP00000434898 homo_sapiens core
#> 5 NA <NA> <NA> <NA>
#> 6 3418 ENSP00000439902 homo_sapiens core
#> Translation.end Translation.Parent Translation.start Translation.object_type
#> 1 32972907 ENST00000380152 32890598 Translation
#> 2 32907428 ENST00000530893 32899266 Translation
#> 3 32950807 ENST00000528762 32945108 Translation
#> 4 32970229 ENST00000470094 32953977 Translation
#> 5 NA <NA> NA <NA>
#> 6 32972907 ENST00000544455 32890598 Translation
#> id species Exon assembly_name
#> 1 ENST00000380152 homo_sapiens c(328896.... GRCh37
#> 2 ENST00000530893 homo_sapiens c("Exon".... GRCh37
#> 3 ENST00000528762 homo_sapiens c("homo_.... GRCh37
#> 4 ENST00000470094 homo_sapiens c("core".... GRCh37
#> 5 ENST00000533776 homo_sapiens c("13", .... GRCh37
#> 6 ENST00000544455 homo_sapiens c("Exon".... GRCh37
#> biotype logic_name
#> 1 protein_coding ensembl_havana_transcript
#> 2 protein_coding havana_homo_sapiens_37
#> 3 nonsense_mediated_decay havana_homo_sapiens_37
#> 4 nonsense_mediated_decay havana_homo_sapiens_37
#> 5 retained_intron havana_homo_sapiens_37
#> 6 protein_coding ensembl_homo_sapiens_37
#>
#> $display_name
#> [1] "BRCA2"
#>
#> $seq_region_name
#> [1] "13"
#>
#> $object_type
#> [1] "Gene"
#>
#> $start
#> [1] 32889611
#>
#> $strand
#> [1] 1
#>
#> $version
#> [1] 10
#>
#> $id
#> [1] "ENSG00000139618"
#>
#> $species
#> [1] "homo_sapiens"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $db_type
#> [1] "core"
#>
#> $end
#> [1] 32973805
#>
event <- "SE_17_-_41251792_41249306_41249261_41246877_BRCA1"
queryEnsemblByEvent(event, species="human", assembly="hg19")
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>
#> $Transcript
#> end object_type id biotype start
#> 1 41277387 Transcript ENST00000357654 protein_coding 41196312
#> 2 41277468 Transcript ENST00000468300 protein_coding 41196822
#> 3 41277346 Transcript ENST00000586385 protein_coding 41197580
#> 4 41277346 Transcript ENST00000591534 protein_coding 41197580
#> 5 41277346 Transcript ENST00000591849 protein_coding 41197580
#> 6 41277419 Transcript ENST00000493795 protein_coding 41197646
#> 7 41277500 Transcript ENST00000471181 protein_coding 41197646
#> 8 41277305 Transcript ENST00000461221 nonsense_mediated_decay 41197695
#> 9 41277373 Transcript ENST00000491747 protein_coding 41197695
#> 10 41256933 Transcript ENST00000484087 protein_coding 41215361
#> 11 41277376 Transcript ENST00000478531 protein_coding 41215361
#> 12 41277419 Transcript ENST00000493919 protein_coding 41215377
#> 13 41223083 Transcript ENST00000472490 retained_intron 41219291
#> 14 41256933 Transcript ENST00000487825 protein_coding 41228505
#> 15 41243841 Transcript ENST00000461574 protein_coding 41228554
#> 16 41277332 Transcript ENST00000467274 retained_intron 41243115
#> 17 41247883 Transcript ENST00000412061 non_stop_decay 41245587
#> 18 41277340 Transcript ENST00000470026 protein_coding 41245601
#> 19 41277381 Transcript ENST00000477152 protein_coding 41245603
#> 20 41277317 Transcript ENST00000492859 nonsense_mediated_decay 41246129
#> 21 41277317 Transcript ENST00000497488 protein_coding 41246129
#> 22 41277467 Transcript ENST00000494123 protein_coding 41246129
#> 23 41256908 Transcript ENST00000473961 protein_coding 41246187
#> 24 41277370 Transcript ENST00000476777 protein_coding 41247863
#> 25 41277387 Transcript ENST00000461798 nonsense_mediated_decay 41251848
#> 26 41277338 Transcript ENST00000489037 protein_coding 41256206
#> 27 41277500 Transcript ENST00000354071 protein_coding 41196313
#> 28 41277500 Transcript ENST00000352993 protein_coding 41196313
#> 29 41277468 Transcript ENST00000346315 protein_coding 41196313
#> 30 41276132 Transcript ENST00000351666 protein_coding 41196313
#> 31 41277468 Transcript ENST00000309486 protein_coding 41196313
#> version logic_name Translation.species Translation.length
#> 1 3 ensembl_havana_transcript human 1863
#> 2 1 ensembl_havana_transcript human 699
#> 3 1 havana_homo_sapiens_37 human 173
#> 4 1 havana_homo_sapiens_37 human 354
#> 5 1 havana_homo_sapiens_37 human 96
#> 6 1 ensembl_havana_transcript human 1816
#> 7 2 ensembl_havana_transcript human 1884
#> 8 1 havana_homo_sapiens_37 human 63
#> 9 2 havana_homo_sapiens_37 human 759
#> 10 1 havana_homo_sapiens_37 human 498
#> 11 1 havana_homo_sapiens_37 human 623
#> 12 1 havana_homo_sapiens_37 human 572
#> 13 1 havana_homo_sapiens_37 <NA> NA
#> 14 1 havana_homo_sapiens_37 human 266
#> 15 1 havana_homo_sapiens_37 human 242
#> 16 1 havana_homo_sapiens_37 <NA> NA
#> 17 3 havana_homo_sapiens_37 human 437
#> 18 1 havana_homo_sapiens_37 human 649
#> 19 1 havana_homo_sapiens_37 human 622
#> 20 1 havana_homo_sapiens_37 human 59
#> 21 1 havana_homo_sapiens_37 human 177
#> 22 1 havana_homo_sapiens_37 human 473
#> 23 1 havana_homo_sapiens_37 human 319
#> 24 1 havana_homo_sapiens_37 human 222
#> 25 1 havana_homo_sapiens_37 human 63
#> 26 1 havana_homo_sapiens_37 human 98
#> 27 3 ensembl_homo_sapiens_37 human 1598
#> 28 3 ensembl_homo_sapiens_37 human 721
#> 29 3 ensembl_homo_sapiens_37 human 1624
#> 30 3 ensembl_homo_sapiens_37 human 680
#> 31 4 ensembl_homo_sapiens_37 human 1567
#> Translation.version Translation.start Translation.Parent
#> 1 3 41197695 ENST00000357654
#> 2 1 41197801 ENST00000468300
#> 3 1 41197695 ENST00000586385
#> 4 1 41197695 ENST00000591534
#> 5 1 41197695 ENST00000591849
#> 6 1 41197695 ENST00000493795
#> 7 2 41197695 ENST00000471181
#> 8 1 41256972 ENST00000461221
#> 9 2 41197695 ENST00000491747
#> 10 1 41215361 ENST00000484087
#> 11 1 41215361 ENST00000478531
#> 12 1 41215377 ENST00000493919
#> 13 NA NA <NA>
#> 14 1 41228505 ENST00000487825
#> 15 1 41228554 ENST00000461574
#> 16 NA NA <NA>
#> 17 3 41245587 ENST00000412061
#> 18 1 41245601 ENST00000470026
#> 19 1 41245603 ENST00000477152
#> 20 1 41262552 ENST00000492859
#> 21 1 41246129 ENST00000497488
#> 22 1 41246129 ENST00000494123
#> 23 1 41246187 ENST00000473961
#> 24 1 41247863 ENST00000476777
#> 25 1 41256972 ENST00000461798
#> 26 1 41256206 ENST00000489037
#> 27 6 41197695 ENST00000354071
#> 28 5 41197695 ENST00000352993
#> 29 4 41197695 ENST00000346315
#> 30 3 41197695 ENST00000351666
#> 31 4 41197695 ENST00000309486
#> Translation.object_type Translation.end Translation.id Translation.db_type
#> 1 Translation 41276113 ENSP00000350283 core
#> 2 Translation 41276113 ENSP00000417148 core
#> 3 Translation 41277202 ENSP00000465818 core
#> 4 Translation 41226495 ENSP00000467329 core
#> 5 Translation 41202109 ENSP00000465347 core
#> 6 Translation 41258543 ENSP00000418775 core
#> 7 Translation 41276113 ENSP00000418960 core
#> 8 Translation 41276113 ENSP00000418548 core
#> 9 Translation 41276113 ENSP00000420705 core
#> 10 Translation 41256933 ENSP00000419481 core
#> 11 Translation 41276113 ENSP00000420412 core
#> 12 Translation 41258543 ENSP00000418819 core
#> 13 <NA> NA <NA> <NA>
#> 14 Translation 41256933 ENSP00000418212 core
#> 15 Translation 41243841 ENSP00000417241 core
#> 16 <NA> NA <NA> <NA>
#> 17 Translation 41247883 ENSP00000397145 core
#> 18 Translation 41276113 ENSP00000419274 core
#> 19 Translation 41276113 ENSP00000419988 core
#> 20 Translation 41276113 ENSP00000420253 core
#> 21 Translation 41246659 ENSP00000418986 core
#> 22 Translation 41276113 ENSP00000419103 core
#> 23 Translation 41256908 ENSP00000420201 core
#> 24 Translation 41276113 ENSP00000417554 core
#> 25 Translation 41276113 ENSP00000417988 core
#> 26 Translation 41276113 ENSP00000420781 core
#> 27 Translation 41276113 ENSP00000326002 core
#> 28 Translation 41276113 ENSP00000312236 core
#> 29 Translation 41276113 ENSP00000246907 core
#> 30 Translation 41276113 ENSP00000338007 core
#> 31 Translation 41246659 ENSP00000310938 core
#> display_name species strand db_type source Parent
#> 1 BRCA1-001 human -1 core ensembl_havana ENSG00000012048
#> 2 BRCA1-007 human -1 core ensembl_havana ENSG00000012048
#> 3 BRCA1-023 human -1 core havana ENSG00000012048
#> 4 BRCA1-024 human -1 core havana ENSG00000012048
#> 5 BRCA1-025 human -1 core havana ENSG00000012048
#> 6 BRCA1-006 human -1 core ensembl_havana ENSG00000012048
#> 7 BRCA1-005 human -1 core ensembl_havana ENSG00000012048
#> 8 BRCA1-010 human -1 core havana ENSG00000012048
#> 9 BRCA1-014 human -1 core havana ENSG00000012048
#> 10 BRCA1-015 human -1 core havana ENSG00000012048
#> 11 BRCA1-009 human -1 core havana ENSG00000012048
#> 12 BRCA1-008 human -1 core havana ENSG00000012048
#> 13 BRCA1-021 human -1 core havana ENSG00000012048
#> 14 BRCA1-019 human -1 core havana ENSG00000012048
#> 15 BRCA1-022 human -1 core havana ENSG00000012048
#> 16 BRCA1-012 human -1 core havana ENSG00000012048
#> 17 BRCA1-026 human -1 core havana ENSG00000012048
#> 18 BRCA1-011 human -1 core havana ENSG00000012048
#> 19 BRCA1-004 human -1 core havana ENSG00000012048
#> 20 BRCA1-002 human -1 core havana ENSG00000012048
#> 21 BRCA1-003 human -1 core havana ENSG00000012048
#> 22 BRCA1-013 human -1 core havana ENSG00000012048
#> 23 BRCA1-018 human -1 core havana ENSG00000012048
#> 24 BRCA1-017 human -1 core havana ENSG00000012048
#> 25 BRCA1-020 human -1 core havana ENSG00000012048
#> 26 BRCA1-016 human -1 core havana ENSG00000012048
#> 27 BRCA1-205 human -1 core ensembl ENSG00000012048
#> 28 BRCA1-204 human -1 core ensembl ENSG00000012048
#> 29 BRCA1-202 human -1 core ensembl ENSG00000012048
#> 30 BRCA1-203 human -1 core ensembl ENSG00000012048
#> 31 BRCA1-201 human -1 core ensembl ENSG00000012048
#> Exon seq_region_name assembly_name is_canonical
#> 1 c(412773.... 17 GRCh37 0
#> 2 c(-1, -1.... 17 GRCh37 0
#> 3 c(412773.... 17 GRCh37 0
#> 4 c(412772.... 17 GRCh37 0
#> 5 c(-1, -1.... 17 GRCh37 0
#> 6 c("core".... 17 GRCh37 0
#> 7 c(412772.... 17 GRCh37 1
#> 8 c(412771.... 17 GRCh37 0
#> 9 c("human.... 17 GRCh37 0
#> 10 c("GRCh3.... 17 GRCh37 0
#> 11 c("Exon".... 17 GRCh37 0
#> 12 c("core".... 17 GRCh37 0
#> 13 c(-1, -1.... 17 GRCh37 0
#> 14 c(-1, -1.... 17 GRCh37 0
#> 15 c("Exon".... 17 GRCh37 0
#> 16 c(1, 1, .... 17 GRCh37 0
#> 17 c(412478.... 17 GRCh37 0
#> 18 c("human.... 17 GRCh37 0
#> 19 c(1, 1, .... 17 GRCh37 0
#> 20 c(412772.... 17 GRCh37 0
#> 21 c(-1, -1.... 17 GRCh37 0
#> 22 c("Exon".... 17 GRCh37 0
#> 23 c("Exon".... 17 GRCh37 0
#> 24 c("human.... 17 GRCh37 0
#> 25 c("human.... 17 GRCh37 0
#> 26 c("human.... 17 GRCh37 0
#> 27 c(412775.... 17 GRCh37 0
#> 28 c(412772.... 17 GRCh37 0
#> 29 c(412774.... 17 GRCh37 0
#> 30 c(1, 1, .... 17 GRCh37 0
#> 31 c(412772.... 17 GRCh37 0
#>
#> $id
#> [1] "ENSG00000012048"
#>
#> $end
#> [1] 41277500
#>
#> $object_type
#> [1] "Gene"
#>
#> $start
#> [1] 41196312
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $version
#> [1] 15
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $display_name
#> [1] "BRCA1"
#>
#> $species
#> [1] "human"
#>
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $db_type
#> [1] "core"
#>
#> $strand
#> [1] -1
#>
#> $seq_region_name
#> [1] "17"
#>
#> $assembly_name
#> [1] "GRCh37"
#>