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")
#> $id
#> [1] "ENSG00000012048"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $strand
#> [1] -1
#>
#> $Transcript
#> length end display_name version start assembly_name source
#> 1 7094 41277387 BRCA1-001 3 41196312 GRCh37 ensembl_havana
#> 2 3273 41277468 BRCA1-007 1 41196822 GRCh37 ensembl_havana
#> 3 781 41277346 BRCA1-023 1 41197580 GRCh37 havana
#> 4 1282 41277346 BRCA1-024 1 41197580 GRCh37 havana
#> 5 563 41277346 BRCA1-025 1 41197580 GRCh37 havana
#> 6 5732 41277419 BRCA1-006 1 41197646 GRCh37 ensembl_havana
#> 7 5936 41277500 BRCA1-005 2 41197646 GRCh37 ensembl_havana
#> 8 5693 41277305 BRCA1-010 1 41197695 GRCh37 havana
#> 9 2379 41277373 BRCA1-014 2 41197695 GRCh37 havana
#> 10 1495 41256933 BRCA1-015 1 41215361 GRCh37 havana
#> 11 1972 41277376 BRCA1-009 1 41215361 GRCh37 havana
#> 12 1948 41277419 BRCA1-008 1 41215377 GRCh37 havana
#> 13 561 41223083 BRCA1-021 1 41219291 GRCh37 havana
#> 14 800 41256933 BRCA1-019 1 41228505 GRCh37 havana
#> 15 726 41243841 BRCA1-022 1 41228554 GRCh37 havana
#> 16 4497 41277332 BRCA1-012 1 41243115 GRCh37 havana
#> 17 1312 41247883 BRCA1-026 3 41245587 GRCh37 havana
#> 18 2108 41277340 BRCA1-011 1 41245601 GRCh37 havana
#> 19 1980 41277381 BRCA1-004 1 41245603 GRCh37 havana
#> 20 1584 41277317 BRCA1-002 1 41246129 GRCh37 havana
#> 21 779 41277317 BRCA1-003 1 41246129 GRCh37 havana
#> 22 1612 41277467 BRCA1-013 1 41246129 GRCh37 havana
#> 23 958 41256908 BRCA1-018 1 41246187 GRCh37 havana
#> 24 769 41277370 BRCA1-017 1 41247863 GRCh37 havana
#> 25 582 41277387 BRCA1-020 1 41251848 GRCh37 havana
#> 26 455 41277338 BRCA1-016 1 41256206 GRCh37 havana
#> 27 6411 41277500 BRCA1-205 3 41196313 GRCh37 ensembl
#> 28 3780 41277500 BRCA1-204 3 41196313 GRCh37 ensembl
#> 29 6451 41277468 BRCA1-202 3 41196313 GRCh37 ensembl
#> 30 3444 41276132 BRCA1-203 3 41196313 GRCh37 ensembl
#> 31 7114 41277468 BRCA1-201 4 41196313 GRCh37 ensembl
#> db_type object_type Parent Translation.Parent Translation.id
#> 1 core Transcript ENSG00000012048 ENST00000357654 ENSP00000350283
#> 2 core Transcript ENSG00000012048 ENST00000468300 ENSP00000417148
#> 3 core Transcript ENSG00000012048 ENST00000586385 ENSP00000465818
#> 4 core Transcript ENSG00000012048 ENST00000591534 ENSP00000467329
#> 5 core Transcript ENSG00000012048 ENST00000591849 ENSP00000465347
#> 6 core Transcript ENSG00000012048 ENST00000493795 ENSP00000418775
#> 7 core Transcript ENSG00000012048 ENST00000471181 ENSP00000418960
#> 8 core Transcript ENSG00000012048 ENST00000461221 ENSP00000418548
#> 9 core Transcript ENSG00000012048 ENST00000491747 ENSP00000420705
#> 10 core Transcript ENSG00000012048 ENST00000484087 ENSP00000419481
#> 11 core Transcript ENSG00000012048 ENST00000478531 ENSP00000420412
#> 12 core Transcript ENSG00000012048 ENST00000493919 ENSP00000418819
#> 13 core Transcript ENSG00000012048 <NA> <NA>
#> 14 core Transcript ENSG00000012048 ENST00000487825 ENSP00000418212
#> 15 core Transcript ENSG00000012048 ENST00000461574 ENSP00000417241
#> 16 core Transcript ENSG00000012048 <NA> <NA>
#> 17 core Transcript ENSG00000012048 ENST00000412061 ENSP00000397145
#> 18 core Transcript ENSG00000012048 ENST00000470026 ENSP00000419274
#> 19 core Transcript ENSG00000012048 ENST00000477152 ENSP00000419988
#> 20 core Transcript ENSG00000012048 ENST00000492859 ENSP00000420253
#> 21 core Transcript ENSG00000012048 ENST00000497488 ENSP00000418986
#> 22 core Transcript ENSG00000012048 ENST00000494123 ENSP00000419103
#> 23 core Transcript ENSG00000012048 ENST00000473961 ENSP00000420201
#> 24 core Transcript ENSG00000012048 ENST00000476777 ENSP00000417554
#> 25 core Transcript ENSG00000012048 ENST00000461798 ENSP00000417988
#> 26 core Transcript ENSG00000012048 ENST00000489037 ENSP00000420781
#> 27 core Transcript ENSG00000012048 ENST00000354071 ENSP00000326002
#> 28 core Transcript ENSG00000012048 ENST00000352993 ENSP00000312236
#> 29 core Transcript ENSG00000012048 ENST00000346315 ENSP00000246907
#> 30 core Transcript ENSG00000012048 ENST00000351666 ENSP00000338007
#> 31 core Transcript ENSG00000012048 ENST00000309486 ENSP00000310938
#> Translation.db_type Translation.object_type Translation.species
#> 1 core Translation human
#> 2 core Translation human
#> 3 core Translation human
#> 4 core Translation human
#> 5 core Translation human
#> 6 core Translation human
#> 7 core Translation human
#> 8 core Translation human
#> 9 core Translation human
#> 10 core Translation human
#> 11 core Translation human
#> 12 core Translation human
#> 13 <NA> <NA> <NA>
#> 14 core Translation human
#> 15 core Translation human
#> 16 <NA> <NA> <NA>
#> 17 core Translation human
#> 18 core Translation human
#> 19 core Translation human
#> 20 core Translation human
#> 21 core Translation human
#> 22 core Translation human
#> 23 core Translation human
#> 24 core Translation human
#> 25 core Translation human
#> 26 core Translation human
#> 27 core Translation human
#> 28 core Translation human
#> 29 core Translation human
#> 30 core Translation human
#> 31 core Translation human
#> Translation.start Translation.version Translation.length Translation.end
#> 1 41197695 3 1863 41276113
#> 2 41197801 1 699 41276113
#> 3 41197695 1 173 41277202
#> 4 41197695 1 354 41226495
#> 5 41197695 1 96 41202109
#> 6 41197695 1 1816 41258543
#> 7 41197695 2 1884 41276113
#> 8 41256972 1 63 41276113
#> 9 41197695 2 759 41276113
#> 10 41215361 1 498 41256933
#> 11 41215361 1 623 41276113
#> 12 41215377 1 572 41258543
#> 13 NA NA NA NA
#> 14 41228505 1 266 41256933
#> 15 41228554 1 242 41243841
#> 16 NA NA NA NA
#> 17 41245587 3 437 41247883
#> 18 41245601 1 649 41276113
#> 19 41245603 1 622 41276113
#> 20 41262552 1 59 41276113
#> 21 41246129 1 177 41246659
#> 22 41246129 1 473 41276113
#> 23 41246187 1 319 41256908
#> 24 41247863 1 222 41276113
#> 25 41256972 1 63 41276113
#> 26 41256206 1 98 41276113
#> 27 41197695 6 1598 41276113
#> 28 41197695 5 721 41276113
#> 29 41197695 4 1624 41276113
#> 30 41197695 3 680 41276113
#> 31 41197695 4 1567 41246659
#> strand Exon seq_region_name is_canonical species gencode_primary
#> 1 -1 c("17", .... 17 0 human 0
#> 2 -1 c(1, 1, .... 17 0 human 0
#> 3 -1 c("ENSE0.... 17 0 human 0
#> 4 -1 c("ENSE0.... 17 0 human 0
#> 5 -1 c("ENSE0.... 17 0 human 0
#> 6 -1 c("17", .... 17 0 human 0
#> 7 -1 c("core".... 17 1 human 0
#> 8 -1 c(-1, -1.... 17 0 human 0
#> 9 -1 c(-1, -1.... 17 0 human 0
#> 10 -1 c("ENSE0.... 17 0 human 0
#> 11 -1 c(1, 1, .... 17 0 human 0
#> 12 -1 c("core".... 17 0 human 0
#> 13 -1 c("ENSE0.... 17 0 human 0
#> 14 -1 c("core".... 17 0 human 0
#> 15 -1 c("Exon".... 17 0 human 0
#> 16 -1 c(412772.... 17 0 human 0
#> 17 -1 c("17", .... 17 0 human 0
#> 18 -1 c("GRCh3.... 17 0 human 0
#> 19 -1 c(412773.... 17 0 human 0
#> 20 -1 c("Exon".... 17 0 human 0
#> 21 -1 c(1, 1),.... 17 0 human 0
#> 22 -1 c("Exon".... 17 0 human 0
#> 23 -1 c("ENSE0.... 17 0 human 0
#> 24 -1 c(1, 1, .... 17 0 human 0
#> 25 -1 c("core".... 17 0 human 0
#> 26 -1 c("GRCh3.... 17 0 human 0
#> 27 -1 c("core".... 17 0 human 0
#> 28 -1 c(412772.... 17 0 human 0
#> 29 -1 c("GRCh3.... 17 0 human 0
#> 30 -1 c("17", .... 17 0 human 0
#> 31 -1 c(412774.... 17 0 human 0
#> logic_name biotype id
#> 1 ensembl_havana_transcript protein_coding ENST00000357654
#> 2 ensembl_havana_transcript protein_coding ENST00000468300
#> 3 havana_homo_sapiens_37 protein_coding ENST00000586385
#> 4 havana_homo_sapiens_37 protein_coding ENST00000591534
#> 5 havana_homo_sapiens_37 protein_coding ENST00000591849
#> 6 ensembl_havana_transcript protein_coding ENST00000493795
#> 7 ensembl_havana_transcript protein_coding ENST00000471181
#> 8 havana_homo_sapiens_37 nonsense_mediated_decay ENST00000461221
#> 9 havana_homo_sapiens_37 protein_coding ENST00000491747
#> 10 havana_homo_sapiens_37 protein_coding ENST00000484087
#> 11 havana_homo_sapiens_37 protein_coding ENST00000478531
#> 12 havana_homo_sapiens_37 protein_coding ENST00000493919
#> 13 havana_homo_sapiens_37 retained_intron ENST00000472490
#> 14 havana_homo_sapiens_37 protein_coding ENST00000487825
#> 15 havana_homo_sapiens_37 protein_coding ENST00000461574
#> 16 havana_homo_sapiens_37 retained_intron ENST00000467274
#> 17 havana_homo_sapiens_37 non_stop_decay ENST00000412061
#> 18 havana_homo_sapiens_37 protein_coding ENST00000470026
#> 19 havana_homo_sapiens_37 protein_coding ENST00000477152
#> 20 havana_homo_sapiens_37 nonsense_mediated_decay ENST00000492859
#> 21 havana_homo_sapiens_37 protein_coding ENST00000497488
#> 22 havana_homo_sapiens_37 protein_coding ENST00000494123
#> 23 havana_homo_sapiens_37 protein_coding ENST00000473961
#> 24 havana_homo_sapiens_37 protein_coding ENST00000476777
#> 25 havana_homo_sapiens_37 nonsense_mediated_decay ENST00000461798
#> 26 havana_homo_sapiens_37 protein_coding ENST00000489037
#> 27 ensembl_homo_sapiens_37 protein_coding ENST00000354071
#> 28 ensembl_homo_sapiens_37 protein_coding ENST00000352993
#> 29 ensembl_homo_sapiens_37 protein_coding ENST00000346315
#> 30 ensembl_homo_sapiens_37 protein_coding ENST00000351666
#> 31 ensembl_homo_sapiens_37 protein_coding ENST00000309486
#>
#> $species
#> [1] "human"
#>
#> $seq_region_name
#> [1] "17"
#>
#> $object_type
#> [1] "Gene"
#>
#> $db_type
#> [1] "core"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#>
#> $version
#> [1] 15
#>
#> $display_name
#> [1] "BRCA1"
#>
#> $end
#> [1] 41277500
#>
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $start
#> [1] 41196312
#>
queryEnsemblByGene("ENSG00000139618")
#> $object_type
#> [1] "Gene"
#>
#> $db_type
#> [1] "core"
#>
#> $Transcript
#> id assembly_name display_name start length gencode_primary
#> 1 ENST00000380152 GRCh37 BRCA2-001 32889611 10930 0
#> 2 ENST00000530893 GRCh37 BRCA2-003 32889642 2011 0
#> 3 ENST00000528762 GRCh37 BRCA2-005 32945108 495 0
#> 4 ENST00000470094 GRCh37 BRCA2-002 32953977 842 0
#> 5 ENST00000533776 GRCh37 BRCA2-006 32970946 523 0
#> 6 ENST00000544455 GRCh37 BRCA2-201 32889617 10984 0
#> version db_type Exon object_type Translation.object_type
#> 1 3 core c("GRCh3.... Transcript Translation
#> 2 2 core c("core".... Transcript Translation
#> 3 1 core c("Exon".... Transcript Translation
#> 4 1 core c("homo_.... Transcript Translation
#> 5 1 core c("ENSE0.... Transcript <NA>
#> 6 1 core c("core".... Transcript Translation
#> Translation.db_type Translation.species Translation.version
#> 1 core homo_sapiens 3
#> 2 core homo_sapiens 2
#> 3 core homo_sapiens 1
#> 4 core homo_sapiens 1
#> 5 <NA> <NA> NA
#> 6 core homo_sapiens 1
#> Translation.Parent Translation.length Translation.start Translation.end
#> 1 ENST00000380152 3418 32890598 32972907
#> 2 ENST00000530893 481 32899266 32907428
#> 3 ENST00000528762 64 32945108 32950807
#> 4 ENST00000470094 186 32953977 32970229
#> 5 <NA> NA NA NA
#> 6 ENST00000544455 3418 32890598 32972907
#> Translation.id strand logic_name end Parent
#> 1 ENSP00000369497 1 ensembl_havana_transcript 32973347 ENSG00000139618
#> 2 ENSP00000435699 1 havana_homo_sapiens_37 32907428 ENSG00000139618
#> 3 ENSP00000433168 1 havana_homo_sapiens_37 32953632 ENSG00000139618
#> 4 ENSP00000434898 1 havana_homo_sapiens_37 32972409 ENSG00000139618
#> 5 <NA> 1 havana_homo_sapiens_37 32972585 ENSG00000139618
#> 6 ENSP00000439902 1 ensembl_homo_sapiens_37 32973805 ENSG00000139618
#> seq_region_name biotype species is_canonical
#> 1 13 protein_coding homo_sapiens 0
#> 2 13 protein_coding homo_sapiens 0
#> 3 13 nonsense_mediated_decay homo_sapiens 0
#> 4 13 nonsense_mediated_decay homo_sapiens 0
#> 5 13 retained_intron homo_sapiens 0
#> 6 13 protein_coding homo_sapiens 1
#> source
#> 1 ensembl_havana
#> 2 havana
#> 3 havana
#> 4 havana
#> 5 havana
#> 6 ensembl
#>
#> $version
#> [1] 10
#>
#> $start
#> [1] 32889611
#>
#> $display_name
#> [1] "BRCA2"
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $id
#> [1] "ENSG00000139618"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $species
#> [1] "homo_sapiens"
#>
#> $seq_region_name
#> [1] "13"
#>
#> $description
#> [1] "breast cancer 2, early onset [Source:HGNC Symbol;Acc:1101]"
#>
#> $canonical_transcript
#> [1] "ENST00000544455.1"
#>
#> $end
#> [1] 32973805
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $strand
#> [1] 1
#>
event <- "SE_17_-_41251792_41249306_41249261_41246877_BRCA1"
queryEnsemblByEvent(event, species="human", assembly="hg19")
#> $object_type
#> [1] "Gene"
#>
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $db_type
#> [1] "core"
#>
#> $end
#> [1] 41277500
#>
#> $Transcript
#> version species strand is_canonical seq_region_name Translation.length
#> 1 3 human -1 0 17 1863
#> 2 1 human -1 0 17 699
#> 3 1 human -1 0 17 173
#> 4 1 human -1 0 17 354
#> 5 1 human -1 0 17 96
#> 6 1 human -1 0 17 1816
#> 7 2 human -1 1 17 1884
#> 8 1 human -1 0 17 63
#> 9 2 human -1 0 17 759
#> 10 1 human -1 0 17 498
#> 11 1 human -1 0 17 623
#> 12 1 human -1 0 17 572
#> 13 1 human -1 0 17 NA
#> 14 1 human -1 0 17 266
#> 15 1 human -1 0 17 242
#> 16 1 human -1 0 17 NA
#> 17 3 human -1 0 17 437
#> 18 1 human -1 0 17 649
#> 19 1 human -1 0 17 622
#> 20 1 human -1 0 17 59
#> 21 1 human -1 0 17 177
#> 22 1 human -1 0 17 473
#> 23 1 human -1 0 17 319
#> 24 1 human -1 0 17 222
#> 25 1 human -1 0 17 63
#> 26 1 human -1 0 17 98
#> 27 3 human -1 0 17 1598
#> 28 3 human -1 0 17 721
#> 29 3 human -1 0 17 1624
#> 30 3 human -1 0 17 680
#> 31 4 human -1 0 17 1567
#> Translation.id Translation.Parent Translation.object_type Translation.start
#> 1 ENSP00000350283 ENST00000357654 Translation 41197695
#> 2 ENSP00000417148 ENST00000468300 Translation 41197801
#> 3 ENSP00000465818 ENST00000586385 Translation 41197695
#> 4 ENSP00000467329 ENST00000591534 Translation 41197695
#> 5 ENSP00000465347 ENST00000591849 Translation 41197695
#> 6 ENSP00000418775 ENST00000493795 Translation 41197695
#> 7 ENSP00000418960 ENST00000471181 Translation 41197695
#> 8 ENSP00000418548 ENST00000461221 Translation 41256972
#> 9 ENSP00000420705 ENST00000491747 Translation 41197695
#> 10 ENSP00000419481 ENST00000484087 Translation 41215361
#> 11 ENSP00000420412 ENST00000478531 Translation 41215361
#> 12 ENSP00000418819 ENST00000493919 Translation 41215377
#> 13 <NA> <NA> <NA> NA
#> 14 ENSP00000418212 ENST00000487825 Translation 41228505
#> 15 ENSP00000417241 ENST00000461574 Translation 41228554
#> 16 <NA> <NA> <NA> NA
#> 17 ENSP00000397145 ENST00000412061 Translation 41245587
#> 18 ENSP00000419274 ENST00000470026 Translation 41245601
#> 19 ENSP00000419988 ENST00000477152 Translation 41245603
#> 20 ENSP00000420253 ENST00000492859 Translation 41262552
#> 21 ENSP00000418986 ENST00000497488 Translation 41246129
#> 22 ENSP00000419103 ENST00000494123 Translation 41246129
#> 23 ENSP00000420201 ENST00000473961 Translation 41246187
#> 24 ENSP00000417554 ENST00000476777 Translation 41247863
#> 25 ENSP00000417988 ENST00000461798 Translation 41256972
#> 26 ENSP00000420781 ENST00000489037 Translation 41256206
#> 27 ENSP00000326002 ENST00000354071 Translation 41197695
#> 28 ENSP00000312236 ENST00000352993 Translation 41197695
#> 29 ENSP00000246907 ENST00000346315 Translation 41197695
#> 30 ENSP00000338007 ENST00000351666 Translation 41197695
#> 31 ENSP00000310938 ENST00000309486 Translation 41197695
#> Translation.end Translation.db_type Translation.version Translation.species
#> 1 41276113 core 3 human
#> 2 41276113 core 1 human
#> 3 41277202 core 1 human
#> 4 41226495 core 1 human
#> 5 41202109 core 1 human
#> 6 41258543 core 1 human
#> 7 41276113 core 2 human
#> 8 41276113 core 1 human
#> 9 41276113 core 2 human
#> 10 41256933 core 1 human
#> 11 41276113 core 1 human
#> 12 41258543 core 1 human
#> 13 NA <NA> NA <NA>
#> 14 41256933 core 1 human
#> 15 41243841 core 1 human
#> 16 NA <NA> NA <NA>
#> 17 41247883 core 3 human
#> 18 41276113 core 1 human
#> 19 41276113 core 1 human
#> 20 41276113 core 1 human
#> 21 41246659 core 1 human
#> 22 41276113 core 1 human
#> 23 41256908 core 1 human
#> 24 41276113 core 1 human
#> 25 41276113 core 1 human
#> 26 41276113 core 1 human
#> 27 41276113 core 6 human
#> 28 41276113 core 5 human
#> 29 41276113 core 4 human
#> 30 41276113 core 3 human
#> 31 41246659 core 4 human
#> id source Parent assembly_name display_name
#> 1 ENST00000357654 ensembl_havana ENSG00000012048 GRCh37 BRCA1-001
#> 2 ENST00000468300 ensembl_havana ENSG00000012048 GRCh37 BRCA1-007
#> 3 ENST00000586385 havana ENSG00000012048 GRCh37 BRCA1-023
#> 4 ENST00000591534 havana ENSG00000012048 GRCh37 BRCA1-024
#> 5 ENST00000591849 havana ENSG00000012048 GRCh37 BRCA1-025
#> 6 ENST00000493795 ensembl_havana ENSG00000012048 GRCh37 BRCA1-006
#> 7 ENST00000471181 ensembl_havana ENSG00000012048 GRCh37 BRCA1-005
#> 8 ENST00000461221 havana ENSG00000012048 GRCh37 BRCA1-010
#> 9 ENST00000491747 havana ENSG00000012048 GRCh37 BRCA1-014
#> 10 ENST00000484087 havana ENSG00000012048 GRCh37 BRCA1-015
#> 11 ENST00000478531 havana ENSG00000012048 GRCh37 BRCA1-009
#> 12 ENST00000493919 havana ENSG00000012048 GRCh37 BRCA1-008
#> 13 ENST00000472490 havana ENSG00000012048 GRCh37 BRCA1-021
#> 14 ENST00000487825 havana ENSG00000012048 GRCh37 BRCA1-019
#> 15 ENST00000461574 havana ENSG00000012048 GRCh37 BRCA1-022
#> 16 ENST00000467274 havana ENSG00000012048 GRCh37 BRCA1-012
#> 17 ENST00000412061 havana ENSG00000012048 GRCh37 BRCA1-026
#> 18 ENST00000470026 havana ENSG00000012048 GRCh37 BRCA1-011
#> 19 ENST00000477152 havana ENSG00000012048 GRCh37 BRCA1-004
#> 20 ENST00000492859 havana ENSG00000012048 GRCh37 BRCA1-002
#> 21 ENST00000497488 havana ENSG00000012048 GRCh37 BRCA1-003
#> 22 ENST00000494123 havana ENSG00000012048 GRCh37 BRCA1-013
#> 23 ENST00000473961 havana ENSG00000012048 GRCh37 BRCA1-018
#> 24 ENST00000476777 havana ENSG00000012048 GRCh37 BRCA1-017
#> 25 ENST00000461798 havana ENSG00000012048 GRCh37 BRCA1-020
#> 26 ENST00000489037 havana ENSG00000012048 GRCh37 BRCA1-016
#> 27 ENST00000354071 ensembl ENSG00000012048 GRCh37 BRCA1-205
#> 28 ENST00000352993 ensembl ENSG00000012048 GRCh37 BRCA1-204
#> 29 ENST00000346315 ensembl ENSG00000012048 GRCh37 BRCA1-202
#> 30 ENST00000351666 ensembl ENSG00000012048 GRCh37 BRCA1-203
#> 31 ENST00000309486 ensembl ENSG00000012048 GRCh37 BRCA1-201
#> Exon gencode_primary logic_name length
#> 1 c(-1, -1.... 0 ensembl_havana_transcript 7094
#> 2 c(1, 1, .... 0 ensembl_havana_transcript 3273
#> 3 c(1, 1, .... 0 havana_homo_sapiens_37 781
#> 4 c(-1, -1.... 0 havana_homo_sapiens_37 1282
#> 5 c("Exon".... 0 havana_homo_sapiens_37 563
#> 6 c("GRCh3.... 0 ensembl_havana_transcript 5732
#> 7 c("human.... 0 ensembl_havana_transcript 5936
#> 8 c("Exon".... 0 havana_homo_sapiens_37 5693
#> 9 c("GRCh3.... 0 havana_homo_sapiens_37 2379
#> 10 c(1, 1, .... 0 havana_homo_sapiens_37 1495
#> 11 c("GRCh3.... 0 havana_homo_sapiens_37 1972
#> 12 c(-1, -1.... 0 havana_homo_sapiens_37 1948
#> 13 c(1, 1),.... 0 havana_homo_sapiens_37 561
#> 14 c(-1, -1.... 0 havana_homo_sapiens_37 800
#> 15 c(412434.... 0 havana_homo_sapiens_37 726
#> 16 c("core".... 0 havana_homo_sapiens_37 4497
#> 17 c("human.... 0 havana_homo_sapiens_37 1312
#> 18 c(412773.... 0 havana_homo_sapiens_37 2108
#> 19 c(412773.... 0 havana_homo_sapiens_37 1980
#> 20 c(412772.... 0 havana_homo_sapiens_37 1584
#> 21 c(412773.... 0 havana_homo_sapiens_37 779
#> 22 c("human.... 0 havana_homo_sapiens_37 1612
#> 23 c(1, 1, .... 0 havana_homo_sapiens_37 958
#> 24 c(1, 1, .... 0 havana_homo_sapiens_37 769
#> 25 c(1, 1, .... 0 havana_homo_sapiens_37 582
#> 26 c("Exon".... 0 havana_homo_sapiens_37 455
#> 27 c(-1, -1.... 0 ensembl_homo_sapiens_37 6411
#> 28 c(1, 1, .... 0 ensembl_homo_sapiens_37 3780
#> 29 c(412772.... 0 ensembl_homo_sapiens_37 6451
#> 30 c("Exon".... 0 ensembl_homo_sapiens_37 3444
#> 31 c(412774.... 0 ensembl_homo_sapiens_37 7114
#> biotype object_type start db_type end
#> 1 protein_coding Transcript 41196312 core 41277387
#> 2 protein_coding Transcript 41196822 core 41277468
#> 3 protein_coding Transcript 41197580 core 41277346
#> 4 protein_coding Transcript 41197580 core 41277346
#> 5 protein_coding Transcript 41197580 core 41277346
#> 6 protein_coding Transcript 41197646 core 41277419
#> 7 protein_coding Transcript 41197646 core 41277500
#> 8 nonsense_mediated_decay Transcript 41197695 core 41277305
#> 9 protein_coding Transcript 41197695 core 41277373
#> 10 protein_coding Transcript 41215361 core 41256933
#> 11 protein_coding Transcript 41215361 core 41277376
#> 12 protein_coding Transcript 41215377 core 41277419
#> 13 retained_intron Transcript 41219291 core 41223083
#> 14 protein_coding Transcript 41228505 core 41256933
#> 15 protein_coding Transcript 41228554 core 41243841
#> 16 retained_intron Transcript 41243115 core 41277332
#> 17 non_stop_decay Transcript 41245587 core 41247883
#> 18 protein_coding Transcript 41245601 core 41277340
#> 19 protein_coding Transcript 41245603 core 41277381
#> 20 nonsense_mediated_decay Transcript 41246129 core 41277317
#> 21 protein_coding Transcript 41246129 core 41277317
#> 22 protein_coding Transcript 41246129 core 41277467
#> 23 protein_coding Transcript 41246187 core 41256908
#> 24 protein_coding Transcript 41247863 core 41277370
#> 25 nonsense_mediated_decay Transcript 41251848 core 41277387
#> 26 protein_coding Transcript 41256206 core 41277338
#> 27 protein_coding Transcript 41196313 core 41277500
#> 28 protein_coding Transcript 41196313 core 41277500
#> 29 protein_coding Transcript 41196313 core 41277468
#> 30 protein_coding Transcript 41196313 core 41276132
#> 31 protein_coding Transcript 41196313 core 41277468
#>
#> $start
#> [1] 41196312
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $id
#> [1] "ENSG00000012048"
#>
#> $seq_region_name
#> [1] "17"
#>
#> $display_name
#> [1] "BRCA1"
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $species
#> [1] "human"
#>
#> $strand
#> [1] -1
#>
#> $version
#> [1] 15
#>
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>