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")
#> $display_name
#> [1] "BRCA1"
#>
#> $object_type
#> [1] "Gene"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $start
#> [1] 41196312
#>
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#>
#> $version
#> [1] 15
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $species
#> [1] "human"
#>
#> $Transcript
#> Parent Exon is_canonical display_name object_type
#> 1 ENSG00000012048 c(412773.... 0 BRCA1-001 Transcript
#> 2 ENSG00000012048 c("17", .... 0 BRCA1-007 Transcript
#> 3 ENSG00000012048 c("17", .... 0 BRCA1-023 Transcript
#> 4 ENSG00000012048 c("human.... 0 BRCA1-024 Transcript
#> 5 ENSG00000012048 c("core".... 0 BRCA1-025 Transcript
#> 6 ENSG00000012048 c("GRCh3.... 0 BRCA1-006 Transcript
#> 7 ENSG00000012048 c(1, 1, .... 1 BRCA1-005 Transcript
#> 8 ENSG00000012048 c(412773.... 0 BRCA1-010 Transcript
#> 9 ENSG00000012048 c(412773.... 0 BRCA1-014 Transcript
#> 10 ENSG00000012048 c(412568.... 0 BRCA1-015 Transcript
#> 11 ENSG00000012048 c("GRCh3.... 0 BRCA1-009 Transcript
#> 12 ENSG00000012048 c(412774.... 0 BRCA1-008 Transcript
#> 13 ENSG00000012048 c(412230.... 0 BRCA1-021 Transcript
#> 14 ENSG00000012048 c(412568.... 0 BRCA1-019 Transcript
#> 15 ENSG00000012048 c("GRCh3.... 0 BRCA1-022 Transcript
#> 16 ENSG00000012048 c("core".... 0 BRCA1-012 Transcript
#> 17 ENSG00000012048 c(-1, -1.... 0 BRCA1-026 Transcript
#> 18 ENSG00000012048 c(-1, -1.... 0 BRCA1-011 Transcript
#> 19 ENSG00000012048 c(1, 1, .... 0 BRCA1-004 Transcript
#> 20 ENSG00000012048 c(1, 1, .... 0 BRCA1-002 Transcript
#> 21 ENSG00000012048 c(-1, -1.... 0 BRCA1-003 Transcript
#> 22 ENSG00000012048 c(412774.... 0 BRCA1-013 Transcript
#> 23 ENSG00000012048 c(412569.... 0 BRCA1-018 Transcript
#> 24 ENSG00000012048 c("GRCh3.... 0 BRCA1-017 Transcript
#> 25 ENSG00000012048 c("GRCh3.... 0 BRCA1-020 Transcript
#> 26 ENSG00000012048 c(412771.... 0 BRCA1-016 Transcript
#> 27 ENSG00000012048 c("core".... 0 BRCA1-205 Transcript
#> 28 ENSG00000012048 c("GRCh3.... 0 BRCA1-204 Transcript
#> 29 ENSG00000012048 c(412774.... 0 BRCA1-202 Transcript
#> 30 ENSG00000012048 c("human.... 0 BRCA1-203 Transcript
#> 31 ENSG00000012048 c(-1, -1.... 0 BRCA1-201 Transcript
#> Translation.version Translation.start Translation.length Translation.end
#> 1 3 41197695 1863 41276113
#> 2 1 41197801 699 41276113
#> 3 1 41197695 173 41277202
#> 4 1 41197695 354 41226495
#> 5 1 41197695 96 41202109
#> 6 1 41197695 1816 41258543
#> 7 2 41197695 1884 41276113
#> 8 1 41256972 63 41276113
#> 9 2 41197695 759 41276113
#> 10 1 41215361 498 41256933
#> 11 1 41215361 623 41276113
#> 12 1 41215377 572 41258543
#> 13 NA NA NA NA
#> 14 1 41228505 266 41256933
#> 15 1 41228554 242 41243841
#> 16 NA NA NA NA
#> 17 3 41245587 437 41247883
#> 18 1 41245601 649 41276113
#> 19 1 41245603 622 41276113
#> 20 1 41262552 59 41276113
#> 21 1 41246129 177 41246659
#> 22 1 41246129 473 41276113
#> 23 1 41246187 319 41256908
#> 24 1 41247863 222 41276113
#> 25 1 41256972 63 41276113
#> 26 1 41256206 98 41276113
#> 27 6 41197695 1598 41276113
#> 28 5 41197695 721 41276113
#> 29 4 41197695 1624 41276113
#> 30 3 41197695 680 41276113
#> 31 4 41197695 1567 41246659
#> Translation.db_type Translation.id Translation.object_type
#> 1 core ENSP00000350283 Translation
#> 2 core ENSP00000417148 Translation
#> 3 core ENSP00000465818 Translation
#> 4 core ENSP00000467329 Translation
#> 5 core ENSP00000465347 Translation
#> 6 core ENSP00000418775 Translation
#> 7 core ENSP00000418960 Translation
#> 8 core ENSP00000418548 Translation
#> 9 core ENSP00000420705 Translation
#> 10 core ENSP00000419481 Translation
#> 11 core ENSP00000420412 Translation
#> 12 core ENSP00000418819 Translation
#> 13 <NA> <NA> <NA>
#> 14 core ENSP00000418212 Translation
#> 15 core ENSP00000417241 Translation
#> 16 <NA> <NA> <NA>
#> 17 core ENSP00000397145 Translation
#> 18 core ENSP00000419274 Translation
#> 19 core ENSP00000419988 Translation
#> 20 core ENSP00000420253 Translation
#> 21 core ENSP00000418986 Translation
#> 22 core ENSP00000419103 Translation
#> 23 core ENSP00000420201 Translation
#> 24 core ENSP00000417554 Translation
#> 25 core ENSP00000417988 Translation
#> 26 core ENSP00000420781 Translation
#> 27 core ENSP00000326002 Translation
#> 28 core ENSP00000312236 Translation
#> 29 core ENSP00000246907 Translation
#> 30 core ENSP00000338007 Translation
#> 31 core ENSP00000310938 Translation
#> Translation.species Translation.Parent start biotype
#> 1 human ENST00000357654 41196312 protein_coding
#> 2 human ENST00000468300 41196822 protein_coding
#> 3 human ENST00000586385 41197580 protein_coding
#> 4 human ENST00000591534 41197580 protein_coding
#> 5 human ENST00000591849 41197580 protein_coding
#> 6 human ENST00000493795 41197646 protein_coding
#> 7 human ENST00000471181 41197646 protein_coding
#> 8 human ENST00000461221 41197695 nonsense_mediated_decay
#> 9 human ENST00000491747 41197695 protein_coding
#> 10 human ENST00000484087 41215361 protein_coding
#> 11 human ENST00000478531 41215361 protein_coding
#> 12 human ENST00000493919 41215377 protein_coding
#> 13 <NA> <NA> 41219291 retained_intron
#> 14 human ENST00000487825 41228505 protein_coding
#> 15 human ENST00000461574 41228554 protein_coding
#> 16 <NA> <NA> 41243115 retained_intron
#> 17 human ENST00000412061 41245587 non_stop_decay
#> 18 human ENST00000470026 41245601 protein_coding
#> 19 human ENST00000477152 41245603 protein_coding
#> 20 human ENST00000492859 41246129 nonsense_mediated_decay
#> 21 human ENST00000497488 41246129 protein_coding
#> 22 human ENST00000494123 41246129 protein_coding
#> 23 human ENST00000473961 41246187 protein_coding
#> 24 human ENST00000476777 41247863 protein_coding
#> 25 human ENST00000461798 41251848 nonsense_mediated_decay
#> 26 human ENST00000489037 41256206 protein_coding
#> 27 human ENST00000354071 41196313 protein_coding
#> 28 human ENST00000352993 41196313 protein_coding
#> 29 human ENST00000346315 41196313 protein_coding
#> 30 human ENST00000351666 41196313 protein_coding
#> 31 human ENST00000309486 41196313 protein_coding
#> length version species seq_region_name assembly_name strand gencode_primary
#> 1 7094 3 human 17 GRCh37 -1 0
#> 2 3273 1 human 17 GRCh37 -1 0
#> 3 781 1 human 17 GRCh37 -1 0
#> 4 1282 1 human 17 GRCh37 -1 0
#> 5 563 1 human 17 GRCh37 -1 0
#> 6 5732 1 human 17 GRCh37 -1 0
#> 7 5936 2 human 17 GRCh37 -1 0
#> 8 5693 1 human 17 GRCh37 -1 0
#> 9 2379 2 human 17 GRCh37 -1 0
#> 10 1495 1 human 17 GRCh37 -1 0
#> 11 1972 1 human 17 GRCh37 -1 0
#> 12 1948 1 human 17 GRCh37 -1 0
#> 13 561 1 human 17 GRCh37 -1 0
#> 14 800 1 human 17 GRCh37 -1 0
#> 15 726 1 human 17 GRCh37 -1 0
#> 16 4497 1 human 17 GRCh37 -1 0
#> 17 1312 3 human 17 GRCh37 -1 0
#> 18 2108 1 human 17 GRCh37 -1 0
#> 19 1980 1 human 17 GRCh37 -1 0
#> 20 1584 1 human 17 GRCh37 -1 0
#> 21 779 1 human 17 GRCh37 -1 0
#> 22 1612 1 human 17 GRCh37 -1 0
#> 23 958 1 human 17 GRCh37 -1 0
#> 24 769 1 human 17 GRCh37 -1 0
#> 25 582 1 human 17 GRCh37 -1 0
#> 26 455 1 human 17 GRCh37 -1 0
#> 27 6411 3 human 17 GRCh37 -1 0
#> 28 3780 3 human 17 GRCh37 -1 0
#> 29 6451 3 human 17 GRCh37 -1 0
#> 30 3444 3 human 17 GRCh37 -1 0
#> 31 7114 4 human 17 GRCh37 -1 0
#> id db_type logic_name end source
#> 1 ENST00000357654 core ensembl_havana_transcript 41277387 ensembl_havana
#> 2 ENST00000468300 core ensembl_havana_transcript 41277468 ensembl_havana
#> 3 ENST00000586385 core havana_homo_sapiens_37 41277346 havana
#> 4 ENST00000591534 core havana_homo_sapiens_37 41277346 havana
#> 5 ENST00000591849 core havana_homo_sapiens_37 41277346 havana
#> 6 ENST00000493795 core ensembl_havana_transcript 41277419 ensembl_havana
#> 7 ENST00000471181 core ensembl_havana_transcript 41277500 ensembl_havana
#> 8 ENST00000461221 core havana_homo_sapiens_37 41277305 havana
#> 9 ENST00000491747 core havana_homo_sapiens_37 41277373 havana
#> 10 ENST00000484087 core havana_homo_sapiens_37 41256933 havana
#> 11 ENST00000478531 core havana_homo_sapiens_37 41277376 havana
#> 12 ENST00000493919 core havana_homo_sapiens_37 41277419 havana
#> 13 ENST00000472490 core havana_homo_sapiens_37 41223083 havana
#> 14 ENST00000487825 core havana_homo_sapiens_37 41256933 havana
#> 15 ENST00000461574 core havana_homo_sapiens_37 41243841 havana
#> 16 ENST00000467274 core havana_homo_sapiens_37 41277332 havana
#> 17 ENST00000412061 core havana_homo_sapiens_37 41247883 havana
#> 18 ENST00000470026 core havana_homo_sapiens_37 41277340 havana
#> 19 ENST00000477152 core havana_homo_sapiens_37 41277381 havana
#> 20 ENST00000492859 core havana_homo_sapiens_37 41277317 havana
#> 21 ENST00000497488 core havana_homo_sapiens_37 41277317 havana
#> 22 ENST00000494123 core havana_homo_sapiens_37 41277467 havana
#> 23 ENST00000473961 core havana_homo_sapiens_37 41256908 havana
#> 24 ENST00000476777 core havana_homo_sapiens_37 41277370 havana
#> 25 ENST00000461798 core havana_homo_sapiens_37 41277387 havana
#> 26 ENST00000489037 core havana_homo_sapiens_37 41277338 havana
#> 27 ENST00000354071 core ensembl_homo_sapiens_37 41277500 ensembl
#> 28 ENST00000352993 core ensembl_homo_sapiens_37 41277500 ensembl
#> 29 ENST00000346315 core ensembl_homo_sapiens_37 41277468 ensembl
#> 30 ENST00000351666 core ensembl_homo_sapiens_37 41276132 ensembl
#> 31 ENST00000309486 core ensembl_homo_sapiens_37 41277468 ensembl
#>
#> $seq_region_name
#> [1] "17"
#>
#> $db_type
#> [1] "core"
#>
#> $id
#> [1] "ENSG00000012048"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $strand
#> [1] -1
#>
#> $end
#> [1] 41277500
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>
queryEnsemblByGene("ENSG00000139618")
#> $start
#> [1] 32889611
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $version
#> [1] 10
#>
#> $canonical_transcript
#> [1] "ENST00000544455.1"
#>
#> $end
#> [1] 32973805
#>
#> $display_name
#> [1] "BRCA2"
#>
#> $description
#> [1] "breast cancer 2, early onset [Source:HGNC Symbol;Acc:1101]"
#>
#> $db_type
#> [1] "core"
#>
#> $object_type
#> [1] "Gene"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $species
#> [1] "homo_sapiens"
#>
#> $Transcript
#> source db_type object_type Parent end length
#> 1 ensembl_havana core Transcript ENSG00000139618 32973347 10930
#> 2 havana core Transcript ENSG00000139618 32907428 2011
#> 3 havana core Transcript ENSG00000139618 32953632 495
#> 4 havana core Transcript ENSG00000139618 32972409 842
#> 5 havana core Transcript ENSG00000139618 32972585 523
#> 6 ensembl core Transcript ENSG00000139618 32973805 10984
#> display_name version start assembly_name gencode_primary
#> 1 BRCA2-001 3 32889611 GRCh37 0
#> 2 BRCA2-003 2 32889642 GRCh37 0
#> 3 BRCA2-005 1 32945108 GRCh37 0
#> 4 BRCA2-002 1 32953977 GRCh37 0
#> 5 BRCA2-006 1 32970946 GRCh37 0
#> 6 BRCA2-201 1 32889617 GRCh37 0
#> biotype logic_name id
#> 1 protein_coding ensembl_havana_transcript ENST00000380152
#> 2 protein_coding havana_homo_sapiens_37 ENST00000530893
#> 3 nonsense_mediated_decay havana_homo_sapiens_37 ENST00000528762
#> 4 nonsense_mediated_decay havana_homo_sapiens_37 ENST00000470094
#> 5 retained_intron havana_homo_sapiens_37 ENST00000533776
#> 6 protein_coding ensembl_homo_sapiens_37 ENST00000544455
#> Translation.length Translation.end Translation.version Translation.species
#> 1 3418 32972907 3 homo_sapiens
#> 2 481 32907428 2 homo_sapiens
#> 3 64 32950807 1 homo_sapiens
#> 4 186 32970229 1 homo_sapiens
#> 5 NA NA NA <NA>
#> 6 3418 32972907 1 homo_sapiens
#> Translation.start Translation.db_type Translation.object_type
#> 1 32890598 core Translation
#> 2 32899266 core Translation
#> 3 32945108 core Translation
#> 4 32953977 core Translation
#> 5 NA <NA> <NA>
#> 6 32890598 core Translation
#> Translation.Parent Translation.id strand Exon seq_region_name
#> 1 ENST00000380152 ENSP00000369497 1 c(1, 1, .... 13
#> 2 ENST00000530893 ENSP00000435699 1 c("ENSE0.... 13
#> 3 ENST00000528762 ENSP00000433168 1 c("13", .... 13
#> 4 ENST00000470094 ENSP00000434898 1 c("Exon".... 13
#> 5 <NA> <NA> 1 c(329709.... 13
#> 6 ENST00000544455 ENSP00000439902 1 c(328898.... 13
#> is_canonical species
#> 1 0 homo_sapiens
#> 2 0 homo_sapiens
#> 3 0 homo_sapiens
#> 4 0 homo_sapiens
#> 5 0 homo_sapiens
#> 6 1 homo_sapiens
#>
#> $seq_region_name
#> [1] "13"
#>
#> $strand
#> [1] 1
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $id
#> [1] "ENSG00000139618"
#>
event <- "SE_17_-_41251792_41249306_41249261_41246877_BRCA1"
queryEnsemblByEvent(event, species="human", assembly="hg19")
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>
#> $Transcript
#> start Translation.Parent Translation.id Translation.end
#> 1 41196312 ENST00000357654 ENSP00000350283 41276113
#> 2 41196822 ENST00000468300 ENSP00000417148 41276113
#> 3 41197580 ENST00000586385 ENSP00000465818 41277202
#> 4 41197580 ENST00000591534 ENSP00000467329 41226495
#> 5 41197580 ENST00000591849 ENSP00000465347 41202109
#> 6 41197646 ENST00000493795 ENSP00000418775 41258543
#> 7 41197646 ENST00000471181 ENSP00000418960 41276113
#> 8 41197695 ENST00000461221 ENSP00000418548 41276113
#> 9 41197695 ENST00000491747 ENSP00000420705 41276113
#> 10 41215361 ENST00000484087 ENSP00000419481 41256933
#> 11 41215361 ENST00000478531 ENSP00000420412 41276113
#> 12 41215377 ENST00000493919 ENSP00000418819 41258543
#> 13 41219291 <NA> <NA> NA
#> 14 41228505 ENST00000487825 ENSP00000418212 41256933
#> 15 41228554 ENST00000461574 ENSP00000417241 41243841
#> 16 41243115 <NA> <NA> NA
#> 17 41245587 ENST00000412061 ENSP00000397145 41247883
#> 18 41245601 ENST00000470026 ENSP00000419274 41276113
#> 19 41245603 ENST00000477152 ENSP00000419988 41276113
#> 20 41246129 ENST00000492859 ENSP00000420253 41276113
#> 21 41246129 ENST00000497488 ENSP00000418986 41246659
#> 22 41246129 ENST00000494123 ENSP00000419103 41276113
#> 23 41246187 ENST00000473961 ENSP00000420201 41256908
#> 24 41247863 ENST00000476777 ENSP00000417554 41276113
#> 25 41251848 ENST00000461798 ENSP00000417988 41276113
#> 26 41256206 ENST00000489037 ENSP00000420781 41276113
#> 27 41196313 ENST00000354071 ENSP00000326002 41276113
#> 28 41196313 ENST00000352993 ENSP00000312236 41276113
#> 29 41196313 ENST00000346315 ENSP00000246907 41276113
#> 30 41196313 ENST00000351666 ENSP00000338007 41276113
#> 31 41196313 ENST00000309486 ENSP00000310938 41246659
#> Translation.version Translation.object_type Translation.db_type
#> 1 3 Translation core
#> 2 1 Translation core
#> 3 1 Translation core
#> 4 1 Translation core
#> 5 1 Translation core
#> 6 1 Translation core
#> 7 2 Translation core
#> 8 1 Translation core
#> 9 2 Translation core
#> 10 1 Translation core
#> 11 1 Translation core
#> 12 1 Translation core
#> 13 NA <NA> <NA>
#> 14 1 Translation core
#> 15 1 Translation core
#> 16 NA <NA> <NA>
#> 17 3 Translation core
#> 18 1 Translation core
#> 19 1 Translation core
#> 20 1 Translation core
#> 21 1 Translation core
#> 22 1 Translation core
#> 23 1 Translation core
#> 24 1 Translation core
#> 25 1 Translation core
#> 26 1 Translation core
#> 27 6 Translation core
#> 28 5 Translation core
#> 29 4 Translation core
#> 30 3 Translation core
#> 31 4 Translation core
#> Translation.length Translation.start Translation.species display_name
#> 1 1863 41197695 human BRCA1-001
#> 2 699 41197801 human BRCA1-007
#> 3 173 41197695 human BRCA1-023
#> 4 354 41197695 human BRCA1-024
#> 5 96 41197695 human BRCA1-025
#> 6 1816 41197695 human BRCA1-006
#> 7 1884 41197695 human BRCA1-005
#> 8 63 41256972 human BRCA1-010
#> 9 759 41197695 human BRCA1-014
#> 10 498 41215361 human BRCA1-015
#> 11 623 41215361 human BRCA1-009
#> 12 572 41215377 human BRCA1-008
#> 13 NA NA <NA> BRCA1-021
#> 14 266 41228505 human BRCA1-019
#> 15 242 41228554 human BRCA1-022
#> 16 NA NA <NA> BRCA1-012
#> 17 437 41245587 human BRCA1-026
#> 18 649 41245601 human BRCA1-011
#> 19 622 41245603 human BRCA1-004
#> 20 59 41262552 human BRCA1-002
#> 21 177 41246129 human BRCA1-003
#> 22 473 41246129 human BRCA1-013
#> 23 319 41246187 human BRCA1-018
#> 24 222 41247863 human BRCA1-017
#> 25 63 41256972 human BRCA1-020
#> 26 98 41256206 human BRCA1-016
#> 27 1598 41197695 human BRCA1-205
#> 28 721 41197695 human BRCA1-204
#> 29 1624 41197695 human BRCA1-202
#> 30 680 41197695 human BRCA1-203
#> 31 1567 41197695 human BRCA1-201
#> source length assembly_name version logic_name
#> 1 ensembl_havana 7094 GRCh37 3 ensembl_havana_transcript
#> 2 ensembl_havana 3273 GRCh37 1 ensembl_havana_transcript
#> 3 havana 781 GRCh37 1 havana_homo_sapiens_37
#> 4 havana 1282 GRCh37 1 havana_homo_sapiens_37
#> 5 havana 563 GRCh37 1 havana_homo_sapiens_37
#> 6 ensembl_havana 5732 GRCh37 1 ensembl_havana_transcript
#> 7 ensembl_havana 5936 GRCh37 2 ensembl_havana_transcript
#> 8 havana 5693 GRCh37 1 havana_homo_sapiens_37
#> 9 havana 2379 GRCh37 2 havana_homo_sapiens_37
#> 10 havana 1495 GRCh37 1 havana_homo_sapiens_37
#> 11 havana 1972 GRCh37 1 havana_homo_sapiens_37
#> 12 havana 1948 GRCh37 1 havana_homo_sapiens_37
#> 13 havana 561 GRCh37 1 havana_homo_sapiens_37
#> 14 havana 800 GRCh37 1 havana_homo_sapiens_37
#> 15 havana 726 GRCh37 1 havana_homo_sapiens_37
#> 16 havana 4497 GRCh37 1 havana_homo_sapiens_37
#> 17 havana 1312 GRCh37 3 havana_homo_sapiens_37
#> 18 havana 2108 GRCh37 1 havana_homo_sapiens_37
#> 19 havana 1980 GRCh37 1 havana_homo_sapiens_37
#> 20 havana 1584 GRCh37 1 havana_homo_sapiens_37
#> 21 havana 779 GRCh37 1 havana_homo_sapiens_37
#> 22 havana 1612 GRCh37 1 havana_homo_sapiens_37
#> 23 havana 958 GRCh37 1 havana_homo_sapiens_37
#> 24 havana 769 GRCh37 1 havana_homo_sapiens_37
#> 25 havana 582 GRCh37 1 havana_homo_sapiens_37
#> 26 havana 455 GRCh37 1 havana_homo_sapiens_37
#> 27 ensembl 6411 GRCh37 3 ensembl_homo_sapiens_37
#> 28 ensembl 3780 GRCh37 3 ensembl_homo_sapiens_37
#> 29 ensembl 6451 GRCh37 3 ensembl_homo_sapiens_37
#> 30 ensembl 3444 GRCh37 3 ensembl_homo_sapiens_37
#> 31 ensembl 7114 GRCh37 4 ensembl_homo_sapiens_37
#> object_type biotype gencode_primary id
#> 1 Transcript protein_coding 0 ENST00000357654
#> 2 Transcript protein_coding 0 ENST00000468300
#> 3 Transcript protein_coding 0 ENST00000586385
#> 4 Transcript protein_coding 0 ENST00000591534
#> 5 Transcript protein_coding 0 ENST00000591849
#> 6 Transcript protein_coding 0 ENST00000493795
#> 7 Transcript protein_coding 0 ENST00000471181
#> 8 Transcript nonsense_mediated_decay 0 ENST00000461221
#> 9 Transcript protein_coding 0 ENST00000491747
#> 10 Transcript protein_coding 0 ENST00000484087
#> 11 Transcript protein_coding 0 ENST00000478531
#> 12 Transcript protein_coding 0 ENST00000493919
#> 13 Transcript retained_intron 0 ENST00000472490
#> 14 Transcript protein_coding 0 ENST00000487825
#> 15 Transcript protein_coding 0 ENST00000461574
#> 16 Transcript retained_intron 0 ENST00000467274
#> 17 Transcript non_stop_decay 0 ENST00000412061
#> 18 Transcript protein_coding 0 ENST00000470026
#> 19 Transcript protein_coding 0 ENST00000477152
#> 20 Transcript nonsense_mediated_decay 0 ENST00000492859
#> 21 Transcript protein_coding 0 ENST00000497488
#> 22 Transcript protein_coding 0 ENST00000494123
#> 23 Transcript protein_coding 0 ENST00000473961
#> 24 Transcript protein_coding 0 ENST00000476777
#> 25 Transcript nonsense_mediated_decay 0 ENST00000461798
#> 26 Transcript protein_coding 0 ENST00000489037
#> 27 Transcript protein_coding 0 ENST00000354071
#> 28 Transcript protein_coding 0 ENST00000352993
#> 29 Transcript protein_coding 0 ENST00000346315
#> 30 Transcript protein_coding 0 ENST00000351666
#> 31 Transcript protein_coding 0 ENST00000309486
#> is_canonical species Exon strand db_type Parent
#> 1 0 human c(-1, -1.... -1 core ENSG00000012048
#> 2 0 human c(1, 1, .... -1 core ENSG00000012048
#> 3 0 human c("Exon".... -1 core ENSG00000012048
#> 4 0 human c(-1, -1.... -1 core ENSG00000012048
#> 5 0 human c(-1, -1.... -1 core ENSG00000012048
#> 6 0 human c(-1, -1.... -1 core ENSG00000012048
#> 7 1 human c(-1, -1.... -1 core ENSG00000012048
#> 8 0 human c(412773.... -1 core ENSG00000012048
#> 9 0 human c(412772.... -1 core ENSG00000012048
#> 10 0 human c(-1, -1.... -1 core ENSG00000012048
#> 11 0 human c(1, 1, .... -1 core ENSG00000012048
#> 12 0 human c("human.... -1 core ENSG00000012048
#> 13 0 human c(412229.... -1 core ENSG00000012048
#> 14 0 human c(412568.... -1 core ENSG00000012048
#> 15 0 human c(412434.... -1 core ENSG00000012048
#> 16 0 human c(-1, -1.... -1 core ENSG00000012048
#> 17 0 human c("GRCh3.... -1 core ENSG00000012048
#> 18 0 human c("17", .... -1 core ENSG00000012048
#> 19 0 human c("core".... -1 core ENSG00000012048
#> 20 0 human c("Exon".... -1 core ENSG00000012048
#> 21 0 human c(1, 1),.... -1 core ENSG00000012048
#> 22 0 human c("17", .... -1 core ENSG00000012048
#> 23 0 human c(412568.... -1 core ENSG00000012048
#> 24 0 human c(-1, -1.... -1 core ENSG00000012048
#> 25 0 human c(412772.... -1 core ENSG00000012048
#> 26 0 human c(412771.... -1 core ENSG00000012048
#> 27 0 human c(-1, -1.... -1 core ENSG00000012048
#> 28 0 human c("core".... -1 core ENSG00000012048
#> 29 0 human c(1, 1, .... -1 core ENSG00000012048
#> 30 0 human c("17", .... -1 core ENSG00000012048
#> 31 0 human c("17", .... -1 core ENSG00000012048
#> seq_region_name end
#> 1 17 41277387
#> 2 17 41277468
#> 3 17 41277346
#> 4 17 41277346
#> 5 17 41277346
#> 6 17 41277419
#> 7 17 41277500
#> 8 17 41277305
#> 9 17 41277373
#> 10 17 41256933
#> 11 17 41277376
#> 12 17 41277419
#> 13 17 41223083
#> 14 17 41256933
#> 15 17 41243841
#> 16 17 41277332
#> 17 17 41247883
#> 18 17 41277340
#> 19 17 41277381
#> 20 17 41277317
#> 21 17 41277317
#> 22 17 41277467
#> 23 17 41256908
#> 24 17 41277370
#> 25 17 41277387
#> 26 17 41277338
#> 27 17 41277500
#> 28 17 41277500
#> 29 17 41277468
#> 30 17 41276132
#> 31 17 41277468
#>
#> $id
#> [1] "ENSG00000012048"
#>
#> $version
#> [1] 15
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $object_type
#> [1] "Gene"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $start
#> [1] 41196312
#>
#> $display_name
#> [1] "BRCA1"
#>
#> $seq_region_name
#> [1] "17"
#>
#> $end
#> [1] 41277500
#>
#> $db_type
#> [1] "core"
#>
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#>
#> $strand
#> [1] -1
#>
#> $species
#> [1] "human"
#>