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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 NULL for 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

Value

Information from Ensembl

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"
#>