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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")
#> $biotype
#> [1] "protein_coding"
#> 
#> $id
#> [1] "ENSG00000012048"
#> 
#> $Transcript
#>         end db_type is_canonical assembly_name    start species         source
#> 1  41277387    core            0        GRCh37 41196312   human ensembl_havana
#> 2  41277468    core            0        GRCh37 41196822   human ensembl_havana
#> 3  41277346    core            0        GRCh37 41197580   human         havana
#> 4  41277346    core            0        GRCh37 41197580   human         havana
#> 5  41277346    core            0        GRCh37 41197580   human         havana
#> 6  41277419    core            0        GRCh37 41197646   human ensembl_havana
#> 7  41277500    core            1        GRCh37 41197646   human ensembl_havana
#> 8  41277305    core            0        GRCh37 41197695   human         havana
#> 9  41277373    core            0        GRCh37 41197695   human         havana
#> 10 41256933    core            0        GRCh37 41215361   human         havana
#> 11 41277376    core            0        GRCh37 41215361   human         havana
#> 12 41277419    core            0        GRCh37 41215377   human         havana
#> 13 41223083    core            0        GRCh37 41219291   human         havana
#> 14 41256933    core            0        GRCh37 41228505   human         havana
#> 15 41243841    core            0        GRCh37 41228554   human         havana
#> 16 41277332    core            0        GRCh37 41243115   human         havana
#> 17 41247883    core            0        GRCh37 41245587   human         havana
#> 18 41277340    core            0        GRCh37 41245601   human         havana
#> 19 41277381    core            0        GRCh37 41245603   human         havana
#> 20 41277317    core            0        GRCh37 41246129   human         havana
#> 21 41277317    core            0        GRCh37 41246129   human         havana
#> 22 41277467    core            0        GRCh37 41246129   human         havana
#> 23 41256908    core            0        GRCh37 41246187   human         havana
#> 24 41277370    core            0        GRCh37 41247863   human         havana
#> 25 41277387    core            0        GRCh37 41251848   human         havana
#> 26 41277338    core            0        GRCh37 41256206   human         havana
#> 27 41277500    core            0        GRCh37 41196313   human        ensembl
#> 28 41277500    core            0        GRCh37 41196313   human        ensembl
#> 29 41277468    core            0        GRCh37 41196313   human        ensembl
#> 30 41276132    core            0        GRCh37 41196313   human        ensembl
#> 31 41277468    core            0        GRCh37 41196313   human        ensembl
#>    version strand object_type         Exon                logic_name
#> 1        3     -1  Transcript c(-1, -1.... ensembl_havana_transcript
#> 2        1     -1  Transcript c("ENSE0.... ensembl_havana_transcript
#> 3        1     -1  Transcript c(-1, -1....    havana_homo_sapiens_37
#> 4        1     -1  Transcript c(412773....    havana_homo_sapiens_37
#> 5        1     -1  Transcript c(-1, -1....    havana_homo_sapiens_37
#> 6        1     -1  Transcript c("Exon".... ensembl_havana_transcript
#> 7        2     -1  Transcript c("Exon".... ensembl_havana_transcript
#> 8        1     -1  Transcript c("Exon"....    havana_homo_sapiens_37
#> 9        2     -1  Transcript c(1, 1, ....    havana_homo_sapiens_37
#> 10       1     -1  Transcript c("ENSE0....    havana_homo_sapiens_37
#> 11       1     -1  Transcript c("Exon"....    havana_homo_sapiens_37
#> 12       1     -1  Transcript c(412774....    havana_homo_sapiens_37
#> 13       1     -1  Transcript c("ENSE0....    havana_homo_sapiens_37
#> 14       1     -1  Transcript c("human....    havana_homo_sapiens_37
#> 15       1     -1  Transcript c(-1, -1....    havana_homo_sapiens_37
#> 16       1     -1  Transcript c("Exon"....    havana_homo_sapiens_37
#> 17       3     -1  Transcript c(412478....    havana_homo_sapiens_37
#> 18       1     -1  Transcript c("Exon"....    havana_homo_sapiens_37
#> 19       1     -1  Transcript c("17", ....    havana_homo_sapiens_37
#> 20       1     -1  Transcript c(412773....    havana_homo_sapiens_37
#> 21       1     -1  Transcript c(412773....    havana_homo_sapiens_37
#> 22       1     -1  Transcript c("GRCh3....    havana_homo_sapiens_37
#> 23       1     -1  Transcript c("GRCh3....    havana_homo_sapiens_37
#> 24       1     -1  Transcript c("Exon"....    havana_homo_sapiens_37
#> 25       1     -1  Transcript c(412772....    havana_homo_sapiens_37
#> 26       1     -1  Transcript c(-1, -1....    havana_homo_sapiens_37
#> 27       3     -1  Transcript c("Exon"....   ensembl_homo_sapiens_37
#> 28       3     -1  Transcript c("GRCh3....   ensembl_homo_sapiens_37
#> 29       3     -1  Transcript c("Exon"....   ensembl_homo_sapiens_37
#> 30       3     -1  Transcript c(-1, -1....   ensembl_homo_sapiens_37
#> 31       4     -1  Transcript c(412774....   ensembl_homo_sapiens_37
#>    seq_region_name Translation.db_type Translation.end Translation.species
#> 1               17                core        41276113               human
#> 2               17                core        41276113               human
#> 3               17                core        41277202               human
#> 4               17                core        41226495               human
#> 5               17                core        41202109               human
#> 6               17                core        41258543               human
#> 7               17                core        41276113               human
#> 8               17                core        41276113               human
#> 9               17                core        41276113               human
#> 10              17                core        41256933               human
#> 11              17                core        41276113               human
#> 12              17                core        41258543               human
#> 13              17                <NA>              NA                <NA>
#> 14              17                core        41256933               human
#> 15              17                core        41243841               human
#> 16              17                <NA>              NA                <NA>
#> 17              17                core        41247883               human
#> 18              17                core        41276113               human
#> 19              17                core        41276113               human
#> 20              17                core        41276113               human
#> 21              17                core        41246659               human
#> 22              17                core        41276113               human
#> 23              17                core        41256908               human
#> 24              17                core        41276113               human
#> 25              17                core        41276113               human
#> 26              17                core        41276113               human
#> 27              17                core        41276113               human
#> 28              17                core        41276113               human
#> 29              17                core        41276113               human
#> 30              17                core        41276113               human
#> 31              17                core        41246659               human
#>    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.id Translation.length display_name
#> 1              Translation ENSP00000350283               1863    BRCA1-001
#> 2              Translation ENSP00000417148                699    BRCA1-007
#> 3              Translation ENSP00000465818                173    BRCA1-023
#> 4              Translation ENSP00000467329                354    BRCA1-024
#> 5              Translation ENSP00000465347                 96    BRCA1-025
#> 6              Translation ENSP00000418775               1816    BRCA1-006
#> 7              Translation ENSP00000418960               1884    BRCA1-005
#> 8              Translation ENSP00000418548                 63    BRCA1-010
#> 9              Translation ENSP00000420705                759    BRCA1-014
#> 10             Translation ENSP00000419481                498    BRCA1-015
#> 11             Translation ENSP00000420412                623    BRCA1-009
#> 12             Translation ENSP00000418819                572    BRCA1-008
#> 13                    <NA>            <NA>                 NA    BRCA1-021
#> 14             Translation ENSP00000418212                266    BRCA1-019
#> 15             Translation ENSP00000417241                242    BRCA1-022
#> 16                    <NA>            <NA>                 NA    BRCA1-012
#> 17             Translation ENSP00000397145                437    BRCA1-026
#> 18             Translation ENSP00000419274                649    BRCA1-011
#> 19             Translation ENSP00000419988                622    BRCA1-004
#> 20             Translation ENSP00000420253                 59    BRCA1-002
#> 21             Translation ENSP00000418986                177    BRCA1-003
#> 22             Translation ENSP00000419103                473    BRCA1-013
#> 23             Translation ENSP00000420201                319    BRCA1-018
#> 24             Translation ENSP00000417554                222    BRCA1-017
#> 25             Translation ENSP00000417988                 63    BRCA1-020
#> 26             Translation ENSP00000420781                 98    BRCA1-016
#> 27             Translation ENSP00000326002               1598    BRCA1-205
#> 28             Translation ENSP00000312236                721    BRCA1-204
#> 29             Translation ENSP00000246907               1624    BRCA1-202
#> 30             Translation ENSP00000338007                680    BRCA1-203
#> 31             Translation ENSP00000310938               1567    BRCA1-201
#>             Parent                 biotype              id
#> 1  ENSG00000012048          protein_coding ENST00000357654
#> 2  ENSG00000012048          protein_coding ENST00000468300
#> 3  ENSG00000012048          protein_coding ENST00000586385
#> 4  ENSG00000012048          protein_coding ENST00000591534
#> 5  ENSG00000012048          protein_coding ENST00000591849
#> 6  ENSG00000012048          protein_coding ENST00000493795
#> 7  ENSG00000012048          protein_coding ENST00000471181
#> 8  ENSG00000012048 nonsense_mediated_decay ENST00000461221
#> 9  ENSG00000012048          protein_coding ENST00000491747
#> 10 ENSG00000012048          protein_coding ENST00000484087
#> 11 ENSG00000012048          protein_coding ENST00000478531
#> 12 ENSG00000012048          protein_coding ENST00000493919
#> 13 ENSG00000012048         retained_intron ENST00000472490
#> 14 ENSG00000012048          protein_coding ENST00000487825
#> 15 ENSG00000012048          protein_coding ENST00000461574
#> 16 ENSG00000012048         retained_intron ENST00000467274
#> 17 ENSG00000012048          non_stop_decay ENST00000412061
#> 18 ENSG00000012048          protein_coding ENST00000470026
#> 19 ENSG00000012048          protein_coding ENST00000477152
#> 20 ENSG00000012048 nonsense_mediated_decay ENST00000492859
#> 21 ENSG00000012048          protein_coding ENST00000497488
#> 22 ENSG00000012048          protein_coding ENST00000494123
#> 23 ENSG00000012048          protein_coding ENST00000473961
#> 24 ENSG00000012048          protein_coding ENST00000476777
#> 25 ENSG00000012048 nonsense_mediated_decay ENST00000461798
#> 26 ENSG00000012048          protein_coding ENST00000489037
#> 27 ENSG00000012048          protein_coding ENST00000354071
#> 28 ENSG00000012048          protein_coding ENST00000352993
#> 29 ENSG00000012048          protein_coding ENST00000346315
#> 30 ENSG00000012048          protein_coding ENST00000351666
#> 31 ENSG00000012048          protein_coding ENST00000309486
#> 
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#> 
#> $seq_region_name
#> [1] "17"
#> 
#> $display_name
#> [1] "BRCA1"
#> 
#> $strand
#> [1] -1
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#> 
#> $end
#> [1] 41277500
#> 
#> $db_type
#> [1] "core"
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $start
#> [1] 41196312
#> 
#> $species
#> [1] "human"
#> 
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#> 
#> $source
#> [1] "ensembl_havana"
#> 
#> $version
#> [1] 15
#> 
queryEnsemblByGene("ENSG00000139618")
#> $display_name
#> [1] "BRCA2"
#> 
#> $strand
#> [1] 1
#> 
#> $seq_region_name
#> [1] "13"
#> 
#> $start
#> [1] 32889611
#> 
#> $canonical_transcript
#> [1] "ENST00000544455.1"
#> 
#> $description
#> [1] "breast cancer 2, early onset [Source:HGNC Symbol;Acc:1101]"
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $id
#> [1] "ENSG00000139618"
#> 
#> $end
#> [1] 32973805
#> 
#> $biotype
#> [1] "protein_coding"
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $source
#> [1] "ensembl_havana"
#> 
#> $Transcript
#>           source assembly_name         Exon                 biotype
#> 1 ensembl_havana        GRCh37 c(328898....          protein_coding
#> 2         havana        GRCh37 c(328898....          protein_coding
#> 3         havana        GRCh37 c("core".... nonsense_mediated_decay
#> 4         havana        GRCh37 c("13", .... nonsense_mediated_decay
#> 5         havana        GRCh37 c("core"....         retained_intron
#> 6        ensembl        GRCh37 c("core"....          protein_coding
#>                id object_type      end is_canonical seq_region_name    start
#> 1 ENST00000380152  Transcript 32973347            0              13 32889611
#> 2 ENST00000530893  Transcript 32907428            0              13 32889642
#> 3 ENST00000528762  Transcript 32953632            0              13 32945108
#> 4 ENST00000470094  Transcript 32972409            0              13 32953977
#> 5 ENST00000533776  Transcript 32972585            0              13 32970946
#> 6 ENST00000544455  Transcript 32973805            1              13 32889617
#>   display_name strand db_type                logic_name version          Parent
#> 1    BRCA2-001      1    core ensembl_havana_transcript       3 ENSG00000139618
#> 2    BRCA2-003      1    core    havana_homo_sapiens_37       2 ENSG00000139618
#> 3    BRCA2-005      1    core    havana_homo_sapiens_37       1 ENSG00000139618
#> 4    BRCA2-002      1    core    havana_homo_sapiens_37       1 ENSG00000139618
#> 5    BRCA2-006      1    core    havana_homo_sapiens_37       1 ENSG00000139618
#> 6    BRCA2-201      1    core   ensembl_homo_sapiens_37       1 ENSG00000139618
#>        species Translation.start Translation.end Translation.species
#> 1 homo_sapiens          32890598        32972907        homo_sapiens
#> 2 homo_sapiens          32899266        32907428        homo_sapiens
#> 3 homo_sapiens          32945108        32950807        homo_sapiens
#> 4 homo_sapiens          32953977        32970229        homo_sapiens
#> 5 homo_sapiens                NA              NA                <NA>
#> 6 homo_sapiens          32890598        32972907        homo_sapiens
#>   Translation.Parent Translation.object_type  Translation.id
#> 1    ENST00000380152             Translation ENSP00000369497
#> 2    ENST00000530893             Translation ENSP00000435699
#> 3    ENST00000528762             Translation ENSP00000433168
#> 4    ENST00000470094             Translation ENSP00000434898
#> 5               <NA>                    <NA>            <NA>
#> 6    ENST00000544455             Translation ENSP00000439902
#>   Translation.version Translation.db_type Translation.length
#> 1                   3                core               3418
#> 2                   2                core                481
#> 3                   1                core                 64
#> 4                   1                core                186
#> 5                  NA                <NA>                 NA
#> 6                   1                core               3418
#> 
#> $version
#> [1] 10
#> 
#> $species
#> [1] "homo_sapiens"
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#> 
#> $db_type
#> [1] "core"
#> 
event <- "SE_17_-_41251792_41249306_41249261_41246877_BRCA1"
queryEnsemblByEvent(event, species="human", assembly="hg19")
#> $strand
#> [1] -1
#> 
#> $seq_region_name
#> [1] "17"
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $species
#> [1] "human"
#> 
#> $biotype
#> [1] "protein_coding"
#> 
#> $source
#> [1] "ensembl_havana"
#> 
#> $display_name
#> [1] "BRCA1"
#> 
#> $version
#> [1] 15
#> 
#> $id
#> [1] "ENSG00000012048"
#> 
#> $end
#> [1] 41277500
#> 
#> $Transcript
#>                   logic_name db_type is_canonical object_type version
#> 1  ensembl_havana_transcript    core            0  Transcript       3
#> 2  ensembl_havana_transcript    core            0  Transcript       1
#> 3     havana_homo_sapiens_37    core            0  Transcript       1
#> 4     havana_homo_sapiens_37    core            0  Transcript       1
#> 5     havana_homo_sapiens_37    core            0  Transcript       1
#> 6  ensembl_havana_transcript    core            0  Transcript       1
#> 7  ensembl_havana_transcript    core            1  Transcript       2
#> 8     havana_homo_sapiens_37    core            0  Transcript       1
#> 9     havana_homo_sapiens_37    core            0  Transcript       2
#> 10    havana_homo_sapiens_37    core            0  Transcript       1
#> 11    havana_homo_sapiens_37    core            0  Transcript       1
#> 12    havana_homo_sapiens_37    core            0  Transcript       1
#> 13    havana_homo_sapiens_37    core            0  Transcript       1
#> 14    havana_homo_sapiens_37    core            0  Transcript       1
#> 15    havana_homo_sapiens_37    core            0  Transcript       1
#> 16    havana_homo_sapiens_37    core            0  Transcript       1
#> 17    havana_homo_sapiens_37    core            0  Transcript       3
#> 18    havana_homo_sapiens_37    core            0  Transcript       1
#> 19    havana_homo_sapiens_37    core            0  Transcript       1
#> 20    havana_homo_sapiens_37    core            0  Transcript       1
#> 21    havana_homo_sapiens_37    core            0  Transcript       1
#> 22    havana_homo_sapiens_37    core            0  Transcript       1
#> 23    havana_homo_sapiens_37    core            0  Transcript       1
#> 24    havana_homo_sapiens_37    core            0  Transcript       1
#> 25    havana_homo_sapiens_37    core            0  Transcript       1
#> 26    havana_homo_sapiens_37    core            0  Transcript       1
#> 27   ensembl_homo_sapiens_37    core            0  Transcript       3
#> 28   ensembl_homo_sapiens_37    core            0  Transcript       3
#> 29   ensembl_homo_sapiens_37    core            0  Transcript       3
#> 30   ensembl_homo_sapiens_37    core            0  Transcript       3
#> 31   ensembl_homo_sapiens_37    core            0  Transcript       4
#>    display_name              id      end    start          Parent
#> 1     BRCA1-001 ENST00000357654 41277387 41196312 ENSG00000012048
#> 2     BRCA1-007 ENST00000468300 41277468 41196822 ENSG00000012048
#> 3     BRCA1-023 ENST00000586385 41277346 41197580 ENSG00000012048
#> 4     BRCA1-024 ENST00000591534 41277346 41197580 ENSG00000012048
#> 5     BRCA1-025 ENST00000591849 41277346 41197580 ENSG00000012048
#> 6     BRCA1-006 ENST00000493795 41277419 41197646 ENSG00000012048
#> 7     BRCA1-005 ENST00000471181 41277500 41197646 ENSG00000012048
#> 8     BRCA1-010 ENST00000461221 41277305 41197695 ENSG00000012048
#> 9     BRCA1-014 ENST00000491747 41277373 41197695 ENSG00000012048
#> 10    BRCA1-015 ENST00000484087 41256933 41215361 ENSG00000012048
#> 11    BRCA1-009 ENST00000478531 41277376 41215361 ENSG00000012048
#> 12    BRCA1-008 ENST00000493919 41277419 41215377 ENSG00000012048
#> 13    BRCA1-021 ENST00000472490 41223083 41219291 ENSG00000012048
#> 14    BRCA1-019 ENST00000487825 41256933 41228505 ENSG00000012048
#> 15    BRCA1-022 ENST00000461574 41243841 41228554 ENSG00000012048
#> 16    BRCA1-012 ENST00000467274 41277332 41243115 ENSG00000012048
#> 17    BRCA1-026 ENST00000412061 41247883 41245587 ENSG00000012048
#> 18    BRCA1-011 ENST00000470026 41277340 41245601 ENSG00000012048
#> 19    BRCA1-004 ENST00000477152 41277381 41245603 ENSG00000012048
#> 20    BRCA1-002 ENST00000492859 41277317 41246129 ENSG00000012048
#> 21    BRCA1-003 ENST00000497488 41277317 41246129 ENSG00000012048
#> 22    BRCA1-013 ENST00000494123 41277467 41246129 ENSG00000012048
#> 23    BRCA1-018 ENST00000473961 41256908 41246187 ENSG00000012048
#> 24    BRCA1-017 ENST00000476777 41277370 41247863 ENSG00000012048
#> 25    BRCA1-020 ENST00000461798 41277387 41251848 ENSG00000012048
#> 26    BRCA1-016 ENST00000489037 41277338 41256206 ENSG00000012048
#> 27    BRCA1-205 ENST00000354071 41277500 41196313 ENSG00000012048
#> 28    BRCA1-204 ENST00000352993 41277500 41196313 ENSG00000012048
#> 29    BRCA1-202 ENST00000346315 41277468 41196313 ENSG00000012048
#> 30    BRCA1-203 ENST00000351666 41276132 41196313 ENSG00000012048
#> 31    BRCA1-201 ENST00000309486 41277468 41196313 ENSG00000012048
#>    Translation.object_type Translation.db_type Translation.species
#> 1              Translation                core               human
#> 2              Translation                core               human
#> 3              Translation                core               human
#> 4              Translation                core               human
#> 5              Translation                core               human
#> 6              Translation                core               human
#> 7              Translation                core               human
#> 8              Translation                core               human
#> 9              Translation                core               human
#> 10             Translation                core               human
#> 11             Translation                core               human
#> 12             Translation                core               human
#> 13                    <NA>                <NA>                <NA>
#> 14             Translation                core               human
#> 15             Translation                core               human
#> 16                    <NA>                <NA>                <NA>
#> 17             Translation                core               human
#> 18             Translation                core               human
#> 19             Translation                core               human
#> 20             Translation                core               human
#> 21             Translation                core               human
#> 22             Translation                core               human
#> 23             Translation                core               human
#> 24             Translation                core               human
#> 25             Translation                core               human
#> 26             Translation                core               human
#> 27             Translation                core               human
#> 28             Translation                core               human
#> 29             Translation                core               human
#> 30             Translation                core               human
#> 31             Translation                core               human
#>    Translation.Parent Translation.start Translation.length Translation.version
#> 1     ENST00000357654          41197695               1863                   3
#> 2     ENST00000468300          41197801                699                   1
#> 3     ENST00000586385          41197695                173                   1
#> 4     ENST00000591534          41197695                354                   1
#> 5     ENST00000591849          41197695                 96                   1
#> 6     ENST00000493795          41197695               1816                   1
#> 7     ENST00000471181          41197695               1884                   2
#> 8     ENST00000461221          41256972                 63                   1
#> 9     ENST00000491747          41197695                759                   2
#> 10    ENST00000484087          41215361                498                   1
#> 11    ENST00000478531          41215361                623                   1
#> 12    ENST00000493919          41215377                572                   1
#> 13               <NA>                NA                 NA                  NA
#> 14    ENST00000487825          41228505                266                   1
#> 15    ENST00000461574          41228554                242                   1
#> 16               <NA>                NA                 NA                  NA
#> 17    ENST00000412061          41245587                437                   3
#> 18    ENST00000470026          41245601                649                   1
#> 19    ENST00000477152          41245603                622                   1
#> 20    ENST00000492859          41262552                 59                   1
#> 21    ENST00000497488          41246129                177                   1
#> 22    ENST00000494123          41246129                473                   1
#> 23    ENST00000473961          41246187                319                   1
#> 24    ENST00000476777          41247863                222                   1
#> 25    ENST00000461798          41256972                 63                   1
#> 26    ENST00000489037          41256206                 98                   1
#> 27    ENST00000354071          41197695               1598                   6
#> 28    ENST00000352993          41197695                721                   5
#> 29    ENST00000346315          41197695               1624                   4
#> 30    ENST00000351666          41197695                680                   3
#> 31    ENST00000309486          41197695               1567                   4
#>    Translation.end  Translation.id seq_region_name strand species assembly_name
#> 1         41276113 ENSP00000350283              17     -1   human        GRCh37
#> 2         41276113 ENSP00000417148              17     -1   human        GRCh37
#> 3         41277202 ENSP00000465818              17     -1   human        GRCh37
#> 4         41226495 ENSP00000467329              17     -1   human        GRCh37
#> 5         41202109 ENSP00000465347              17     -1   human        GRCh37
#> 6         41258543 ENSP00000418775              17     -1   human        GRCh37
#> 7         41276113 ENSP00000418960              17     -1   human        GRCh37
#> 8         41276113 ENSP00000418548              17     -1   human        GRCh37
#> 9         41276113 ENSP00000420705              17     -1   human        GRCh37
#> 10        41256933 ENSP00000419481              17     -1   human        GRCh37
#> 11        41276113 ENSP00000420412              17     -1   human        GRCh37
#> 12        41258543 ENSP00000418819              17     -1   human        GRCh37
#> 13              NA            <NA>              17     -1   human        GRCh37
#> 14        41256933 ENSP00000418212              17     -1   human        GRCh37
#> 15        41243841 ENSP00000417241              17     -1   human        GRCh37
#> 16              NA            <NA>              17     -1   human        GRCh37
#> 17        41247883 ENSP00000397145              17     -1   human        GRCh37
#> 18        41276113 ENSP00000419274              17     -1   human        GRCh37
#> 19        41276113 ENSP00000419988              17     -1   human        GRCh37
#> 20        41276113 ENSP00000420253              17     -1   human        GRCh37
#> 21        41246659 ENSP00000418986              17     -1   human        GRCh37
#> 22        41276113 ENSP00000419103              17     -1   human        GRCh37
#> 23        41256908 ENSP00000420201              17     -1   human        GRCh37
#> 24        41276113 ENSP00000417554              17     -1   human        GRCh37
#> 25        41276113 ENSP00000417988              17     -1   human        GRCh37
#> 26        41276113 ENSP00000420781              17     -1   human        GRCh37
#> 27        41276113 ENSP00000326002              17     -1   human        GRCh37
#> 28        41276113 ENSP00000312236              17     -1   human        GRCh37
#> 29        41276113 ENSP00000246907              17     -1   human        GRCh37
#> 30        41276113 ENSP00000338007              17     -1   human        GRCh37
#> 31        41246659 ENSP00000310938              17     -1   human        GRCh37
#>            Exon                 biotype         source
#> 1  c(1, 1, ....          protein_coding ensembl_havana
#> 2  c(1, 1, ....          protein_coding ensembl_havana
#> 3  c("human....          protein_coding         havana
#> 4  c("17", ....          protein_coding         havana
#> 5  c(412772....          protein_coding         havana
#> 6  c("Exon"....          protein_coding ensembl_havana
#> 7  c("human....          protein_coding ensembl_havana
#> 8  c(412771.... nonsense_mediated_decay         havana
#> 9  c("GRCh3....          protein_coding         havana
#> 10 c("Exon"....          protein_coding         havana
#> 11 c(1, 1, ....          protein_coding         havana
#> 12 c("GRCh3....          protein_coding         havana
#> 13 c("Exon"....         retained_intron         havana
#> 14 c("Exon"....          protein_coding         havana
#> 15 c("GRCh3....          protein_coding         havana
#> 16 c(412772....         retained_intron         havana
#> 17 c("Exon"....          non_stop_decay         havana
#> 18 c(-1, -1....          protein_coding         havana
#> 19 c("Exon"....          protein_coding         havana
#> 20 c(412772.... nonsense_mediated_decay         havana
#> 21 c(412772....          protein_coding         havana
#> 22 c(412772....          protein_coding         havana
#> 23 c("GRCh3....          protein_coding         havana
#> 24 c(412773....          protein_coding         havana
#> 25 c(412772.... nonsense_mediated_decay         havana
#> 26 c("ENSE0....          protein_coding         havana
#> 27 c(412772....          protein_coding        ensembl
#> 28 c("core"....          protein_coding        ensembl
#> 29 c(412772....          protein_coding        ensembl
#> 30 c("Exon"....          protein_coding        ensembl
#> 31 c(412772....          protein_coding        ensembl
#> 
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#> 
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#> 
#> $start
#> [1] 41196312
#> 
#> $db_type
#> [1] "core"
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>