Skip to contents

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