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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")
#> $strand
#> [1] -1
#> 
#> $seq_region_name
#> [1] "17"
#> 
#> $id
#> [1] "ENSG00000012048"
#> 
#> $end
#> [1] 41277500
#> 
#> $Transcript
#>    display_name db_type seq_region_name strand      end              id
#> 1     BRCA1-001    core              17     -1 41277387 ENST00000357654
#> 2     BRCA1-007    core              17     -1 41277468 ENST00000468300
#> 3     BRCA1-023    core              17     -1 41277346 ENST00000586385
#> 4     BRCA1-024    core              17     -1 41277346 ENST00000591534
#> 5     BRCA1-025    core              17     -1 41277346 ENST00000591849
#> 6     BRCA1-006    core              17     -1 41277419 ENST00000493795
#> 7     BRCA1-005    core              17     -1 41277500 ENST00000471181
#> 8     BRCA1-010    core              17     -1 41277305 ENST00000461221
#> 9     BRCA1-014    core              17     -1 41277373 ENST00000491747
#> 10    BRCA1-015    core              17     -1 41256933 ENST00000484087
#> 11    BRCA1-009    core              17     -1 41277376 ENST00000478531
#> 12    BRCA1-008    core              17     -1 41277419 ENST00000493919
#> 13    BRCA1-021    core              17     -1 41223083 ENST00000472490
#> 14    BRCA1-019    core              17     -1 41256933 ENST00000487825
#> 15    BRCA1-022    core              17     -1 41243841 ENST00000461574
#> 16    BRCA1-012    core              17     -1 41277332 ENST00000467274
#> 17    BRCA1-026    core              17     -1 41247883 ENST00000412061
#> 18    BRCA1-011    core              17     -1 41277340 ENST00000470026
#> 19    BRCA1-004    core              17     -1 41277381 ENST00000477152
#> 20    BRCA1-002    core              17     -1 41277317 ENST00000492859
#> 21    BRCA1-003    core              17     -1 41277317 ENST00000497488
#> 22    BRCA1-013    core              17     -1 41277467 ENST00000494123
#> 23    BRCA1-018    core              17     -1 41256908 ENST00000473961
#> 24    BRCA1-017    core              17     -1 41277370 ENST00000476777
#> 25    BRCA1-020    core              17     -1 41277387 ENST00000461798
#> 26    BRCA1-016    core              17     -1 41277338 ENST00000489037
#> 27    BRCA1-205    core              17     -1 41277500 ENST00000354071
#> 28    BRCA1-204    core              17     -1 41277500 ENST00000352993
#> 29    BRCA1-202    core              17     -1 41277468 ENST00000346315
#> 30    BRCA1-203    core              17     -1 41276132 ENST00000351666
#> 31    BRCA1-201    core              17     -1 41277468 ENST00000309486
#>    assembly_name         source         Exon                logic_name
#> 1         GRCh37 ensembl_havana c(412772.... ensembl_havana_transcript
#> 2         GRCh37 ensembl_havana c("Exon".... ensembl_havana_transcript
#> 3         GRCh37         havana c("GRCh3....    havana_homo_sapiens_37
#> 4         GRCh37         havana c("GRCh3....    havana_homo_sapiens_37
#> 5         GRCh37         havana c("ENSE0....    havana_homo_sapiens_37
#> 6         GRCh37 ensembl_havana c(412772.... ensembl_havana_transcript
#> 7         GRCh37 ensembl_havana c(412775.... ensembl_havana_transcript
#> 8         GRCh37         havana c("ENSE0....    havana_homo_sapiens_37
#> 9         GRCh37         havana c("GRCh3....    havana_homo_sapiens_37
#> 10        GRCh37         havana c(412568....    havana_homo_sapiens_37
#> 11        GRCh37         havana c(412772....    havana_homo_sapiens_37
#> 12        GRCh37         havana c("ENSE0....    havana_homo_sapiens_37
#> 13        GRCh37         havana c(1, 1),....    havana_homo_sapiens_37
#> 14        GRCh37         havana c("GRCh3....    havana_homo_sapiens_37
#> 15        GRCh37         havana c("GRCh3....    havana_homo_sapiens_37
#> 16        GRCh37         havana c("GRCh3....    havana_homo_sapiens_37
#> 17        GRCh37         havana c(-1, -1....    havana_homo_sapiens_37
#> 18        GRCh37         havana c("human....    havana_homo_sapiens_37
#> 19        GRCh37         havana c("17", ....    havana_homo_sapiens_37
#> 20        GRCh37         havana c("Exon"....    havana_homo_sapiens_37
#> 21        GRCh37         havana c("GRCh3....    havana_homo_sapiens_37
#> 22        GRCh37         havana c("Exon"....    havana_homo_sapiens_37
#> 23        GRCh37         havana c("GRCh3....    havana_homo_sapiens_37
#> 24        GRCh37         havana c(412772....    havana_homo_sapiens_37
#> 25        GRCh37         havana c(412772....    havana_homo_sapiens_37
#> 26        GRCh37         havana c(1, 1, ....    havana_homo_sapiens_37
#> 27        GRCh37        ensembl c(412772....   ensembl_homo_sapiens_37
#> 28        GRCh37        ensembl c(1, 1, ....   ensembl_homo_sapiens_37
#> 29        GRCh37        ensembl c(412772....   ensembl_homo_sapiens_37
#> 30        GRCh37        ensembl c("GRCh3....   ensembl_homo_sapiens_37
#> 31        GRCh37        ensembl c("GRCh3....   ensembl_homo_sapiens_37
#>    object_type version species    start                 biotype          Parent
#> 1   Transcript       3   human 41196312          protein_coding ENSG00000012048
#> 2   Transcript       1   human 41196822          protein_coding ENSG00000012048
#> 3   Transcript       1   human 41197580          protein_coding ENSG00000012048
#> 4   Transcript       1   human 41197580          protein_coding ENSG00000012048
#> 5   Transcript       1   human 41197580          protein_coding ENSG00000012048
#> 6   Transcript       1   human 41197646          protein_coding ENSG00000012048
#> 7   Transcript       2   human 41197646          protein_coding ENSG00000012048
#> 8   Transcript       1   human 41197695 nonsense_mediated_decay ENSG00000012048
#> 9   Transcript       2   human 41197695          protein_coding ENSG00000012048
#> 10  Transcript       1   human 41215361          protein_coding ENSG00000012048
#> 11  Transcript       1   human 41215361          protein_coding ENSG00000012048
#> 12  Transcript       1   human 41215377          protein_coding ENSG00000012048
#> 13  Transcript       1   human 41219291         retained_intron ENSG00000012048
#> 14  Transcript       1   human 41228505          protein_coding ENSG00000012048
#> 15  Transcript       1   human 41228554          protein_coding ENSG00000012048
#> 16  Transcript       1   human 41243115         retained_intron ENSG00000012048
#> 17  Transcript       3   human 41245587          non_stop_decay ENSG00000012048
#> 18  Transcript       1   human 41245601          protein_coding ENSG00000012048
#> 19  Transcript       1   human 41245603          protein_coding ENSG00000012048
#> 20  Transcript       1   human 41246129 nonsense_mediated_decay ENSG00000012048
#> 21  Transcript       1   human 41246129          protein_coding ENSG00000012048
#> 22  Transcript       1   human 41246129          protein_coding ENSG00000012048
#> 23  Transcript       1   human 41246187          protein_coding ENSG00000012048
#> 24  Transcript       1   human 41247863          protein_coding ENSG00000012048
#> 25  Transcript       1   human 41251848 nonsense_mediated_decay ENSG00000012048
#> 26  Transcript       1   human 41256206          protein_coding ENSG00000012048
#> 27  Transcript       3   human 41196313          protein_coding ENSG00000012048
#> 28  Transcript       3   human 41196313          protein_coding ENSG00000012048
#> 29  Transcript       3   human 41196313          protein_coding ENSG00000012048
#> 30  Transcript       3   human 41196313          protein_coding ENSG00000012048
#> 31  Transcript       4   human 41196313          protein_coding ENSG00000012048
#>    is_canonical Translation.Parent Translation.length Translation.start
#> 1             0    ENST00000357654               1863          41197695
#> 2             0    ENST00000468300                699          41197801
#> 3             0    ENST00000586385                173          41197695
#> 4             0    ENST00000591534                354          41197695
#> 5             0    ENST00000591849                 96          41197695
#> 6             0    ENST00000493795               1816          41197695
#> 7             1    ENST00000471181               1884          41197695
#> 8             0    ENST00000461221                 63          41256972
#> 9             0    ENST00000491747                759          41197695
#> 10            0    ENST00000484087                498          41215361
#> 11            0    ENST00000478531                623          41215361
#> 12            0    ENST00000493919                572          41215377
#> 13            0               <NA>                 NA                NA
#> 14            0    ENST00000487825                266          41228505
#> 15            0    ENST00000461574                242          41228554
#> 16            0               <NA>                 NA                NA
#> 17            0    ENST00000412061                437          41245587
#> 18            0    ENST00000470026                649          41245601
#> 19            0    ENST00000477152                622          41245603
#> 20            0    ENST00000492859                 59          41262552
#> 21            0    ENST00000497488                177          41246129
#> 22            0    ENST00000494123                473          41246129
#> 23            0    ENST00000473961                319          41246187
#> 24            0    ENST00000476777                222          41247863
#> 25            0    ENST00000461798                 63          41256972
#> 26            0    ENST00000489037                 98          41256206
#> 27            0    ENST00000354071               1598          41197695
#> 28            0    ENST00000352993                721          41197695
#> 29            0    ENST00000346315               1624          41197695
#> 30            0    ENST00000351666                680          41197695
#> 31            0    ENST00000309486               1567          41197695
#>     Translation.id Translation.end Translation.species Translation.version
#> 1  ENSP00000350283        41276113               human                   3
#> 2  ENSP00000417148        41276113               human                   1
#> 3  ENSP00000465818        41277202               human                   1
#> 4  ENSP00000467329        41226495               human                   1
#> 5  ENSP00000465347        41202109               human                   1
#> 6  ENSP00000418775        41258543               human                   1
#> 7  ENSP00000418960        41276113               human                   2
#> 8  ENSP00000418548        41276113               human                   1
#> 9  ENSP00000420705        41276113               human                   2
#> 10 ENSP00000419481        41256933               human                   1
#> 11 ENSP00000420412        41276113               human                   1
#> 12 ENSP00000418819        41258543               human                   1
#> 13            <NA>              NA                <NA>                  NA
#> 14 ENSP00000418212        41256933               human                   1
#> 15 ENSP00000417241        41243841               human                   1
#> 16            <NA>              NA                <NA>                  NA
#> 17 ENSP00000397145        41247883               human                   3
#> 18 ENSP00000419274        41276113               human                   1
#> 19 ENSP00000419988        41276113               human                   1
#> 20 ENSP00000420253        41276113               human                   1
#> 21 ENSP00000418986        41246659               human                   1
#> 22 ENSP00000419103        41276113               human                   1
#> 23 ENSP00000420201        41256908               human                   1
#> 24 ENSP00000417554        41276113               human                   1
#> 25 ENSP00000417988        41276113               human                   1
#> 26 ENSP00000420781        41276113               human                   1
#> 27 ENSP00000326002        41276113               human                   6
#> 28 ENSP00000312236        41276113               human                   5
#> 29 ENSP00000246907        41276113               human                   4
#> 30 ENSP00000338007        41276113               human                   3
#> 31 ENSP00000310938        41246659               human                   4
#>    Translation.object_type Translation.db_type
#> 1              Translation                core
#> 2              Translation                core
#> 3              Translation                core
#> 4              Translation                core
#> 5              Translation                core
#> 6              Translation                core
#> 7              Translation                core
#> 8              Translation                core
#> 9              Translation                core
#> 10             Translation                core
#> 11             Translation                core
#> 12             Translation                core
#> 13                    <NA>                <NA>
#> 14             Translation                core
#> 15             Translation                core
#> 16                    <NA>                <NA>
#> 17             Translation                core
#> 18             Translation                core
#> 19             Translation                core
#> 20             Translation                core
#> 21             Translation                core
#> 22             Translation                core
#> 23             Translation                core
#> 24             Translation                core
#> 25             Translation                core
#> 26             Translation                core
#> 27             Translation                core
#> 28             Translation                core
#> 29             Translation                core
#> 30             Translation                core
#> 31             Translation                core
#> 
#> $display_name
#> [1] "BRCA1"
#> 
#> $db_type
#> [1] "core"
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#> 
#> $source
#> [1] "ensembl_havana"
#> 
#> $species
#> [1] "human"
#> 
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $version
#> [1] 15
#> 
#> $start
#> [1] 41196312
#> 
#> $biotype
#> [1] "protein_coding"
#> 
queryEnsemblByGene("ENSG00000139618")
#> $species
#> [1] "homo_sapiens"
#> 
#> $end
#> [1] 32973805
#> 
#> $seq_region_name
#> [1] "13"
#> 
#> $canonical_transcript
#> [1] "ENST00000544455.1"
#> 
#> $start
#> [1] 32889611
#> 
#> $Transcript
#>        end seq_region_name      species         Exon display_name version
#> 1 32973347              13 homo_sapiens c(328896....    BRCA2-001       3
#> 2 32907428              13 homo_sapiens c(328896....    BRCA2-003       2
#> 3 32953632              13 homo_sapiens c("Exon"....    BRCA2-005       1
#> 4 32972409              13 homo_sapiens c("Exon"....    BRCA2-002       1
#> 5 32972585              13 homo_sapiens c("ENSE0....    BRCA2-006       1
#> 6 32973805              13 homo_sapiens c(328896....    BRCA2-201       1
#>                id          Parent    start                logic_name db_type
#> 1 ENST00000380152 ENSG00000139618 32889611 ensembl_havana_transcript    core
#> 2 ENST00000530893 ENSG00000139618 32889642    havana_homo_sapiens_37    core
#> 3 ENST00000528762 ENSG00000139618 32945108    havana_homo_sapiens_37    core
#> 4 ENST00000470094 ENSG00000139618 32953977    havana_homo_sapiens_37    core
#> 5 ENST00000533776 ENSG00000139618 32970946    havana_homo_sapiens_37    core
#> 6 ENST00000544455 ENSG00000139618 32889617   ensembl_homo_sapiens_37    core
#>   object_type is_canonical strand assembly_name         source
#> 1  Transcript            0      1        GRCh37 ensembl_havana
#> 2  Transcript            0      1        GRCh37         havana
#> 3  Transcript            0      1        GRCh37         havana
#> 4  Transcript            0      1        GRCh37         havana
#> 5  Transcript            0      1        GRCh37         havana
#> 6  Transcript            1      1        GRCh37        ensembl
#>                   biotype Translation.length  Translation.id
#> 1          protein_coding               3418 ENSP00000369497
#> 2          protein_coding                481 ENSP00000435699
#> 3 nonsense_mediated_decay                 64 ENSP00000433168
#> 4 nonsense_mediated_decay                186 ENSP00000434898
#> 5         retained_intron                 NA            <NA>
#> 6          protein_coding               3418 ENSP00000439902
#>   Translation.version Translation.Parent Translation.start Translation.end
#> 1                   3    ENST00000380152          32890598        32972907
#> 2                   2    ENST00000530893          32899266        32907428
#> 3                   1    ENST00000528762          32945108        32950807
#> 4                   1    ENST00000470094          32953977        32970229
#> 5                  NA               <NA>                NA              NA
#> 6                   1    ENST00000544455          32890598        32972907
#>   Translation.species Translation.db_type Translation.object_type
#> 1        homo_sapiens                core             Translation
#> 2        homo_sapiens                core             Translation
#> 3        homo_sapiens                core             Translation
#> 4        homo_sapiens                core             Translation
#> 5                <NA>                <NA>                    <NA>
#> 6        homo_sapiens                core             Translation
#> 
#> $display_name
#> [1] "BRCA2"
#> 
#> $id
#> [1] "ENSG00000139618"
#> 
#> $version
#> [1] 10
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#> 
#> $db_type
#> [1] "core"
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $description
#> [1] "breast cancer 2, early onset [Source:HGNC Symbol;Acc:1101]"
#> 
#> $strand
#> [1] 1
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $source
#> [1] "ensembl_havana"
#> 
#> $biotype
#> [1] "protein_coding"
#> 
event <- "SE_17_-_41251792_41249306_41249261_41246877_BRCA1"
queryEnsemblByEvent(event, species="human", assembly="hg19")
#> $start
#> [1] 41196312
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#> 
#> $source
#> [1] "ensembl_havana"
#> 
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#> 
#> $species
#> [1] "human"
#> 
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $biotype
#> [1] "protein_coding"
#> 
#> $version
#> [1] 15
#> 
#> $end
#> [1] 41277500
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $strand
#> [1] -1
#> 
#> $Transcript
#>    strand object_type display_name              id seq_region_name db_type
#> 1      -1  Transcript    BRCA1-001 ENST00000357654              17    core
#> 2      -1  Transcript    BRCA1-007 ENST00000468300              17    core
#> 3      -1  Transcript    BRCA1-023 ENST00000586385              17    core
#> 4      -1  Transcript    BRCA1-024 ENST00000591534              17    core
#> 5      -1  Transcript    BRCA1-025 ENST00000591849              17    core
#> 6      -1  Transcript    BRCA1-006 ENST00000493795              17    core
#> 7      -1  Transcript    BRCA1-005 ENST00000471181              17    core
#> 8      -1  Transcript    BRCA1-010 ENST00000461221              17    core
#> 9      -1  Transcript    BRCA1-014 ENST00000491747              17    core
#> 10     -1  Transcript    BRCA1-015 ENST00000484087              17    core
#> 11     -1  Transcript    BRCA1-009 ENST00000478531              17    core
#> 12     -1  Transcript    BRCA1-008 ENST00000493919              17    core
#> 13     -1  Transcript    BRCA1-021 ENST00000472490              17    core
#> 14     -1  Transcript    BRCA1-019 ENST00000487825              17    core
#> 15     -1  Transcript    BRCA1-022 ENST00000461574              17    core
#> 16     -1  Transcript    BRCA1-012 ENST00000467274              17    core
#> 17     -1  Transcript    BRCA1-026 ENST00000412061              17    core
#> 18     -1  Transcript    BRCA1-011 ENST00000470026              17    core
#> 19     -1  Transcript    BRCA1-004 ENST00000477152              17    core
#> 20     -1  Transcript    BRCA1-002 ENST00000492859              17    core
#> 21     -1  Transcript    BRCA1-003 ENST00000497488              17    core
#> 22     -1  Transcript    BRCA1-013 ENST00000494123              17    core
#> 23     -1  Transcript    BRCA1-018 ENST00000473961              17    core
#> 24     -1  Transcript    BRCA1-017 ENST00000476777              17    core
#> 25     -1  Transcript    BRCA1-020 ENST00000461798              17    core
#> 26     -1  Transcript    BRCA1-016 ENST00000489037              17    core
#> 27     -1  Transcript    BRCA1-205 ENST00000354071              17    core
#> 28     -1  Transcript    BRCA1-204 ENST00000352993              17    core
#> 29     -1  Transcript    BRCA1-202 ENST00000346315              17    core
#> 30     -1  Transcript    BRCA1-203 ENST00000351666              17    core
#> 31     -1  Transcript    BRCA1-201 ENST00000309486              17    core
#>       start         source                logic_name         Exon
#> 1  41196312 ensembl_havana ensembl_havana_transcript c("17", ....
#> 2  41196822 ensembl_havana ensembl_havana_transcript c("GRCh3....
#> 3  41197580         havana    havana_homo_sapiens_37 c("17", ....
#> 4  41197580         havana    havana_homo_sapiens_37 c("human....
#> 5  41197580         havana    havana_homo_sapiens_37 c("human....
#> 6  41197646 ensembl_havana ensembl_havana_transcript c(1, 1, ....
#> 7  41197646 ensembl_havana ensembl_havana_transcript c("human....
#> 8  41197695         havana    havana_homo_sapiens_37 c("ENSE0....
#> 9  41197695         havana    havana_homo_sapiens_37 c(1, 1, ....
#> 10 41215361         havana    havana_homo_sapiens_37 c("GRCh3....
#> 11 41215361         havana    havana_homo_sapiens_37 c("ENSE0....
#> 12 41215377         havana    havana_homo_sapiens_37 c("human....
#> 13 41219291         havana    havana_homo_sapiens_37 c("human....
#> 14 41228505         havana    havana_homo_sapiens_37 c("core"....
#> 15 41228554         havana    havana_homo_sapiens_37 c(412438....
#> 16 41243115         havana    havana_homo_sapiens_37 c("Exon"....
#> 17 41245587         havana    havana_homo_sapiens_37 c("human....
#> 18 41245601         havana    havana_homo_sapiens_37 c("human....
#> 19 41245603         havana    havana_homo_sapiens_37 c("GRCh3....
#> 20 41246129         havana    havana_homo_sapiens_37 c("human....
#> 21 41246129         havana    havana_homo_sapiens_37 c("17", ....
#> 22 41246129         havana    havana_homo_sapiens_37 c(412772....
#> 23 41246187         havana    havana_homo_sapiens_37 c(-1, -1....
#> 24 41247863         havana    havana_homo_sapiens_37 c("GRCh3....
#> 25 41251848         havana    havana_homo_sapiens_37 c("human....
#> 26 41256206         havana    havana_homo_sapiens_37 c("human....
#> 27 41196313        ensembl   ensembl_homo_sapiens_37 c(412772....
#> 28 41196313        ensembl   ensembl_homo_sapiens_37 c("human....
#> 29 41196313        ensembl   ensembl_homo_sapiens_37 c("human....
#> 30 41196313        ensembl   ensembl_homo_sapiens_37 c(412760....
#> 31 41196313        ensembl   ensembl_homo_sapiens_37 c("core"....
#>    Translation.species Translation.object_type Translation.start
#> 1                human             Translation          41197695
#> 2                human             Translation          41197801
#> 3                human             Translation          41197695
#> 4                human             Translation          41197695
#> 5                human             Translation          41197695
#> 6                human             Translation          41197695
#> 7                human             Translation          41197695
#> 8                human             Translation          41256972
#> 9                human             Translation          41197695
#> 10               human             Translation          41215361
#> 11               human             Translation          41215361
#> 12               human             Translation          41215377
#> 13                <NA>                    <NA>                NA
#> 14               human             Translation          41228505
#> 15               human             Translation          41228554
#> 16                <NA>                    <NA>                NA
#> 17               human             Translation          41245587
#> 18               human             Translation          41245601
#> 19               human             Translation          41245603
#> 20               human             Translation          41262552
#> 21               human             Translation          41246129
#> 22               human             Translation          41246129
#> 23               human             Translation          41246187
#> 24               human             Translation          41247863
#> 25               human             Translation          41256972
#> 26               human             Translation          41256206
#> 27               human             Translation          41197695
#> 28               human             Translation          41197695
#> 29               human             Translation          41197695
#> 30               human             Translation          41197695
#> 31               human             Translation          41197695
#>    Translation.length Translation.end Translation.version Translation.db_type
#> 1                1863        41276113                   3                core
#> 2                 699        41276113                   1                core
#> 3                 173        41277202                   1                core
#> 4                 354        41226495                   1                core
#> 5                  96        41202109                   1                core
#> 6                1816        41258543                   1                core
#> 7                1884        41276113                   2                core
#> 8                  63        41276113                   1                core
#> 9                 759        41276113                   2                core
#> 10                498        41256933                   1                core
#> 11                623        41276113                   1                core
#> 12                572        41258543                   1                core
#> 13                 NA              NA                  NA                <NA>
#> 14                266        41256933                   1                core
#> 15                242        41243841                   1                core
#> 16                 NA              NA                  NA                <NA>
#> 17                437        41247883                   3                core
#> 18                649        41276113                   1                core
#> 19                622        41276113                   1                core
#> 20                 59        41276113                   1                core
#> 21                177        41246659                   1                core
#> 22                473        41276113                   1                core
#> 23                319        41256908                   1                core
#> 24                222        41276113                   1                core
#> 25                 63        41276113                   1                core
#> 26                 98        41276113                   1                core
#> 27               1598        41276113                   6                core
#> 28                721        41276113                   5                core
#> 29               1624        41276113                   4                core
#> 30                680        41276113                   3                core
#> 31               1567        41246659                   4                core
#>     Translation.id Translation.Parent species assembly_name          Parent
#> 1  ENSP00000350283    ENST00000357654   human        GRCh37 ENSG00000012048
#> 2  ENSP00000417148    ENST00000468300   human        GRCh37 ENSG00000012048
#> 3  ENSP00000465818    ENST00000586385   human        GRCh37 ENSG00000012048
#> 4  ENSP00000467329    ENST00000591534   human        GRCh37 ENSG00000012048
#> 5  ENSP00000465347    ENST00000591849   human        GRCh37 ENSG00000012048
#> 6  ENSP00000418775    ENST00000493795   human        GRCh37 ENSG00000012048
#> 7  ENSP00000418960    ENST00000471181   human        GRCh37 ENSG00000012048
#> 8  ENSP00000418548    ENST00000461221   human        GRCh37 ENSG00000012048
#> 9  ENSP00000420705    ENST00000491747   human        GRCh37 ENSG00000012048
#> 10 ENSP00000419481    ENST00000484087   human        GRCh37 ENSG00000012048
#> 11 ENSP00000420412    ENST00000478531   human        GRCh37 ENSG00000012048
#> 12 ENSP00000418819    ENST00000493919   human        GRCh37 ENSG00000012048
#> 13            <NA>               <NA>   human        GRCh37 ENSG00000012048
#> 14 ENSP00000418212    ENST00000487825   human        GRCh37 ENSG00000012048
#> 15 ENSP00000417241    ENST00000461574   human        GRCh37 ENSG00000012048
#> 16            <NA>               <NA>   human        GRCh37 ENSG00000012048
#> 17 ENSP00000397145    ENST00000412061   human        GRCh37 ENSG00000012048
#> 18 ENSP00000419274    ENST00000470026   human        GRCh37 ENSG00000012048
#> 19 ENSP00000419988    ENST00000477152   human        GRCh37 ENSG00000012048
#> 20 ENSP00000420253    ENST00000492859   human        GRCh37 ENSG00000012048
#> 21 ENSP00000418986    ENST00000497488   human        GRCh37 ENSG00000012048
#> 22 ENSP00000419103    ENST00000494123   human        GRCh37 ENSG00000012048
#> 23 ENSP00000420201    ENST00000473961   human        GRCh37 ENSG00000012048
#> 24 ENSP00000417554    ENST00000476777   human        GRCh37 ENSG00000012048
#> 25 ENSP00000417988    ENST00000461798   human        GRCh37 ENSG00000012048
#> 26 ENSP00000420781    ENST00000489037   human        GRCh37 ENSG00000012048
#> 27 ENSP00000326002    ENST00000354071   human        GRCh37 ENSG00000012048
#> 28 ENSP00000312236    ENST00000352993   human        GRCh37 ENSG00000012048
#> 29 ENSP00000246907    ENST00000346315   human        GRCh37 ENSG00000012048
#> 30 ENSP00000338007    ENST00000351666   human        GRCh37 ENSG00000012048
#> 31 ENSP00000310938    ENST00000309486   human        GRCh37 ENSG00000012048
#>    is_canonical                 biotype version      end
#> 1             0          protein_coding       3 41277387
#> 2             0          protein_coding       1 41277468
#> 3             0          protein_coding       1 41277346
#> 4             0          protein_coding       1 41277346
#> 5             0          protein_coding       1 41277346
#> 6             0          protein_coding       1 41277419
#> 7             1          protein_coding       2 41277500
#> 8             0 nonsense_mediated_decay       1 41277305
#> 9             0          protein_coding       2 41277373
#> 10            0          protein_coding       1 41256933
#> 11            0          protein_coding       1 41277376
#> 12            0          protein_coding       1 41277419
#> 13            0         retained_intron       1 41223083
#> 14            0          protein_coding       1 41256933
#> 15            0          protein_coding       1 41243841
#> 16            0         retained_intron       1 41277332
#> 17            0          non_stop_decay       3 41247883
#> 18            0          protein_coding       1 41277340
#> 19            0          protein_coding       1 41277381
#> 20            0 nonsense_mediated_decay       1 41277317
#> 21            0          protein_coding       1 41277317
#> 22            0          protein_coding       1 41277467
#> 23            0          protein_coding       1 41256908
#> 24            0          protein_coding       1 41277370
#> 25            0 nonsense_mediated_decay       1 41277387
#> 26            0          protein_coding       1 41277338
#> 27            0          protein_coding       3 41277500
#> 28            0          protein_coding       3 41277500
#> 29            0          protein_coding       3 41277468
#> 30            0          protein_coding       3 41276132
#> 31            0          protein_coding       4 41277468
#> 
#> $id
#> [1] "ENSG00000012048"
#> 
#> $display_name
#> [1] "BRCA1"
#> 
#> $seq_region_name
#> [1] "17"
#> 
#> $db_type
#> [1] "core"
#>