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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")
#> $db_type
#> [1] "core"
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $display_name
#> [1] "BRCA1"
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $id
#> [1] "ENSG00000012048"
#> 
#> $Transcript
#>       start length gencode_primary version              id assembly_name
#> 1  41196312   7094               0       3 ENST00000357654        GRCh37
#> 2  41196822   3273               0       1 ENST00000468300        GRCh37
#> 3  41197580    781               0       1 ENST00000586385        GRCh37
#> 4  41197580   1282               0       1 ENST00000591534        GRCh37
#> 5  41197580    563               0       1 ENST00000591849        GRCh37
#> 6  41197646   5732               0       1 ENST00000493795        GRCh37
#> 7  41197646   5936               0       2 ENST00000471181        GRCh37
#> 8  41197695   5693               0       1 ENST00000461221        GRCh37
#> 9  41197695   2379               0       2 ENST00000491747        GRCh37
#> 10 41215361   1495               0       1 ENST00000484087        GRCh37
#> 11 41215361   1972               0       1 ENST00000478531        GRCh37
#> 12 41215377   1948               0       1 ENST00000493919        GRCh37
#> 13 41219291    561               0       1 ENST00000472490        GRCh37
#> 14 41228505    800               0       1 ENST00000487825        GRCh37
#> 15 41228554    726               0       1 ENST00000461574        GRCh37
#> 16 41243115   4497               0       1 ENST00000467274        GRCh37
#> 17 41245587   1312               0       3 ENST00000412061        GRCh37
#> 18 41245601   2108               0       1 ENST00000470026        GRCh37
#> 19 41245603   1980               0       1 ENST00000477152        GRCh37
#> 20 41246129   1584               0       1 ENST00000492859        GRCh37
#> 21 41246129    779               0       1 ENST00000497488        GRCh37
#> 22 41246129   1612               0       1 ENST00000494123        GRCh37
#> 23 41246187    958               0       1 ENST00000473961        GRCh37
#> 24 41247863    769               0       1 ENST00000476777        GRCh37
#> 25 41251848    582               0       1 ENST00000461798        GRCh37
#> 26 41256206    455               0       1 ENST00000489037        GRCh37
#> 27 41196313   6411               0       3 ENST00000354071        GRCh37
#> 28 41196313   3780               0       3 ENST00000352993        GRCh37
#> 29 41196313   6451               0       3 ENST00000346315        GRCh37
#> 30 41196313   3444               0       3 ENST00000351666        GRCh37
#> 31 41196313   7114               0       4 ENST00000309486        GRCh37
#>    display_name         Exon object_type Translation.object_type
#> 1     BRCA1-001 c("ENSE0....  Transcript             Translation
#> 2     BRCA1-007 c("Exon"....  Transcript             Translation
#> 3     BRCA1-023 c("core"....  Transcript             Translation
#> 4     BRCA1-024 c("Exon"....  Transcript             Translation
#> 5     BRCA1-025 c("Exon"....  Transcript             Translation
#> 6     BRCA1-006 c(412774....  Transcript             Translation
#> 7     BRCA1-005 c("Exon"....  Transcript             Translation
#> 8     BRCA1-010 c(412773....  Transcript             Translation
#> 9     BRCA1-014 c("core"....  Transcript             Translation
#> 10    BRCA1-015 c("Exon"....  Transcript             Translation
#> 11    BRCA1-009 c("core"....  Transcript             Translation
#> 12    BRCA1-008 c("Exon"....  Transcript             Translation
#> 13    BRCA1-021 c("Exon"....  Transcript                    <NA>
#> 14    BRCA1-019 c("GRCh3....  Transcript             Translation
#> 15    BRCA1-022 c("ENSE0....  Transcript             Translation
#> 16    BRCA1-012 c("ENSE0....  Transcript                    <NA>
#> 17    BRCA1-026 c("Exon"....  Transcript             Translation
#> 18    BRCA1-011 c(1, 1, ....  Transcript             Translation
#> 19    BRCA1-004 c("core"....  Transcript             Translation
#> 20    BRCA1-002 c(-1, -1....  Transcript             Translation
#> 21    BRCA1-003 c(412772....  Transcript             Translation
#> 22    BRCA1-013 c("Exon"....  Transcript             Translation
#> 23    BRCA1-018 c("Exon"....  Transcript             Translation
#> 24    BRCA1-017 c("core"....  Transcript             Translation
#> 25    BRCA1-020 c("core"....  Transcript             Translation
#> 26    BRCA1-016 c(-1, -1....  Transcript             Translation
#> 27    BRCA1-205 c("ENSE0....  Transcript             Translation
#> 28    BRCA1-204 c("GRCh3....  Transcript             Translation
#> 29    BRCA1-202 c("core"....  Transcript             Translation
#> 30    BRCA1-203 c(412760....  Transcript             Translation
#> 31    BRCA1-201 c("Exon"....  Transcript             Translation
#>    Translation.db_type Translation.species Translation.version
#> 1                 core               human                   3
#> 2                 core               human                   1
#> 3                 core               human                   1
#> 4                 core               human                   1
#> 5                 core               human                   1
#> 6                 core               human                   1
#> 7                 core               human                   2
#> 8                 core               human                   1
#> 9                 core               human                   2
#> 10                core               human                   1
#> 11                core               human                   1
#> 12                core               human                   1
#> 13                <NA>                <NA>                  NA
#> 14                core               human                   1
#> 15                core               human                   1
#> 16                <NA>                <NA>                  NA
#> 17                core               human                   3
#> 18                core               human                   1
#> 19                core               human                   1
#> 20                core               human                   1
#> 21                core               human                   1
#> 22                core               human                   1
#> 23                core               human                   1
#> 24                core               human                   1
#> 25                core               human                   1
#> 26                core               human                   1
#> 27                core               human                   6
#> 28                core               human                   5
#> 29                core               human                   4
#> 30                core               human                   3
#> 31                core               human                   4
#>    Translation.Parent Translation.length Translation.start Translation.end
#> 1     ENST00000357654               1863          41197695        41276113
#> 2     ENST00000468300                699          41197801        41276113
#> 3     ENST00000586385                173          41197695        41277202
#> 4     ENST00000591534                354          41197695        41226495
#> 5     ENST00000591849                 96          41197695        41202109
#> 6     ENST00000493795               1816          41197695        41258543
#> 7     ENST00000471181               1884          41197695        41276113
#> 8     ENST00000461221                 63          41256972        41276113
#> 9     ENST00000491747                759          41197695        41276113
#> 10    ENST00000484087                498          41215361        41256933
#> 11    ENST00000478531                623          41215361        41276113
#> 12    ENST00000493919                572          41215377        41258543
#> 13               <NA>                 NA                NA              NA
#> 14    ENST00000487825                266          41228505        41256933
#> 15    ENST00000461574                242          41228554        41243841
#> 16               <NA>                 NA                NA              NA
#> 17    ENST00000412061                437          41245587        41247883
#> 18    ENST00000470026                649          41245601        41276113
#> 19    ENST00000477152                622          41245603        41276113
#> 20    ENST00000492859                 59          41262552        41276113
#> 21    ENST00000497488                177          41246129        41246659
#> 22    ENST00000494123                473          41246129        41276113
#> 23    ENST00000473961                319          41246187        41256908
#> 24    ENST00000476777                222          41247863        41276113
#> 25    ENST00000461798                 63          41256972        41276113
#> 26    ENST00000489037                 98          41256206        41276113
#> 27    ENST00000354071               1598          41197695        41276113
#> 28    ENST00000352993                721          41197695        41276113
#> 29    ENST00000346315               1624          41197695        41276113
#> 30    ENST00000351666                680          41197695        41276113
#> 31    ENST00000309486               1567          41197695        41246659
#>     Translation.id db_type          Parent seq_region_name
#> 1  ENSP00000350283    core ENSG00000012048              17
#> 2  ENSP00000417148    core ENSG00000012048              17
#> 3  ENSP00000465818    core ENSG00000012048              17
#> 4  ENSP00000467329    core ENSG00000012048              17
#> 5  ENSP00000465347    core ENSG00000012048              17
#> 6  ENSP00000418775    core ENSG00000012048              17
#> 7  ENSP00000418960    core ENSG00000012048              17
#> 8  ENSP00000418548    core ENSG00000012048              17
#> 9  ENSP00000420705    core ENSG00000012048              17
#> 10 ENSP00000419481    core ENSG00000012048              17
#> 11 ENSP00000420412    core ENSG00000012048              17
#> 12 ENSP00000418819    core ENSG00000012048              17
#> 13            <NA>    core ENSG00000012048              17
#> 14 ENSP00000418212    core ENSG00000012048              17
#> 15 ENSP00000417241    core ENSG00000012048              17
#> 16            <NA>    core ENSG00000012048              17
#> 17 ENSP00000397145    core ENSG00000012048              17
#> 18 ENSP00000419274    core ENSG00000012048              17
#> 19 ENSP00000419988    core ENSG00000012048              17
#> 20 ENSP00000420253    core ENSG00000012048              17
#> 21 ENSP00000418986    core ENSG00000012048              17
#> 22 ENSP00000419103    core ENSG00000012048              17
#> 23 ENSP00000420201    core ENSG00000012048              17
#> 24 ENSP00000417554    core ENSG00000012048              17
#> 25 ENSP00000417988    core ENSG00000012048              17
#> 26 ENSP00000420781    core ENSG00000012048              17
#> 27 ENSP00000326002    core ENSG00000012048              17
#> 28 ENSP00000312236    core ENSG00000012048              17
#> 29 ENSP00000246907    core ENSG00000012048              17
#> 30 ENSP00000338007    core ENSG00000012048              17
#> 31 ENSP00000310938    core ENSG00000012048              17
#>                    biotype species strand                logic_name      end
#> 1           protein_coding   human     -1 ensembl_havana_transcript 41277387
#> 2           protein_coding   human     -1 ensembl_havana_transcript 41277468
#> 3           protein_coding   human     -1    havana_homo_sapiens_37 41277346
#> 4           protein_coding   human     -1    havana_homo_sapiens_37 41277346
#> 5           protein_coding   human     -1    havana_homo_sapiens_37 41277346
#> 6           protein_coding   human     -1 ensembl_havana_transcript 41277419
#> 7           protein_coding   human     -1 ensembl_havana_transcript 41277500
#> 8  nonsense_mediated_decay   human     -1    havana_homo_sapiens_37 41277305
#> 9           protein_coding   human     -1    havana_homo_sapiens_37 41277373
#> 10          protein_coding   human     -1    havana_homo_sapiens_37 41256933
#> 11          protein_coding   human     -1    havana_homo_sapiens_37 41277376
#> 12          protein_coding   human     -1    havana_homo_sapiens_37 41277419
#> 13         retained_intron   human     -1    havana_homo_sapiens_37 41223083
#> 14          protein_coding   human     -1    havana_homo_sapiens_37 41256933
#> 15          protein_coding   human     -1    havana_homo_sapiens_37 41243841
#> 16         retained_intron   human     -1    havana_homo_sapiens_37 41277332
#> 17          non_stop_decay   human     -1    havana_homo_sapiens_37 41247883
#> 18          protein_coding   human     -1    havana_homo_sapiens_37 41277340
#> 19          protein_coding   human     -1    havana_homo_sapiens_37 41277381
#> 20 nonsense_mediated_decay   human     -1    havana_homo_sapiens_37 41277317
#> 21          protein_coding   human     -1    havana_homo_sapiens_37 41277317
#> 22          protein_coding   human     -1    havana_homo_sapiens_37 41277467
#> 23          protein_coding   human     -1    havana_homo_sapiens_37 41256908
#> 24          protein_coding   human     -1    havana_homo_sapiens_37 41277370
#> 25 nonsense_mediated_decay   human     -1    havana_homo_sapiens_37 41277387
#> 26          protein_coding   human     -1    havana_homo_sapiens_37 41277338
#> 27          protein_coding   human     -1   ensembl_homo_sapiens_37 41277500
#> 28          protein_coding   human     -1   ensembl_homo_sapiens_37 41277500
#> 29          protein_coding   human     -1   ensembl_homo_sapiens_37 41277468
#> 30          protein_coding   human     -1   ensembl_homo_sapiens_37 41276132
#> 31          protein_coding   human     -1   ensembl_homo_sapiens_37 41277468
#>            source is_canonical
#> 1  ensembl_havana            0
#> 2  ensembl_havana            0
#> 3          havana            0
#> 4          havana            0
#> 5          havana            0
#> 6  ensembl_havana            0
#> 7  ensembl_havana            1
#> 8          havana            0
#> 9          havana            0
#> 10         havana            0
#> 11         havana            0
#> 12         havana            0
#> 13         havana            0
#> 14         havana            0
#> 15         havana            0
#> 16         havana            0
#> 17         havana            0
#> 18         havana            0
#> 19         havana            0
#> 20         havana            0
#> 21         havana            0
#> 22         havana            0
#> 23         havana            0
#> 24         havana            0
#> 25         havana            0
#> 26         havana            0
#> 27        ensembl            0
#> 28        ensembl            0
#> 29        ensembl            0
#> 30        ensembl            0
#> 31        ensembl            0
#> 
#> $version
#> [1] 15
#> 
#> $start
#> [1] 41196312
#> 
#> $source
#> [1] "ensembl_havana"
#> 
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#> 
#> $end
#> [1] 41277500
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#> 
#> $strand
#> [1] -1
#> 
#> $biotype
#> [1] "protein_coding"
#> 
#> $species
#> [1] "human"
#> 
#> $seq_region_name
#> [1] "17"
#> 
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#> 
queryEnsemblByGene("ENSG00000139618")
#> $description
#> [1] "breast cancer 2, early onset [Source:HGNC Symbol;Acc:1101]"
#> 
#> $db_type
#> [1] "core"
#> 
#> $end
#> [1] 32973805
#> 
#> $seq_region_name
#> [1] "13"
#> 
#> $species
#> [1] "homo_sapiens"
#> 
#> $strand
#> [1] 1
#> 
#> $biotype
#> [1] "protein_coding"
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $version
#> [1] 10
#> 
#> $id
#> [1] "ENSG00000139618"
#> 
#> $Transcript
#>                id gencode_primary                logic_name object_type
#> 1 ENST00000380152               0 ensembl_havana_transcript  Transcript
#> 2 ENST00000530893               0    havana_homo_sapiens_37  Transcript
#> 3 ENST00000528762               0    havana_homo_sapiens_37  Transcript
#> 4 ENST00000470094               0    havana_homo_sapiens_37  Transcript
#> 5 ENST00000533776               0    havana_homo_sapiens_37  Transcript
#> 6 ENST00000544455               0   ensembl_homo_sapiens_37  Transcript
#>                   biotype version assembly_name length         source
#> 1          protein_coding       3        GRCh37  10930 ensembl_havana
#> 2          protein_coding       2        GRCh37   2011         havana
#> 3 nonsense_mediated_decay       1        GRCh37    495         havana
#> 4 nonsense_mediated_decay       1        GRCh37    842         havana
#> 5         retained_intron       1        GRCh37    523         havana
#> 6          protein_coding       1        GRCh37  10984        ensembl
#>   Translation.Parent Translation.end  Translation.id Translation.version
#> 1    ENST00000380152        32972907 ENSP00000369497                   3
#> 2    ENST00000530893        32907428 ENSP00000435699                   2
#> 3    ENST00000528762        32950807 ENSP00000433168                   1
#> 4    ENST00000470094        32970229 ENSP00000434898                   1
#> 5               <NA>              NA            <NA>                  NA
#> 6    ENST00000544455        32972907 ENSP00000439902                   1
#>   Translation.object_type Translation.db_type Translation.length
#> 1             Translation                core               3418
#> 2             Translation                core                481
#> 3             Translation                core                 64
#> 4             Translation                core                186
#> 5                    <NA>                <NA>                 NA
#> 6             Translation                core               3418
#>   Translation.start Translation.species display_name    start      end
#> 1          32890598        homo_sapiens    BRCA2-001 32889611 32973347
#> 2          32899266        homo_sapiens    BRCA2-003 32889642 32907428
#> 3          32945108        homo_sapiens    BRCA2-005 32945108 32953632
#> 4          32953977        homo_sapiens    BRCA2-002 32953977 32972409
#> 5                NA                <NA>    BRCA2-006 32970946 32972585
#> 6          32890598        homo_sapiens    BRCA2-201 32889617 32973805
#>            Parent seq_region_name db_type strand      species         Exon
#> 1 ENSG00000139618              13    core      1 homo_sapiens c("core"....
#> 2 ENSG00000139618              13    core      1 homo_sapiens c(1, 1, ....
#> 3 ENSG00000139618              13    core      1 homo_sapiens c("13", ....
#> 4 ENSG00000139618              13    core      1 homo_sapiens c(1, 1, ....
#> 5 ENSG00000139618              13    core      1 homo_sapiens c("GRCh3....
#> 6 ENSG00000139618              13    core      1 homo_sapiens c("ENSE0....
#>   is_canonical
#> 1            0
#> 2            0
#> 3            0
#> 4            0
#> 5            0
#> 6            1
#> 
#> $canonical_transcript
#> [1] "ENST00000544455.1"
#> 
#> $display_name
#> [1] "BRCA2"
#> 
#> $start
#> [1] 32889611
#> 
#> $source
#> [1] "ensembl_havana"
#> 
event <- "SE_17_-_41251792_41249306_41249261_41246877_BRCA1"
queryEnsemblByEvent(event, species="human", assembly="hg19")
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $db_type
#> [1] "core"
#> 
#> $source
#> [1] "ensembl_havana"
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $start
#> [1] 41196312
#> 
#> $version
#> [1] 15
#> 
#> $display_name
#> [1] "BRCA1"
#> 
#> $end
#> [1] 41277500
#> 
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#> 
#> $id
#> [1] "ENSG00000012048"
#> 
#> $biotype
#> [1] "protein_coding"
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#> 
#> $Transcript
#>             Parent object_type db_type         source assembly_name    start
#> 1  ENSG00000012048  Transcript    core ensembl_havana        GRCh37 41196312
#> 2  ENSG00000012048  Transcript    core ensembl_havana        GRCh37 41196822
#> 3  ENSG00000012048  Transcript    core         havana        GRCh37 41197580
#> 4  ENSG00000012048  Transcript    core         havana        GRCh37 41197580
#> 5  ENSG00000012048  Transcript    core         havana        GRCh37 41197580
#> 6  ENSG00000012048  Transcript    core ensembl_havana        GRCh37 41197646
#> 7  ENSG00000012048  Transcript    core ensembl_havana        GRCh37 41197646
#> 8  ENSG00000012048  Transcript    core         havana        GRCh37 41197695
#> 9  ENSG00000012048  Transcript    core         havana        GRCh37 41197695
#> 10 ENSG00000012048  Transcript    core         havana        GRCh37 41215361
#> 11 ENSG00000012048  Transcript    core         havana        GRCh37 41215361
#> 12 ENSG00000012048  Transcript    core         havana        GRCh37 41215377
#> 13 ENSG00000012048  Transcript    core         havana        GRCh37 41219291
#> 14 ENSG00000012048  Transcript    core         havana        GRCh37 41228505
#> 15 ENSG00000012048  Transcript    core         havana        GRCh37 41228554
#> 16 ENSG00000012048  Transcript    core         havana        GRCh37 41243115
#> 17 ENSG00000012048  Transcript    core         havana        GRCh37 41245587
#> 18 ENSG00000012048  Transcript    core         havana        GRCh37 41245601
#> 19 ENSG00000012048  Transcript    core         havana        GRCh37 41245603
#> 20 ENSG00000012048  Transcript    core         havana        GRCh37 41246129
#> 21 ENSG00000012048  Transcript    core         havana        GRCh37 41246129
#> 22 ENSG00000012048  Transcript    core         havana        GRCh37 41246129
#> 23 ENSG00000012048  Transcript    core         havana        GRCh37 41246187
#> 24 ENSG00000012048  Transcript    core         havana        GRCh37 41247863
#> 25 ENSG00000012048  Transcript    core         havana        GRCh37 41251848
#> 26 ENSG00000012048  Transcript    core         havana        GRCh37 41256206
#> 27 ENSG00000012048  Transcript    core        ensembl        GRCh37 41196313
#> 28 ENSG00000012048  Transcript    core        ensembl        GRCh37 41196313
#> 29 ENSG00000012048  Transcript    core        ensembl        GRCh37 41196313
#> 30 ENSG00000012048  Transcript    core        ensembl        GRCh37 41196313
#> 31 ENSG00000012048  Transcript    core        ensembl        GRCh37 41196313
#>    version display_name length      end              id                 biotype
#> 1        3    BRCA1-001   7094 41277387 ENST00000357654          protein_coding
#> 2        1    BRCA1-007   3273 41277468 ENST00000468300          protein_coding
#> 3        1    BRCA1-023    781 41277346 ENST00000586385          protein_coding
#> 4        1    BRCA1-024   1282 41277346 ENST00000591534          protein_coding
#> 5        1    BRCA1-025    563 41277346 ENST00000591849          protein_coding
#> 6        1    BRCA1-006   5732 41277419 ENST00000493795          protein_coding
#> 7        2    BRCA1-005   5936 41277500 ENST00000471181          protein_coding
#> 8        1    BRCA1-010   5693 41277305 ENST00000461221 nonsense_mediated_decay
#> 9        2    BRCA1-014   2379 41277373 ENST00000491747          protein_coding
#> 10       1    BRCA1-015   1495 41256933 ENST00000484087          protein_coding
#> 11       1    BRCA1-009   1972 41277376 ENST00000478531          protein_coding
#> 12       1    BRCA1-008   1948 41277419 ENST00000493919          protein_coding
#> 13       1    BRCA1-021    561 41223083 ENST00000472490         retained_intron
#> 14       1    BRCA1-019    800 41256933 ENST00000487825          protein_coding
#> 15       1    BRCA1-022    726 41243841 ENST00000461574          protein_coding
#> 16       1    BRCA1-012   4497 41277332 ENST00000467274         retained_intron
#> 17       3    BRCA1-026   1312 41247883 ENST00000412061          non_stop_decay
#> 18       1    BRCA1-011   2108 41277340 ENST00000470026          protein_coding
#> 19       1    BRCA1-004   1980 41277381 ENST00000477152          protein_coding
#> 20       1    BRCA1-002   1584 41277317 ENST00000492859 nonsense_mediated_decay
#> 21       1    BRCA1-003    779 41277317 ENST00000497488          protein_coding
#> 22       1    BRCA1-013   1612 41277467 ENST00000494123          protein_coding
#> 23       1    BRCA1-018    958 41256908 ENST00000473961          protein_coding
#> 24       1    BRCA1-017    769 41277370 ENST00000476777          protein_coding
#> 25       1    BRCA1-020    582 41277387 ENST00000461798 nonsense_mediated_decay
#> 26       1    BRCA1-016    455 41277338 ENST00000489037          protein_coding
#> 27       3    BRCA1-205   6411 41277500 ENST00000354071          protein_coding
#> 28       3    BRCA1-204   3780 41277500 ENST00000352993          protein_coding
#> 29       3    BRCA1-202   6451 41277468 ENST00000346315          protein_coding
#> 30       3    BRCA1-203   3444 41276132 ENST00000351666          protein_coding
#> 31       4    BRCA1-201   7114 41277468 ENST00000309486          protein_coding
#>                   logic_name gencode_primary species is_canonical
#> 1  ensembl_havana_transcript               0   human            0
#> 2  ensembl_havana_transcript               0   human            0
#> 3     havana_homo_sapiens_37               0   human            0
#> 4     havana_homo_sapiens_37               0   human            0
#> 5     havana_homo_sapiens_37               0   human            0
#> 6  ensembl_havana_transcript               0   human            0
#> 7  ensembl_havana_transcript               0   human            1
#> 8     havana_homo_sapiens_37               0   human            0
#> 9     havana_homo_sapiens_37               0   human            0
#> 10    havana_homo_sapiens_37               0   human            0
#> 11    havana_homo_sapiens_37               0   human            0
#> 12    havana_homo_sapiens_37               0   human            0
#> 13    havana_homo_sapiens_37               0   human            0
#> 14    havana_homo_sapiens_37               0   human            0
#> 15    havana_homo_sapiens_37               0   human            0
#> 16    havana_homo_sapiens_37               0   human            0
#> 17    havana_homo_sapiens_37               0   human            0
#> 18    havana_homo_sapiens_37               0   human            0
#> 19    havana_homo_sapiens_37               0   human            0
#> 20    havana_homo_sapiens_37               0   human            0
#> 21    havana_homo_sapiens_37               0   human            0
#> 22    havana_homo_sapiens_37               0   human            0
#> 23    havana_homo_sapiens_37               0   human            0
#> 24    havana_homo_sapiens_37               0   human            0
#> 25    havana_homo_sapiens_37               0   human            0
#> 26    havana_homo_sapiens_37               0   human            0
#> 27   ensembl_homo_sapiens_37               0   human            0
#> 28   ensembl_homo_sapiens_37               0   human            0
#> 29   ensembl_homo_sapiens_37               0   human            0
#> 30   ensembl_homo_sapiens_37               0   human            0
#> 31   ensembl_homo_sapiens_37               0   human            0
#>    seq_region_name         Exon strand Translation.object_type
#> 1               17 c(-1, -1....     -1             Translation
#> 2               17 c(412774....     -1             Translation
#> 3               17 c(412773....     -1             Translation
#> 4               17 c(412773....     -1             Translation
#> 5               17 c(412772....     -1             Translation
#> 6               17 c("core"....     -1             Translation
#> 7               17 c("17", ....     -1             Translation
#> 8               17 c("core"....     -1             Translation
#> 9               17 c("ENSE0....     -1             Translation
#> 10              17 c("Exon"....     -1             Translation
#> 11              17 c(1, 1, ....     -1             Translation
#> 12              17 c("ENSE0....     -1             Translation
#> 13              17 c(412229....     -1                    <NA>
#> 14              17 c(1, 1, ....     -1             Translation
#> 15              17 c("Exon"....     -1             Translation
#> 16              17 c("core"....     -1                    <NA>
#> 17              17 c(412478....     -1             Translation
#> 18              17 c(412771....     -1             Translation
#> 19              17 c("Exon"....     -1             Translation
#> 20              17 c("core"....     -1             Translation
#> 21              17 c(412773....     -1             Translation
#> 22              17 c("core"....     -1             Translation
#> 23              17 c("ENSE0....     -1             Translation
#> 24              17 c(1, 1, ....     -1             Translation
#> 25              17 c("17", ....     -1             Translation
#> 26              17 c("ENSE0....     -1             Translation
#> 27              17 c("ENSE0....     -1             Translation
#> 28              17 c("core"....     -1             Translation
#> 29              17 c("ENSE0....     -1             Translation
#> 30              17 c("ENSE0....     -1             Translation
#> 31              17 c("ENSE0....     -1             Translation
#>    Translation.db_type Translation.Parent  Translation.id Translation.length
#> 1                 core    ENST00000357654 ENSP00000350283               1863
#> 2                 core    ENST00000468300 ENSP00000417148                699
#> 3                 core    ENST00000586385 ENSP00000465818                173
#> 4                 core    ENST00000591534 ENSP00000467329                354
#> 5                 core    ENST00000591849 ENSP00000465347                 96
#> 6                 core    ENST00000493795 ENSP00000418775               1816
#> 7                 core    ENST00000471181 ENSP00000418960               1884
#> 8                 core    ENST00000461221 ENSP00000418548                 63
#> 9                 core    ENST00000491747 ENSP00000420705                759
#> 10                core    ENST00000484087 ENSP00000419481                498
#> 11                core    ENST00000478531 ENSP00000420412                623
#> 12                core    ENST00000493919 ENSP00000418819                572
#> 13                <NA>               <NA>            <NA>                 NA
#> 14                core    ENST00000487825 ENSP00000418212                266
#> 15                core    ENST00000461574 ENSP00000417241                242
#> 16                <NA>               <NA>            <NA>                 NA
#> 17                core    ENST00000412061 ENSP00000397145                437
#> 18                core    ENST00000470026 ENSP00000419274                649
#> 19                core    ENST00000477152 ENSP00000419988                622
#> 20                core    ENST00000492859 ENSP00000420253                 59
#> 21                core    ENST00000497488 ENSP00000418986                177
#> 22                core    ENST00000494123 ENSP00000419103                473
#> 23                core    ENST00000473961 ENSP00000420201                319
#> 24                core    ENST00000476777 ENSP00000417554                222
#> 25                core    ENST00000461798 ENSP00000417988                 63
#> 26                core    ENST00000489037 ENSP00000420781                 98
#> 27                core    ENST00000354071 ENSP00000326002               1598
#> 28                core    ENST00000352993 ENSP00000312236                721
#> 29                core    ENST00000346315 ENSP00000246907               1624
#> 30                core    ENST00000351666 ENSP00000338007                680
#> 31                core    ENST00000309486 ENSP00000310938               1567
#>    Translation.end Translation.version Translation.start Translation.species
#> 1         41276113                   3          41197695               human
#> 2         41276113                   1          41197801               human
#> 3         41277202                   1          41197695               human
#> 4         41226495                   1          41197695               human
#> 5         41202109                   1          41197695               human
#> 6         41258543                   1          41197695               human
#> 7         41276113                   2          41197695               human
#> 8         41276113                   1          41256972               human
#> 9         41276113                   2          41197695               human
#> 10        41256933                   1          41215361               human
#> 11        41276113                   1          41215361               human
#> 12        41258543                   1          41215377               human
#> 13              NA                  NA                NA                <NA>
#> 14        41256933                   1          41228505               human
#> 15        41243841                   1          41228554               human
#> 16              NA                  NA                NA                <NA>
#> 17        41247883                   3          41245587               human
#> 18        41276113                   1          41245601               human
#> 19        41276113                   1          41245603               human
#> 20        41276113                   1          41262552               human
#> 21        41246659                   1          41246129               human
#> 22        41276113                   1          41246129               human
#> 23        41256908                   1          41246187               human
#> 24        41276113                   1          41247863               human
#> 25        41276113                   1          41256972               human
#> 26        41276113                   1          41256206               human
#> 27        41276113                   6          41197695               human
#> 28        41276113                   5          41197695               human
#> 29        41276113                   4          41197695               human
#> 30        41276113                   3          41197695               human
#> 31        41246659                   4          41197695               human
#> 
#> $species
#> [1] "human"
#> 
#> $seq_region_name
#> [1] "17"
#> 
#> $strand
#> [1] -1
#>