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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")
#> $start
#> [1] 41196312
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $biotype
#> [1] "protein_coding"
#> 
#> $end
#> [1] 41277500
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $Transcript
#>                   logic_name version              id db_type species
#> 1  ensembl_havana_transcript       3 ENST00000357654    core   human
#> 2  ensembl_havana_transcript       1 ENST00000468300    core   human
#> 3     havana_homo_sapiens_37       1 ENST00000586385    core   human
#> 4     havana_homo_sapiens_37       1 ENST00000591534    core   human
#> 5     havana_homo_sapiens_37       1 ENST00000591849    core   human
#> 6  ensembl_havana_transcript       1 ENST00000493795    core   human
#> 7  ensembl_havana_transcript       2 ENST00000471181    core   human
#> 8     havana_homo_sapiens_37       1 ENST00000461221    core   human
#> 9     havana_homo_sapiens_37       2 ENST00000491747    core   human
#> 10    havana_homo_sapiens_37       1 ENST00000484087    core   human
#> 11    havana_homo_sapiens_37       1 ENST00000478531    core   human
#> 12    havana_homo_sapiens_37       1 ENST00000493919    core   human
#> 13    havana_homo_sapiens_37       1 ENST00000472490    core   human
#> 14    havana_homo_sapiens_37       1 ENST00000487825    core   human
#> 15    havana_homo_sapiens_37       1 ENST00000461574    core   human
#> 16    havana_homo_sapiens_37       1 ENST00000467274    core   human
#> 17    havana_homo_sapiens_37       3 ENST00000412061    core   human
#> 18    havana_homo_sapiens_37       1 ENST00000470026    core   human
#> 19    havana_homo_sapiens_37       1 ENST00000477152    core   human
#> 20    havana_homo_sapiens_37       1 ENST00000492859    core   human
#> 21    havana_homo_sapiens_37       1 ENST00000497488    core   human
#> 22    havana_homo_sapiens_37       1 ENST00000494123    core   human
#> 23    havana_homo_sapiens_37       1 ENST00000473961    core   human
#> 24    havana_homo_sapiens_37       1 ENST00000476777    core   human
#> 25    havana_homo_sapiens_37       1 ENST00000461798    core   human
#> 26    havana_homo_sapiens_37       1 ENST00000489037    core   human
#> 27   ensembl_homo_sapiens_37       3 ENST00000354071    core   human
#> 28   ensembl_homo_sapiens_37       3 ENST00000352993    core   human
#> 29   ensembl_homo_sapiens_37       3 ENST00000346315    core   human
#> 30   ensembl_homo_sapiens_37       3 ENST00000351666    core   human
#> 31   ensembl_homo_sapiens_37       4 ENST00000309486    core   human
#>    seq_region_name is_canonical assembly_name    start length      end
#> 1               17            0        GRCh37 41196312   7094 41277387
#> 2               17            0        GRCh37 41196822   3273 41277468
#> 3               17            0        GRCh37 41197580    781 41277346
#> 4               17            0        GRCh37 41197580   1282 41277346
#> 5               17            0        GRCh37 41197580    563 41277346
#> 6               17            0        GRCh37 41197646   5732 41277419
#> 7               17            1        GRCh37 41197646   5936 41277500
#> 8               17            0        GRCh37 41197695   5693 41277305
#> 9               17            0        GRCh37 41197695   2379 41277373
#> 10              17            0        GRCh37 41215361   1495 41256933
#> 11              17            0        GRCh37 41215361   1972 41277376
#> 12              17            0        GRCh37 41215377   1948 41277419
#> 13              17            0        GRCh37 41219291    561 41223083
#> 14              17            0        GRCh37 41228505    800 41256933
#> 15              17            0        GRCh37 41228554    726 41243841
#> 16              17            0        GRCh37 41243115   4497 41277332
#> 17              17            0        GRCh37 41245587   1312 41247883
#> 18              17            0        GRCh37 41245601   2108 41277340
#> 19              17            0        GRCh37 41245603   1980 41277381
#> 20              17            0        GRCh37 41246129   1584 41277317
#> 21              17            0        GRCh37 41246129    779 41277317
#> 22              17            0        GRCh37 41246129   1612 41277467
#> 23              17            0        GRCh37 41246187    958 41256908
#> 24              17            0        GRCh37 41247863    769 41277370
#> 25              17            0        GRCh37 41251848    582 41277387
#> 26              17            0        GRCh37 41256206    455 41277338
#> 27              17            0        GRCh37 41196313   6411 41277500
#> 28              17            0        GRCh37 41196313   3780 41277500
#> 29              17            0        GRCh37 41196313   6451 41277468
#> 30              17            0        GRCh37 41196313   3444 41276132
#> 31              17            0        GRCh37 41196313   7114 41277468
#>                    biotype object_type          Parent gencode_primary strand
#> 1           protein_coding  Transcript ENSG00000012048               0     -1
#> 2           protein_coding  Transcript ENSG00000012048               0     -1
#> 3           protein_coding  Transcript ENSG00000012048               0     -1
#> 4           protein_coding  Transcript ENSG00000012048               0     -1
#> 5           protein_coding  Transcript ENSG00000012048               0     -1
#> 6           protein_coding  Transcript ENSG00000012048               0     -1
#> 7           protein_coding  Transcript ENSG00000012048               0     -1
#> 8  nonsense_mediated_decay  Transcript ENSG00000012048               0     -1
#> 9           protein_coding  Transcript ENSG00000012048               0     -1
#> 10          protein_coding  Transcript ENSG00000012048               0     -1
#> 11          protein_coding  Transcript ENSG00000012048               0     -1
#> 12          protein_coding  Transcript ENSG00000012048               0     -1
#> 13         retained_intron  Transcript ENSG00000012048               0     -1
#> 14          protein_coding  Transcript ENSG00000012048               0     -1
#> 15          protein_coding  Transcript ENSG00000012048               0     -1
#> 16         retained_intron  Transcript ENSG00000012048               0     -1
#> 17          non_stop_decay  Transcript ENSG00000012048               0     -1
#> 18          protein_coding  Transcript ENSG00000012048               0     -1
#> 19          protein_coding  Transcript ENSG00000012048               0     -1
#> 20 nonsense_mediated_decay  Transcript ENSG00000012048               0     -1
#> 21          protein_coding  Transcript ENSG00000012048               0     -1
#> 22          protein_coding  Transcript ENSG00000012048               0     -1
#> 23          protein_coding  Transcript ENSG00000012048               0     -1
#> 24          protein_coding  Transcript ENSG00000012048               0     -1
#> 25 nonsense_mediated_decay  Transcript ENSG00000012048               0     -1
#> 26          protein_coding  Transcript ENSG00000012048               0     -1
#> 27          protein_coding  Transcript ENSG00000012048               0     -1
#> 28          protein_coding  Transcript ENSG00000012048               0     -1
#> 29          protein_coding  Transcript ENSG00000012048               0     -1
#> 30          protein_coding  Transcript ENSG00000012048               0     -1
#> 31          protein_coding  Transcript ENSG00000012048               0     -1
#>            source display_name         Exon Translation.species  Translation.id
#> 1  ensembl_havana    BRCA1-001 c("ENSE0....               human ENSP00000350283
#> 2  ensembl_havana    BRCA1-007 c(412774....               human ENSP00000417148
#> 3          havana    BRCA1-023 c("17", ....               human ENSP00000465818
#> 4          havana    BRCA1-024 c("GRCh3....               human ENSP00000467329
#> 5          havana    BRCA1-025 c("GRCh3....               human ENSP00000465347
#> 6  ensembl_havana    BRCA1-006 c(412774....               human ENSP00000418775
#> 7  ensembl_havana    BRCA1-005 c(1, 1, ....               human ENSP00000418960
#> 8          havana    BRCA1-010 c("ENSE0....               human ENSP00000418548
#> 9          havana    BRCA1-014 c(1, 1, ....               human ENSP00000420705
#> 10         havana    BRCA1-015 c("Exon"....               human ENSP00000419481
#> 11         havana    BRCA1-009 c("GRCh3....               human ENSP00000420412
#> 12         havana    BRCA1-008 c(-1, -1....               human ENSP00000418819
#> 13         havana    BRCA1-021 c("ENSE0....                <NA>            <NA>
#> 14         havana    BRCA1-019 c("GRCh3....               human ENSP00000418212
#> 15         havana    BRCA1-022 c("GRCh3....               human ENSP00000417241
#> 16         havana    BRCA1-012 c(412773....                <NA>            <NA>
#> 17         havana    BRCA1-026 c("17", ....               human ENSP00000397145
#> 18         havana    BRCA1-011 c("core"....               human ENSP00000419274
#> 19         havana    BRCA1-004 c(412772....               human ENSP00000419988
#> 20         havana    BRCA1-002 c("17", ....               human ENSP00000420253
#> 21         havana    BRCA1-003 c("17", ....               human ENSP00000418986
#> 22         havana    BRCA1-013 c("ENSE0....               human ENSP00000419103
#> 23         havana    BRCA1-018 c("ENSE0....               human ENSP00000420201
#> 24         havana    BRCA1-017 c("core"....               human ENSP00000417554
#> 25         havana    BRCA1-020 c("17", ....               human ENSP00000417988
#> 26         havana    BRCA1-016 c("17", ....               human ENSP00000420781
#> 27        ensembl    BRCA1-205 c("Exon"....               human ENSP00000326002
#> 28        ensembl    BRCA1-204 c(-1, -1....               human ENSP00000312236
#> 29        ensembl    BRCA1-202 c("GRCh3....               human ENSP00000246907
#> 30        ensembl    BRCA1-203 c("human....               human ENSP00000338007
#> 31        ensembl    BRCA1-201 c("17", ....               human ENSP00000310938
#>    Translation.db_type Translation.end Translation.object_type
#> 1                 core        41276113             Translation
#> 2                 core        41276113             Translation
#> 3                 core        41277202             Translation
#> 4                 core        41226495             Translation
#> 5                 core        41202109             Translation
#> 6                 core        41258543             Translation
#> 7                 core        41276113             Translation
#> 8                 core        41276113             Translation
#> 9                 core        41276113             Translation
#> 10                core        41256933             Translation
#> 11                core        41276113             Translation
#> 12                core        41258543             Translation
#> 13                <NA>              NA                    <NA>
#> 14                core        41256933             Translation
#> 15                core        41243841             Translation
#> 16                <NA>              NA                    <NA>
#> 17                core        41247883             Translation
#> 18                core        41276113             Translation
#> 19                core        41276113             Translation
#> 20                core        41276113             Translation
#> 21                core        41246659             Translation
#> 22                core        41276113             Translation
#> 23                core        41256908             Translation
#> 24                core        41276113             Translation
#> 25                core        41276113             Translation
#> 26                core        41276113             Translation
#> 27                core        41276113             Translation
#> 28                core        41276113             Translation
#> 29                core        41276113             Translation
#> 30                core        41276113             Translation
#> 31                core        41246659             Translation
#>    Translation.Parent Translation.start Translation.length Translation.version
#> 1     ENST00000357654          41197695               1863                   3
#> 2     ENST00000468300          41197801                699                   1
#> 3     ENST00000586385          41197695                173                   1
#> 4     ENST00000591534          41197695                354                   1
#> 5     ENST00000591849          41197695                 96                   1
#> 6     ENST00000493795          41197695               1816                   1
#> 7     ENST00000471181          41197695               1884                   2
#> 8     ENST00000461221          41256972                 63                   1
#> 9     ENST00000491747          41197695                759                   2
#> 10    ENST00000484087          41215361                498                   1
#> 11    ENST00000478531          41215361                623                   1
#> 12    ENST00000493919          41215377                572                   1
#> 13               <NA>                NA                 NA                  NA
#> 14    ENST00000487825          41228505                266                   1
#> 15    ENST00000461574          41228554                242                   1
#> 16               <NA>                NA                 NA                  NA
#> 17    ENST00000412061          41245587                437                   3
#> 18    ENST00000470026          41245601                649                   1
#> 19    ENST00000477152          41245603                622                   1
#> 20    ENST00000492859          41262552                 59                   1
#> 21    ENST00000497488          41246129                177                   1
#> 22    ENST00000494123          41246129                473                   1
#> 23    ENST00000473961          41246187                319                   1
#> 24    ENST00000476777          41247863                222                   1
#> 25    ENST00000461798          41256972                 63                   1
#> 26    ENST00000489037          41256206                 98                   1
#> 27    ENST00000354071          41197695               1598                   6
#> 28    ENST00000352993          41197695                721                   5
#> 29    ENST00000346315          41197695               1624                   4
#> 30    ENST00000351666          41197695                680                   3
#> 31    ENST00000309486          41197695               1567                   4
#> 
#> $display_name
#> [1] "BRCA1"
#> 
#> $strand
#> [1] -1
#> 
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#> 
#> $source
#> [1] "ensembl_havana"
#> 
#> $version
#> [1] 15
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#> 
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#> 
#> $db_type
#> [1] "core"
#> 
#> $id
#> [1] "ENSG00000012048"
#> 
#> $seq_region_name
#> [1] "17"
#> 
#> $species
#> [1] "human"
#> 
queryEnsemblByGene("ENSG00000139618")
#> $biotype
#> [1] "protein_coding"
#> 
#> $end
#> [1] 32973805
#> 
#> $version
#> [1] 10
#> 
#> $description
#> [1] "breast cancer 2, early onset [Source:HGNC Symbol;Acc:1101]"
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $display_name
#> [1] "BRCA2"
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $seq_region_name
#> [1] "13"
#> 
#> $strand
#> [1] 1
#> 
#> $source
#> [1] "ensembl_havana"
#> 
#> $Transcript
#>        species    start         Exon              id db_type gencode_primary
#> 1 homo_sapiens 32889611 c(1, 1, .... ENST00000380152    core               0
#> 2 homo_sapiens 32889642 c(1, 1, .... ENST00000530893    core               0
#> 3 homo_sapiens 32945108 c("core".... ENST00000528762    core               0
#> 4 homo_sapiens 32953977 c(1, 1, .... ENST00000470094    core               0
#> 5 homo_sapiens 32970946 c("GRCh3.... ENST00000533776    core               0
#> 6 homo_sapiens 32889617 c(328898.... ENST00000544455    core               0
#>   length                logic_name version                 biotype      end
#> 1  10930 ensembl_havana_transcript       3          protein_coding 32973347
#> 2   2011    havana_homo_sapiens_37       2          protein_coding 32907428
#> 3    495    havana_homo_sapiens_37       1 nonsense_mediated_decay 32953632
#> 4    842    havana_homo_sapiens_37       1 nonsense_mediated_decay 32972409
#> 5    523    havana_homo_sapiens_37       1         retained_intron 32972585
#> 6  10984   ensembl_homo_sapiens_37       1          protein_coding 32973805
#>   display_name object_type seq_region_name is_canonical assembly_name
#> 1    BRCA2-001  Transcript              13            0        GRCh37
#> 2    BRCA2-003  Transcript              13            0        GRCh37
#> 3    BRCA2-005  Transcript              13            0        GRCh37
#> 4    BRCA2-002  Transcript              13            0        GRCh37
#> 5    BRCA2-006  Transcript              13            0        GRCh37
#> 6    BRCA2-201  Transcript              13            1        GRCh37
#>   Translation.Parent Translation.length  Translation.id Translation.db_type
#> 1    ENST00000380152               3418 ENSP00000369497                core
#> 2    ENST00000530893                481 ENSP00000435699                core
#> 3    ENST00000528762                 64 ENSP00000433168                core
#> 4    ENST00000470094                186 ENSP00000434898                core
#> 5               <NA>                 NA            <NA>                <NA>
#> 6    ENST00000544455               3418 ENSP00000439902                core
#>   Translation.species Translation.object_type Translation.start
#> 1        homo_sapiens             Translation          32890598
#> 2        homo_sapiens             Translation          32899266
#> 3        homo_sapiens             Translation          32945108
#> 4        homo_sapiens             Translation          32953977
#> 5                <NA>                    <NA>                NA
#> 6        homo_sapiens             Translation          32890598
#>   Translation.version Translation.end          Parent strand         source
#> 1                   3        32972907 ENSG00000139618      1 ensembl_havana
#> 2                   2        32907428 ENSG00000139618      1         havana
#> 3                   1        32950807 ENSG00000139618      1         havana
#> 4                   1        32970229 ENSG00000139618      1         havana
#> 5                  NA              NA ENSG00000139618      1         havana
#> 6                   1        32972907 ENSG00000139618      1        ensembl
#> 
#> $start
#> [1] 32889611
#> 
#> $species
#> [1] "homo_sapiens"
#> 
#> $db_type
#> [1] "core"
#> 
#> $id
#> [1] "ENSG00000139618"
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#> 
#> $canonical_transcript
#> [1] "ENST00000544455.1"
#> 
event <- "SE_17_-_41251792_41249306_41249261_41246877_BRCA1"
queryEnsemblByEvent(event, species="human", assembly="hg19")
#> $strand
#> [1] -1
#> 
#> $end
#> [1] 41277500
#> 
#> $Transcript
#>         end         Exon is_canonical strand          Parent    start
#> 1  41277387 c("17", ....            0     -1 ENSG00000012048 41196312
#> 2  41277468 c(-1, -1....            0     -1 ENSG00000012048 41196822
#> 3  41277346 c("human....            0     -1 ENSG00000012048 41197580
#> 4  41277346 c(412773....            0     -1 ENSG00000012048 41197580
#> 5  41277346 c(1, 1, ....            0     -1 ENSG00000012048 41197580
#> 6  41277419 c("human....            0     -1 ENSG00000012048 41197646
#> 7  41277500 c("core"....            1     -1 ENSG00000012048 41197646
#> 8  41277305 c("human....            0     -1 ENSG00000012048 41197695
#> 9  41277373 c(-1, -1....            0     -1 ENSG00000012048 41197695
#> 10 41256933 c(412568....            0     -1 ENSG00000012048 41215361
#> 11 41277376 c(412772....            0     -1 ENSG00000012048 41215361
#> 12 41277419 c("human....            0     -1 ENSG00000012048 41215377
#> 13 41223083 c("Exon"....            0     -1 ENSG00000012048 41219291
#> 14 41256933 c("human....            0     -1 ENSG00000012048 41228505
#> 15 41243841 c("core"....            0     -1 ENSG00000012048 41228554
#> 16 41277332 c(-1, -1....            0     -1 ENSG00000012048 41243115
#> 17 41247883 c("human....            0     -1 ENSG00000012048 41245587
#> 18 41277340 c(412773....            0     -1 ENSG00000012048 41245601
#> 19 41277381 c("ENSE0....            0     -1 ENSG00000012048 41245603
#> 20 41277317 c("human....            0     -1 ENSG00000012048 41246129
#> 21 41277317 c("17", ....            0     -1 ENSG00000012048 41246129
#> 22 41277467 c(412772....            0     -1 ENSG00000012048 41246129
#> 23 41256908 c("GRCh3....            0     -1 ENSG00000012048 41246187
#> 24 41277370 c("ENSE0....            0     -1 ENSG00000012048 41247863
#> 25 41277387 c("human....            0     -1 ENSG00000012048 41251848
#> 26 41277338 c("human....            0     -1 ENSG00000012048 41256206
#> 27 41277500 c(-1, -1....            0     -1 ENSG00000012048 41196313
#> 28 41277500 c(1, 1, ....            0     -1 ENSG00000012048 41196313
#> 29 41277468 c(-1, -1....            0     -1 ENSG00000012048 41196313
#> 30 41276132 c("ENSE0....            0     -1 ENSG00000012048 41196313
#> 31 41277468 c("core"....            0     -1 ENSG00000012048 41196313
#>                 id version gencode_primary seq_region_name object_type
#> 1  ENST00000357654       3               0              17  Transcript
#> 2  ENST00000468300       1               0              17  Transcript
#> 3  ENST00000586385       1               0              17  Transcript
#> 4  ENST00000591534       1               0              17  Transcript
#> 5  ENST00000591849       1               0              17  Transcript
#> 6  ENST00000493795       1               0              17  Transcript
#> 7  ENST00000471181       2               0              17  Transcript
#> 8  ENST00000461221       1               0              17  Transcript
#> 9  ENST00000491747       2               0              17  Transcript
#> 10 ENST00000484087       1               0              17  Transcript
#> 11 ENST00000478531       1               0              17  Transcript
#> 12 ENST00000493919       1               0              17  Transcript
#> 13 ENST00000472490       1               0              17  Transcript
#> 14 ENST00000487825       1               0              17  Transcript
#> 15 ENST00000461574       1               0              17  Transcript
#> 16 ENST00000467274       1               0              17  Transcript
#> 17 ENST00000412061       3               0              17  Transcript
#> 18 ENST00000470026       1               0              17  Transcript
#> 19 ENST00000477152       1               0              17  Transcript
#> 20 ENST00000492859       1               0              17  Transcript
#> 21 ENST00000497488       1               0              17  Transcript
#> 22 ENST00000494123       1               0              17  Transcript
#> 23 ENST00000473961       1               0              17  Transcript
#> 24 ENST00000476777       1               0              17  Transcript
#> 25 ENST00000461798       1               0              17  Transcript
#> 26 ENST00000489037       1               0              17  Transcript
#> 27 ENST00000354071       3               0              17  Transcript
#> 28 ENST00000352993       3               0              17  Transcript
#> 29 ENST00000346315       3               0              17  Transcript
#> 30 ENST00000351666       3               0              17  Transcript
#> 31 ENST00000309486       4               0              17  Transcript
#>    assembly_name display_name Translation.end  Translation.id
#> 1         GRCh37    BRCA1-001        41276113 ENSP00000350283
#> 2         GRCh37    BRCA1-007        41276113 ENSP00000417148
#> 3         GRCh37    BRCA1-023        41277202 ENSP00000465818
#> 4         GRCh37    BRCA1-024        41226495 ENSP00000467329
#> 5         GRCh37    BRCA1-025        41202109 ENSP00000465347
#> 6         GRCh37    BRCA1-006        41258543 ENSP00000418775
#> 7         GRCh37    BRCA1-005        41276113 ENSP00000418960
#> 8         GRCh37    BRCA1-010        41276113 ENSP00000418548
#> 9         GRCh37    BRCA1-014        41276113 ENSP00000420705
#> 10        GRCh37    BRCA1-015        41256933 ENSP00000419481
#> 11        GRCh37    BRCA1-009        41276113 ENSP00000420412
#> 12        GRCh37    BRCA1-008        41258543 ENSP00000418819
#> 13        GRCh37    BRCA1-021              NA            <NA>
#> 14        GRCh37    BRCA1-019        41256933 ENSP00000418212
#> 15        GRCh37    BRCA1-022        41243841 ENSP00000417241
#> 16        GRCh37    BRCA1-012              NA            <NA>
#> 17        GRCh37    BRCA1-026        41247883 ENSP00000397145
#> 18        GRCh37    BRCA1-011        41276113 ENSP00000419274
#> 19        GRCh37    BRCA1-004        41276113 ENSP00000419988
#> 20        GRCh37    BRCA1-002        41276113 ENSP00000420253
#> 21        GRCh37    BRCA1-003        41246659 ENSP00000418986
#> 22        GRCh37    BRCA1-013        41276113 ENSP00000419103
#> 23        GRCh37    BRCA1-018        41256908 ENSP00000420201
#> 24        GRCh37    BRCA1-017        41276113 ENSP00000417554
#> 25        GRCh37    BRCA1-020        41276113 ENSP00000417988
#> 26        GRCh37    BRCA1-016        41276113 ENSP00000420781
#> 27        GRCh37    BRCA1-205        41276113 ENSP00000326002
#> 28        GRCh37    BRCA1-204        41276113 ENSP00000312236
#> 29        GRCh37    BRCA1-202        41276113 ENSP00000246907
#> 30        GRCh37    BRCA1-203        41276113 ENSP00000338007
#> 31        GRCh37    BRCA1-201        41246659 ENSP00000310938
#>    Translation.object_type Translation.version Translation.length
#> 1              Translation                   3               1863
#> 2              Translation                   1                699
#> 3              Translation                   1                173
#> 4              Translation                   1                354
#> 5              Translation                   1                 96
#> 6              Translation                   1               1816
#> 7              Translation                   2               1884
#> 8              Translation                   1                 63
#> 9              Translation                   2                759
#> 10             Translation                   1                498
#> 11             Translation                   1                623
#> 12             Translation                   1                572
#> 13                    <NA>                  NA                 NA
#> 14             Translation                   1                266
#> 15             Translation                   1                242
#> 16                    <NA>                  NA                 NA
#> 17             Translation                   3                437
#> 18             Translation                   1                649
#> 19             Translation                   1                622
#> 20             Translation                   1                 59
#> 21             Translation                   1                177
#> 22             Translation                   1                473
#> 23             Translation                   1                319
#> 24             Translation                   1                222
#> 25             Translation                   1                 63
#> 26             Translation                   1                 98
#> 27             Translation                   6               1598
#> 28             Translation                   5                721
#> 29             Translation                   4               1624
#> 30             Translation                   3                680
#> 31             Translation                   4               1567
#>    Translation.Parent Translation.species Translation.db_type Translation.start
#> 1     ENST00000357654               human                core          41197695
#> 2     ENST00000468300               human                core          41197801
#> 3     ENST00000586385               human                core          41197695
#> 4     ENST00000591534               human                core          41197695
#> 5     ENST00000591849               human                core          41197695
#> 6     ENST00000493795               human                core          41197695
#> 7     ENST00000471181               human                core          41197695
#> 8     ENST00000461221               human                core          41256972
#> 9     ENST00000491747               human                core          41197695
#> 10    ENST00000484087               human                core          41215361
#> 11    ENST00000478531               human                core          41215361
#> 12    ENST00000493919               human                core          41215377
#> 13               <NA>                <NA>                <NA>                NA
#> 14    ENST00000487825               human                core          41228505
#> 15    ENST00000461574               human                core          41228554
#> 16               <NA>                <NA>                <NA>                NA
#> 17    ENST00000412061               human                core          41245587
#> 18    ENST00000470026               human                core          41245601
#> 19    ENST00000477152               human                core          41245603
#> 20    ENST00000492859               human                core          41262552
#> 21    ENST00000497488               human                core          41246129
#> 22    ENST00000494123               human                core          41246129
#> 23    ENST00000473961               human                core          41246187
#> 24    ENST00000476777               human                core          41247863
#> 25    ENST00000461798               human                core          41256972
#> 26    ENST00000489037               human                core          41256206
#> 27    ENST00000354071               human                core          41197695
#> 28    ENST00000352993               human                core          41197695
#> 29    ENST00000346315               human                core          41197695
#> 30    ENST00000351666               human                core          41197695
#> 31    ENST00000309486               human                core          41197695
#>                    biotype length                logic_name db_type species
#> 1           protein_coding   7094 ensembl_havana_transcript    core   human
#> 2           protein_coding   3273 ensembl_havana_transcript    core   human
#> 3           protein_coding    781    havana_homo_sapiens_37    core   human
#> 4           protein_coding   1282    havana_homo_sapiens_37    core   human
#> 5           protein_coding    563    havana_homo_sapiens_37    core   human
#> 6           protein_coding   5732 ensembl_havana_transcript    core   human
#> 7           protein_coding   5936 ensembl_havana_transcript    core   human
#> 8  nonsense_mediated_decay   5693    havana_homo_sapiens_37    core   human
#> 9           protein_coding   2379    havana_homo_sapiens_37    core   human
#> 10          protein_coding   1495    havana_homo_sapiens_37    core   human
#> 11          protein_coding   1972    havana_homo_sapiens_37    core   human
#> 12          protein_coding   1948    havana_homo_sapiens_37    core   human
#> 13         retained_intron    561    havana_homo_sapiens_37    core   human
#> 14          protein_coding    800    havana_homo_sapiens_37    core   human
#> 15          protein_coding    726    havana_homo_sapiens_37    core   human
#> 16         retained_intron   4497    havana_homo_sapiens_37    core   human
#> 17          non_stop_decay   1312    havana_homo_sapiens_37    core   human
#> 18          protein_coding   2108    havana_homo_sapiens_37    core   human
#> 19          protein_coding   1980    havana_homo_sapiens_37    core   human
#> 20 nonsense_mediated_decay   1584    havana_homo_sapiens_37    core   human
#> 21          protein_coding    779    havana_homo_sapiens_37    core   human
#> 22          protein_coding   1612    havana_homo_sapiens_37    core   human
#> 23          protein_coding    958    havana_homo_sapiens_37    core   human
#> 24          protein_coding    769    havana_homo_sapiens_37    core   human
#> 25 nonsense_mediated_decay    582    havana_homo_sapiens_37    core   human
#> 26          protein_coding    455    havana_homo_sapiens_37    core   human
#> 27          protein_coding   6411   ensembl_homo_sapiens_37    core   human
#> 28          protein_coding   3780   ensembl_homo_sapiens_37    core   human
#> 29          protein_coding   6451   ensembl_homo_sapiens_37    core   human
#> 30          protein_coding   3444   ensembl_homo_sapiens_37    core   human
#> 31          protein_coding   7114   ensembl_homo_sapiens_37    core   human
#>            source
#> 1  ensembl_havana
#> 2  ensembl_havana
#> 3          havana
#> 4          havana
#> 5          havana
#> 6  ensembl_havana
#> 7  ensembl_havana
#> 8          havana
#> 9          havana
#> 10         havana
#> 11         havana
#> 12         havana
#> 13         havana
#> 14         havana
#> 15         havana
#> 16         havana
#> 17         havana
#> 18         havana
#> 19         havana
#> 20         havana
#> 21         havana
#> 22         havana
#> 23         havana
#> 24         havana
#> 25         havana
#> 26         havana
#> 27        ensembl
#> 28        ensembl
#> 29        ensembl
#> 30        ensembl
#> 31        ensembl
#> 
#> $start
#> [1] 41196312
#> 
#> $seq_region_name
#> [1] "17"
#> 
#> $version
#> [1] 15
#> 
#> $object_type
#> [1] "Gene"
#> 
#> $assembly_name
#> [1] "GRCh37"
#> 
#> $display_name
#> [1] "BRCA1"
#> 
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#> 
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#> 
#> $biotype
#> [1] "protein_coding"
#> 
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#> 
#> $id
#> [1] "ENSG00000012048"
#> 
#> $source
#> [1] "ensembl_havana"
#> 
#> $db_type
#> [1] "core"
#> 
#> $species
#> [1] "human"
#>