Query information from Ensembl
Usage
queryEnsemblByGene(gene, species = NULL, assembly = NULL)
queryEnsemblByEvent(event, species = NULL, assembly = NULL, data = NULL)See also
Other functions to retrieve external information:
ensemblToUniprot(),
plotProtein(),
plotTranscripts()
Examples
queryEnsemblByGene("BRCA1", "human", "hg19")
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#>
#> $db_type
#> [1] "core"
#>
#> $end
#> [1] 41277500
#>
#> $seq_region_name
#> [1] "17"
#>
#> $species
#> [1] "human"
#>
#> $strand
#> [1] -1
#>
#> $object_type
#> [1] "Gene"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $version
#> [1] 15
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $id
#> [1] "ENSG00000012048"
#>
#> $Transcript
#> strand Exon species is_canonical end seq_region_name
#> 1 -1 c("17", .... human 0 41277387 17
#> 2 -1 c(412772.... human 0 41277468 17
#> 3 -1 c("17", .... human 0 41277346 17
#> 4 -1 c(412772.... human 0 41277346 17
#> 5 -1 c(-1, -1.... human 0 41277346 17
#> 6 -1 c(412772.... human 0 41277419 17
#> 7 -1 c(412775.... human 1 41277500 17
#> 8 -1 c(-1, -1.... human 0 41277305 17
#> 9 -1 c(-1, -1.... human 0 41277373 17
#> 10 -1 c("ENSE0.... human 0 41256933 17
#> 11 -1 c("human.... human 0 41277376 17
#> 12 -1 c("17", .... human 0 41277419 17
#> 13 -1 c("GRCh3.... human 0 41223083 17
#> 14 -1 c(-1, -1.... human 0 41256933 17
#> 15 -1 c("17", .... human 0 41243841 17
#> 16 -1 c(412772.... human 0 41277332 17
#> 17 -1 c("17", .... human 0 41247883 17
#> 18 -1 c("ENSE0.... human 0 41277340 17
#> 19 -1 c("human.... human 0 41277381 17
#> 20 -1 c("human.... human 0 41277317 17
#> 21 -1 c(412772.... human 0 41277317 17
#> 22 -1 c(-1, -1.... human 0 41277467 17
#> 23 -1 c("Exon".... human 0 41256908 17
#> 24 -1 c("core".... human 0 41277370 17
#> 25 -1 c(-1, -1.... human 0 41277387 17
#> 26 -1 c(412773.... human 0 41277338 17
#> 27 -1 c("ENSE0.... human 0 41277500 17
#> 28 -1 c(1, 1, .... human 0 41277500 17
#> 29 -1 c(-1, -1.... human 0 41277468 17
#> 30 -1 c("17", .... human 0 41276132 17
#> 31 -1 c(412772.... human 0 41277468 17
#> Parent db_type source length display_name
#> 1 ENSG00000012048 core ensembl_havana 7094 BRCA1-001
#> 2 ENSG00000012048 core ensembl_havana 3273 BRCA1-007
#> 3 ENSG00000012048 core havana 781 BRCA1-023
#> 4 ENSG00000012048 core havana 1282 BRCA1-024
#> 5 ENSG00000012048 core havana 563 BRCA1-025
#> 6 ENSG00000012048 core ensembl_havana 5732 BRCA1-006
#> 7 ENSG00000012048 core ensembl_havana 5936 BRCA1-005
#> 8 ENSG00000012048 core havana 5693 BRCA1-010
#> 9 ENSG00000012048 core havana 2379 BRCA1-014
#> 10 ENSG00000012048 core havana 1495 BRCA1-015
#> 11 ENSG00000012048 core havana 1972 BRCA1-009
#> 12 ENSG00000012048 core havana 1948 BRCA1-008
#> 13 ENSG00000012048 core havana 561 BRCA1-021
#> 14 ENSG00000012048 core havana 800 BRCA1-019
#> 15 ENSG00000012048 core havana 726 BRCA1-022
#> 16 ENSG00000012048 core havana 4497 BRCA1-012
#> 17 ENSG00000012048 core havana 1312 BRCA1-026
#> 18 ENSG00000012048 core havana 2108 BRCA1-011
#> 19 ENSG00000012048 core havana 1980 BRCA1-004
#> 20 ENSG00000012048 core havana 1584 BRCA1-002
#> 21 ENSG00000012048 core havana 779 BRCA1-003
#> 22 ENSG00000012048 core havana 1612 BRCA1-013
#> 23 ENSG00000012048 core havana 958 BRCA1-018
#> 24 ENSG00000012048 core havana 769 BRCA1-017
#> 25 ENSG00000012048 core havana 582 BRCA1-020
#> 26 ENSG00000012048 core havana 455 BRCA1-016
#> 27 ENSG00000012048 core ensembl 6411 BRCA1-205
#> 28 ENSG00000012048 core ensembl 3780 BRCA1-204
#> 29 ENSG00000012048 core ensembl 6451 BRCA1-202
#> 30 ENSG00000012048 core ensembl 3444 BRCA1-203
#> 31 ENSG00000012048 core ensembl 7114 BRCA1-201
#> Translation.length Translation.start Translation.species Translation.Parent
#> 1 1863 41197695 human ENST00000357654
#> 2 699 41197801 human ENST00000468300
#> 3 173 41197695 human ENST00000586385
#> 4 354 41197695 human ENST00000591534
#> 5 96 41197695 human ENST00000591849
#> 6 1816 41197695 human ENST00000493795
#> 7 1884 41197695 human ENST00000471181
#> 8 63 41256972 human ENST00000461221
#> 9 759 41197695 human ENST00000491747
#> 10 498 41215361 human ENST00000484087
#> 11 623 41215361 human ENST00000478531
#> 12 572 41215377 human ENST00000493919
#> 13 NA NA <NA> <NA>
#> 14 266 41228505 human ENST00000487825
#> 15 242 41228554 human ENST00000461574
#> 16 NA NA <NA> <NA>
#> 17 437 41245587 human ENST00000412061
#> 18 649 41245601 human ENST00000470026
#> 19 622 41245603 human ENST00000477152
#> 20 59 41262552 human ENST00000492859
#> 21 177 41246129 human ENST00000497488
#> 22 473 41246129 human ENST00000494123
#> 23 319 41246187 human ENST00000473961
#> 24 222 41247863 human ENST00000476777
#> 25 63 41256972 human ENST00000461798
#> 26 98 41256206 human ENST00000489037
#> 27 1598 41197695 human ENST00000354071
#> 28 721 41197695 human ENST00000352993
#> 29 1624 41197695 human ENST00000346315
#> 30 680 41197695 human ENST00000351666
#> 31 1567 41197695 human ENST00000309486
#> Translation.end Translation.id Translation.version Translation.db_type
#> 1 41276113 ENSP00000350283 3 core
#> 2 41276113 ENSP00000417148 1 core
#> 3 41277202 ENSP00000465818 1 core
#> 4 41226495 ENSP00000467329 1 core
#> 5 41202109 ENSP00000465347 1 core
#> 6 41258543 ENSP00000418775 1 core
#> 7 41276113 ENSP00000418960 2 core
#> 8 41276113 ENSP00000418548 1 core
#> 9 41276113 ENSP00000420705 2 core
#> 10 41256933 ENSP00000419481 1 core
#> 11 41276113 ENSP00000420412 1 core
#> 12 41258543 ENSP00000418819 1 core
#> 13 NA <NA> NA <NA>
#> 14 41256933 ENSP00000418212 1 core
#> 15 41243841 ENSP00000417241 1 core
#> 16 NA <NA> NA <NA>
#> 17 41247883 ENSP00000397145 3 core
#> 18 41276113 ENSP00000419274 1 core
#> 19 41276113 ENSP00000419988 1 core
#> 20 41276113 ENSP00000420253 1 core
#> 21 41246659 ENSP00000418986 1 core
#> 22 41276113 ENSP00000419103 1 core
#> 23 41256908 ENSP00000420201 1 core
#> 24 41276113 ENSP00000417554 1 core
#> 25 41276113 ENSP00000417988 1 core
#> 26 41276113 ENSP00000420781 1 core
#> 27 41276113 ENSP00000326002 6 core
#> 28 41276113 ENSP00000312236 5 core
#> 29 41276113 ENSP00000246907 4 core
#> 30 41276113 ENSP00000338007 3 core
#> 31 41246659 ENSP00000310938 4 core
#> Translation.object_type start id gencode_primary
#> 1 Translation 41196312 ENST00000357654 0
#> 2 Translation 41196822 ENST00000468300 0
#> 3 Translation 41197580 ENST00000586385 0
#> 4 Translation 41197580 ENST00000591534 0
#> 5 Translation 41197580 ENST00000591849 0
#> 6 Translation 41197646 ENST00000493795 0
#> 7 Translation 41197646 ENST00000471181 0
#> 8 Translation 41197695 ENST00000461221 0
#> 9 Translation 41197695 ENST00000491747 0
#> 10 Translation 41215361 ENST00000484087 0
#> 11 Translation 41215361 ENST00000478531 0
#> 12 Translation 41215377 ENST00000493919 0
#> 13 <NA> 41219291 ENST00000472490 0
#> 14 Translation 41228505 ENST00000487825 0
#> 15 Translation 41228554 ENST00000461574 0
#> 16 <NA> 41243115 ENST00000467274 0
#> 17 Translation 41245587 ENST00000412061 0
#> 18 Translation 41245601 ENST00000470026 0
#> 19 Translation 41245603 ENST00000477152 0
#> 20 Translation 41246129 ENST00000492859 0
#> 21 Translation 41246129 ENST00000497488 0
#> 22 Translation 41246129 ENST00000494123 0
#> 23 Translation 41246187 ENST00000473961 0
#> 24 Translation 41247863 ENST00000476777 0
#> 25 Translation 41251848 ENST00000461798 0
#> 26 Translation 41256206 ENST00000489037 0
#> 27 Translation 41196313 ENST00000354071 0
#> 28 Translation 41196313 ENST00000352993 0
#> 29 Translation 41196313 ENST00000346315 0
#> 30 Translation 41196313 ENST00000351666 0
#> 31 Translation 41196313 ENST00000309486 0
#> logic_name object_type biotype assembly_name
#> 1 ensembl_havana_transcript Transcript protein_coding GRCh37
#> 2 ensembl_havana_transcript Transcript protein_coding GRCh37
#> 3 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 4 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 5 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 6 ensembl_havana_transcript Transcript protein_coding GRCh37
#> 7 ensembl_havana_transcript Transcript protein_coding GRCh37
#> 8 havana_homo_sapiens_37 Transcript nonsense_mediated_decay GRCh37
#> 9 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 10 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 11 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 12 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 13 havana_homo_sapiens_37 Transcript retained_intron GRCh37
#> 14 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 15 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 16 havana_homo_sapiens_37 Transcript retained_intron GRCh37
#> 17 havana_homo_sapiens_37 Transcript non_stop_decay GRCh37
#> 18 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 19 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 20 havana_homo_sapiens_37 Transcript nonsense_mediated_decay GRCh37
#> 21 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 22 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 23 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 24 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 25 havana_homo_sapiens_37 Transcript nonsense_mediated_decay GRCh37
#> 26 havana_homo_sapiens_37 Transcript protein_coding GRCh37
#> 27 ensembl_homo_sapiens_37 Transcript protein_coding GRCh37
#> 28 ensembl_homo_sapiens_37 Transcript protein_coding GRCh37
#> 29 ensembl_homo_sapiens_37 Transcript protein_coding GRCh37
#> 30 ensembl_homo_sapiens_37 Transcript protein_coding GRCh37
#> 31 ensembl_homo_sapiens_37 Transcript protein_coding GRCh37
#> version
#> 1 3
#> 2 1
#> 3 1
#> 4 1
#> 5 1
#> 6 1
#> 7 2
#> 8 1
#> 9 2
#> 10 1
#> 11 1
#> 12 1
#> 13 1
#> 14 1
#> 15 1
#> 16 1
#> 17 3
#> 18 1
#> 19 1
#> 20 1
#> 21 1
#> 22 1
#> 23 1
#> 24 1
#> 25 1
#> 26 1
#> 27 3
#> 28 3
#> 29 3
#> 30 3
#> 31 4
#>
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>
#> $display_name
#> [1] "BRCA1"
#>
#> $start
#> [1] 41196312
#>
#> $source
#> [1] "ensembl_havana"
#>
queryEnsemblByGene("ENSG00000139618")
#> $display_name
#> [1] "BRCA2"
#>
#> $strand
#> [1] 1
#>
#> $object_type
#> [1] "Gene"
#>
#> $start
#> [1] 32889611
#>
#> $canonical_transcript
#> [1] "ENST00000544455.1"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $id
#> [1] "ENSG00000139618"
#>
#> $end
#> [1] 32973805
#>
#> $db_type
#> [1] "core"
#>
#> $description
#> [1] "breast cancer 2, early onset [Source:HGNC Symbol;Acc:1101]"
#>
#> $assembly_name
#> [1] "GRCh37"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $version
#> [1] 10
#>
#> $seq_region_name
#> [1] "13"
#>
#> $species
#> [1] "homo_sapiens"
#>
#> $Transcript
#> start object_type gencode_primary strand display_name is_canonical
#> 1 32889611 Transcript 0 1 BRCA2-001 0
#> 2 32889642 Transcript 0 1 BRCA2-003 0
#> 3 32945108 Transcript 0 1 BRCA2-005 0
#> 4 32953977 Transcript 0 1 BRCA2-002 0
#> 5 32970946 Transcript 0 1 BRCA2-006 0
#> 6 32889617 Transcript 0 1 BRCA2-201 1
#> Translation.object_type Translation.start Translation.Parent
#> 1 Translation 32890598 ENST00000380152
#> 2 Translation 32899266 ENST00000530893
#> 3 Translation 32945108 ENST00000528762
#> 4 Translation 32953977 ENST00000470094
#> 5 <NA> NA <NA>
#> 6 Translation 32890598 ENST00000544455
#> Translation.db_type Translation.end Translation.id Translation.species
#> 1 core 32972907 ENSP00000369497 homo_sapiens
#> 2 core 32907428 ENSP00000435699 homo_sapiens
#> 3 core 32950807 ENSP00000433168 homo_sapiens
#> 4 core 32970229 ENSP00000434898 homo_sapiens
#> 5 <NA> NA <NA> <NA>
#> 6 core 32972907 ENSP00000439902 homo_sapiens
#> Translation.length Translation.version length db_type Parent
#> 1 3418 3 10930 core ENSG00000139618
#> 2 481 2 2011 core ENSG00000139618
#> 3 64 1 495 core ENSG00000139618
#> 4 186 1 842 core ENSG00000139618
#> 5 NA NA 523 core ENSG00000139618
#> 6 3418 1 10984 core ENSG00000139618
#> end logic_name source id
#> 1 32973347 ensembl_havana_transcript ensembl_havana ENST00000380152
#> 2 32907428 havana_homo_sapiens_37 havana ENST00000530893
#> 3 32953632 havana_homo_sapiens_37 havana ENST00000528762
#> 4 32972409 havana_homo_sapiens_37 havana ENST00000470094
#> 5 32972585 havana_homo_sapiens_37 havana ENST00000533776
#> 6 32973805 ensembl_homo_sapiens_37 ensembl ENST00000544455
#> species Exon version biotype assembly_name
#> 1 homo_sapiens c("13", .... 3 protein_coding GRCh37
#> 2 homo_sapiens c("Exon".... 2 protein_coding GRCh37
#> 3 homo_sapiens c("homo_.... 1 nonsense_mediated_decay GRCh37
#> 4 homo_sapiens c("ENSE0.... 1 nonsense_mediated_decay GRCh37
#> 5 homo_sapiens c("Exon".... 1 retained_intron GRCh37
#> 6 homo_sapiens c(1, 1, .... 1 protein_coding GRCh37
#> seq_region_name
#> 1 13
#> 2 13
#> 3 13
#> 4 13
#> 5 13
#> 6 13
#>
event <- "SE_17_-_41251792_41249306_41249261_41246877_BRCA1"
queryEnsemblByEvent(event, species="human", assembly="hg19")
#> $assembly_name
#> [1] "GRCh37"
#>
#> $display_name
#> [1] "BRCA1"
#>
#> $seq_region_name
#> [1] "17"
#>
#> $id
#> [1] "ENSG00000012048"
#>
#> $source
#> [1] "ensembl_havana"
#>
#> $canonical_transcript
#> [1] "ENST00000471181.2"
#>
#> $version
#> [1] 15
#>
#> $species
#> [1] "human"
#>
#> $strand
#> [1] -1
#>
#> $start
#> [1] 41196312
#>
#> $end
#> [1] 41277500
#>
#> $Transcript
#> is_canonical species strand version display_name assembly_name
#> 1 0 human -1 3 BRCA1-001 GRCh37
#> 2 0 human -1 1 BRCA1-007 GRCh37
#> 3 0 human -1 1 BRCA1-023 GRCh37
#> 4 0 human -1 1 BRCA1-024 GRCh37
#> 5 0 human -1 1 BRCA1-025 GRCh37
#> 6 0 human -1 1 BRCA1-006 GRCh37
#> 7 1 human -1 2 BRCA1-005 GRCh37
#> 8 0 human -1 1 BRCA1-010 GRCh37
#> 9 0 human -1 2 BRCA1-014 GRCh37
#> 10 0 human -1 1 BRCA1-015 GRCh37
#> 11 0 human -1 1 BRCA1-009 GRCh37
#> 12 0 human -1 1 BRCA1-008 GRCh37
#> 13 0 human -1 1 BRCA1-021 GRCh37
#> 14 0 human -1 1 BRCA1-019 GRCh37
#> 15 0 human -1 1 BRCA1-022 GRCh37
#> 16 0 human -1 1 BRCA1-012 GRCh37
#> 17 0 human -1 3 BRCA1-026 GRCh37
#> 18 0 human -1 1 BRCA1-011 GRCh37
#> 19 0 human -1 1 BRCA1-004 GRCh37
#> 20 0 human -1 1 BRCA1-002 GRCh37
#> 21 0 human -1 1 BRCA1-003 GRCh37
#> 22 0 human -1 1 BRCA1-013 GRCh37
#> 23 0 human -1 1 BRCA1-018 GRCh37
#> 24 0 human -1 1 BRCA1-017 GRCh37
#> 25 0 human -1 1 BRCA1-020 GRCh37
#> 26 0 human -1 1 BRCA1-016 GRCh37
#> 27 0 human -1 3 BRCA1-205 GRCh37
#> 28 0 human -1 3 BRCA1-204 GRCh37
#> 29 0 human -1 3 BRCA1-202 GRCh37
#> 30 0 human -1 3 BRCA1-203 GRCh37
#> 31 0 human -1 4 BRCA1-201 GRCh37
#> Parent source seq_region_name Translation.object_type
#> 1 ENSG00000012048 ensembl_havana 17 Translation
#> 2 ENSG00000012048 ensembl_havana 17 Translation
#> 3 ENSG00000012048 havana 17 Translation
#> 4 ENSG00000012048 havana 17 Translation
#> 5 ENSG00000012048 havana 17 Translation
#> 6 ENSG00000012048 ensembl_havana 17 Translation
#> 7 ENSG00000012048 ensembl_havana 17 Translation
#> 8 ENSG00000012048 havana 17 Translation
#> 9 ENSG00000012048 havana 17 Translation
#> 10 ENSG00000012048 havana 17 Translation
#> 11 ENSG00000012048 havana 17 Translation
#> 12 ENSG00000012048 havana 17 Translation
#> 13 ENSG00000012048 havana 17 <NA>
#> 14 ENSG00000012048 havana 17 Translation
#> 15 ENSG00000012048 havana 17 Translation
#> 16 ENSG00000012048 havana 17 <NA>
#> 17 ENSG00000012048 havana 17 Translation
#> 18 ENSG00000012048 havana 17 Translation
#> 19 ENSG00000012048 havana 17 Translation
#> 20 ENSG00000012048 havana 17 Translation
#> 21 ENSG00000012048 havana 17 Translation
#> 22 ENSG00000012048 havana 17 Translation
#> 23 ENSG00000012048 havana 17 Translation
#> 24 ENSG00000012048 havana 17 Translation
#> 25 ENSG00000012048 havana 17 Translation
#> 26 ENSG00000012048 havana 17 Translation
#> 27 ENSG00000012048 ensembl 17 Translation
#> 28 ENSG00000012048 ensembl 17 Translation
#> 29 ENSG00000012048 ensembl 17 Translation
#> 30 ENSG00000012048 ensembl 17 Translation
#> 31 ENSG00000012048 ensembl 17 Translation
#> Translation.Parent Translation.id Translation.length Translation.db_type
#> 1 ENST00000357654 ENSP00000350283 1863 core
#> 2 ENST00000468300 ENSP00000417148 699 core
#> 3 ENST00000586385 ENSP00000465818 173 core
#> 4 ENST00000591534 ENSP00000467329 354 core
#> 5 ENST00000591849 ENSP00000465347 96 core
#> 6 ENST00000493795 ENSP00000418775 1816 core
#> 7 ENST00000471181 ENSP00000418960 1884 core
#> 8 ENST00000461221 ENSP00000418548 63 core
#> 9 ENST00000491747 ENSP00000420705 759 core
#> 10 ENST00000484087 ENSP00000419481 498 core
#> 11 ENST00000478531 ENSP00000420412 623 core
#> 12 ENST00000493919 ENSP00000418819 572 core
#> 13 <NA> <NA> NA <NA>
#> 14 ENST00000487825 ENSP00000418212 266 core
#> 15 ENST00000461574 ENSP00000417241 242 core
#> 16 <NA> <NA> NA <NA>
#> 17 ENST00000412061 ENSP00000397145 437 core
#> 18 ENST00000470026 ENSP00000419274 649 core
#> 19 ENST00000477152 ENSP00000419988 622 core
#> 20 ENST00000492859 ENSP00000420253 59 core
#> 21 ENST00000497488 ENSP00000418986 177 core
#> 22 ENST00000494123 ENSP00000419103 473 core
#> 23 ENST00000473961 ENSP00000420201 319 core
#> 24 ENST00000476777 ENSP00000417554 222 core
#> 25 ENST00000461798 ENSP00000417988 63 core
#> 26 ENST00000489037 ENSP00000420781 98 core
#> 27 ENST00000354071 ENSP00000326002 1598 core
#> 28 ENST00000352993 ENSP00000312236 721 core
#> 29 ENST00000346315 ENSP00000246907 1624 core
#> 30 ENST00000351666 ENSP00000338007 680 core
#> 31 ENST00000309486 ENSP00000310938 1567 core
#> Translation.end Translation.start Translation.species Translation.version
#> 1 41276113 41197695 human 3
#> 2 41276113 41197801 human 1
#> 3 41277202 41197695 human 1
#> 4 41226495 41197695 human 1
#> 5 41202109 41197695 human 1
#> 6 41258543 41197695 human 1
#> 7 41276113 41197695 human 2
#> 8 41276113 41256972 human 1
#> 9 41276113 41197695 human 2
#> 10 41256933 41215361 human 1
#> 11 41276113 41215361 human 1
#> 12 41258543 41215377 human 1
#> 13 NA NA <NA> NA
#> 14 41256933 41228505 human 1
#> 15 41243841 41228554 human 1
#> 16 NA NA <NA> NA
#> 17 41247883 41245587 human 3
#> 18 41276113 41245601 human 1
#> 19 41276113 41245603 human 1
#> 20 41276113 41262552 human 1
#> 21 41246659 41246129 human 1
#> 22 41276113 41246129 human 1
#> 23 41256908 41246187 human 1
#> 24 41276113 41247863 human 1
#> 25 41276113 41256972 human 1
#> 26 41276113 41256206 human 1
#> 27 41276113 41197695 human 6
#> 28 41276113 41197695 human 5
#> 29 41276113 41197695 human 4
#> 30 41276113 41197695 human 3
#> 31 41246659 41197695 human 4
#> id logic_name gencode_primary Exon
#> 1 ENST00000357654 ensembl_havana_transcript 0 c("GRCh3....
#> 2 ENST00000468300 ensembl_havana_transcript 0 c(412774....
#> 3 ENST00000586385 havana_homo_sapiens_37 0 c(1, 1, ....
#> 4 ENST00000591534 havana_homo_sapiens_37 0 c("core"....
#> 5 ENST00000591849 havana_homo_sapiens_37 0 c(412773....
#> 6 ENST00000493795 ensembl_havana_transcript 0 c("Exon"....
#> 7 ENST00000471181 ensembl_havana_transcript 0 c(412772....
#> 8 ENST00000461221 havana_homo_sapiens_37 0 c("core"....
#> 9 ENST00000491747 havana_homo_sapiens_37 0 c(412772....
#> 10 ENST00000484087 havana_homo_sapiens_37 0 c("Exon"....
#> 11 ENST00000478531 havana_homo_sapiens_37 0 c(1, 1, ....
#> 12 ENST00000493919 havana_homo_sapiens_37 0 c(412772....
#> 13 ENST00000472490 havana_homo_sapiens_37 0 c("17", ....
#> 14 ENST00000487825 havana_homo_sapiens_37 0 c("17", ....
#> 15 ENST00000461574 havana_homo_sapiens_37 0 c("human....
#> 16 ENST00000467274 havana_homo_sapiens_37 0 c("human....
#> 17 ENST00000412061 havana_homo_sapiens_37 0 c(412478....
#> 18 ENST00000470026 havana_homo_sapiens_37 0 c("human....
#> 19 ENST00000477152 havana_homo_sapiens_37 0 c("ENSE0....
#> 20 ENST00000492859 havana_homo_sapiens_37 0 c("Exon"....
#> 21 ENST00000497488 havana_homo_sapiens_37 0 c("human....
#> 22 ENST00000494123 havana_homo_sapiens_37 0 c("ENSE0....
#> 23 ENST00000473961 havana_homo_sapiens_37 0 c("Exon"....
#> 24 ENST00000476777 havana_homo_sapiens_37 0 c(412773....
#> 25 ENST00000461798 havana_homo_sapiens_37 0 c("human....
#> 26 ENST00000489037 havana_homo_sapiens_37 0 c(412771....
#> 27 ENST00000354071 ensembl_homo_sapiens_37 0 c("ENSE0....
#> 28 ENST00000352993 ensembl_homo_sapiens_37 0 c("Exon"....
#> 29 ENST00000346315 ensembl_homo_sapiens_37 0 c(-1, -1....
#> 30 ENST00000351666 ensembl_homo_sapiens_37 0 c(-1, -1....
#> 31 ENST00000309486 ensembl_homo_sapiens_37 0 c(412774....
#> end db_type start object_type biotype length
#> 1 41277387 core 41196312 Transcript protein_coding 7094
#> 2 41277468 core 41196822 Transcript protein_coding 3273
#> 3 41277346 core 41197580 Transcript protein_coding 781
#> 4 41277346 core 41197580 Transcript protein_coding 1282
#> 5 41277346 core 41197580 Transcript protein_coding 563
#> 6 41277419 core 41197646 Transcript protein_coding 5732
#> 7 41277500 core 41197646 Transcript protein_coding 5936
#> 8 41277305 core 41197695 Transcript nonsense_mediated_decay 5693
#> 9 41277373 core 41197695 Transcript protein_coding 2379
#> 10 41256933 core 41215361 Transcript protein_coding 1495
#> 11 41277376 core 41215361 Transcript protein_coding 1972
#> 12 41277419 core 41215377 Transcript protein_coding 1948
#> 13 41223083 core 41219291 Transcript retained_intron 561
#> 14 41256933 core 41228505 Transcript protein_coding 800
#> 15 41243841 core 41228554 Transcript protein_coding 726
#> 16 41277332 core 41243115 Transcript retained_intron 4497
#> 17 41247883 core 41245587 Transcript non_stop_decay 1312
#> 18 41277340 core 41245601 Transcript protein_coding 2108
#> 19 41277381 core 41245603 Transcript protein_coding 1980
#> 20 41277317 core 41246129 Transcript nonsense_mediated_decay 1584
#> 21 41277317 core 41246129 Transcript protein_coding 779
#> 22 41277467 core 41246129 Transcript protein_coding 1612
#> 23 41256908 core 41246187 Transcript protein_coding 958
#> 24 41277370 core 41247863 Transcript protein_coding 769
#> 25 41277387 core 41251848 Transcript nonsense_mediated_decay 582
#> 26 41277338 core 41256206 Transcript protein_coding 455
#> 27 41277500 core 41196313 Transcript protein_coding 6411
#> 28 41277500 core 41196313 Transcript protein_coding 3780
#> 29 41277468 core 41196313 Transcript protein_coding 6451
#> 30 41276132 core 41196313 Transcript protein_coding 3444
#> 31 41277468 core 41196313 Transcript protein_coding 7114
#>
#> $db_type
#> [1] "core"
#>
#> $biotype
#> [1] "protein_coding"
#>
#> $object_type
#> [1] "Gene"
#>
#> $description
#> [1] "breast cancer 1, early onset [Source:HGNC Symbol;Acc:1100]"
#>
#> $logic_name
#> [1] "ensembl_havana_gene_homo_sapiens_37"
#>