https://www.bioconductor.org/help/workflows/annotation-data/
https://bioconductor.org/help/workflows/annotation/Annotation_Resources/
library(TxDb.Dmelanogaster.UCSC.dm6.ensGene)
library(org.Dm.eg.db)
library(BSgenome.Dmelanogaster.UCSC.dm6)
library(GO.db)
library(rtracklayer)# TxDb object
txdb <- TxDb.Dmelanogaster.UCSC.dm6.ensGene## TxDb object:
## # Db type: TxDb
## # Supporting package: GenomicFeatures
## # Data source: UCSC
## # Genome: dm6
## # Organism: Drosophila melanogaster
## # Taxonomy ID: 7227
## # UCSC Table: ensGene
## # UCSC Track: Ensembl Genes
## # Resource URL: http://genome.ucsc.edu/
## # Type of Gene ID: Ensembl gene ID
## # Full dataset: yes
## # miRBase build ID: NA
## # transcript_nrow: 34703
## # exon_nrow: 83433
## # cds_nrow: 62685
## # Db created by: GenomicFeatures package from Bioconductor
## # Creation time: 2017-04-04 22:11:07 +0000 (Tue, 04 Apr 2017)
## # GenomicFeatures version at creation time: 1.27.13
## # RSQLite version at creation time: 1.1-2
## # DBSCHEMAVERSION: 1.1
# extract ranges
fly_genes <- genes(txdb)
fly_exons <- exonsBy(txdb, by = "gene")
fly_fiveUTR <- fiveUTRsByTranscript(txdb)## GRanges object with 17522 ranges and 1 metadata column:
## seqnames ranges strand | gene_id
## <Rle> <IRanges> <Rle> | <character>
## FBgn0000003 chr3R [ 6822498, 6822796] + | FBgn0000003
## FBgn0000008 chr2R [22136968, 22172834] + | FBgn0000008
## FBgn0000014 chr3R [16807214, 16830049] - | FBgn0000014
## FBgn0000015 chr3R [16927210, 16972236] - | FBgn0000015
## FBgn0000017 chr3L [16615866, 16647882] - | FBgn0000017
## ... ... ... ... . ...
## FBgn0267791 chr2R [20587551, 20606854] + | FBgn0267791
## FBgn0267792 chr2R [ 8600415, 8612295] + | FBgn0267792
## FBgn0267793 chr2R [16297449, 16306695] - | FBgn0267793
## FBgn0267794 chr3L [17934032, 17946114] + | FBgn0267794
## FBgn0267795 chr3L [14053215, 14071583] + | FBgn0267795
## -------
## seqinfo: 1870 sequences (1 circular) from dm6 genome
## GRangesList object of length 17522:
## $FBgn0000003
## GRanges object with 1 range and 2 metadata columns:
## seqnames ranges strand | exon_id exon_name
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] chr3R [6822498, 6822796] + | 49264 <NA>
##
## $FBgn0000008
## GRanges object with 13 ranges and 2 metadata columns:
## seqnames ranges strand | exon_id exon_name
## [1] chr2R [22136968, 22137026] + | 22500 <NA>
## [2] chr2R [22136968, 22137208] + | 22501 <NA>
## [3] chr2R [22137433, 22138251] + | 22502 <NA>
## [4] chr2R [22138000, 22138251] + | 22503 <NA>
## [5] chr2R [22151654, 22151695] + | 22508 <NA>
## ... ... ... ... . ... ...
## [9] chr2R [22170778, 22171259] + | 22512 <NA>
## [10] chr2R [22170778, 22171985] + | 22513 <NA>
## [11] chr2R [22172082, 22172252] + | 22514 <NA>
## [12] chr2R [22172316, 22172433] + | 22515 <NA>
## [13] chr2R [22172497, 22172834] + | 22516 <NA>
##
## ...
## <17520 more elements>
## -------
## seqinfo: 1870 sequences (1 circular) from dm6 genome
## GRangesList object of length 29726:
## $1
## GRanges object with 1 range and 3 metadata columns:
## seqnames ranges strand | exon_id exon_name exon_rank
## <Rle> <IRanges> <Rle> | <integer> <character> <integer>
## [1] chr2L [7529, 7679] + | 1 <NA> 1
##
## $2
## GRanges object with 1 range and 3 metadata columns:
## seqnames ranges strand | exon_id exon_name exon_rank
## [1] chr2L [7529, 7679] + | 1 <NA> 1
##
## $3
## GRanges object with 1 range and 3 metadata columns:
## seqnames ranges strand | exon_id exon_name exon_rank
## [1] chr2L [7529, 7679] + | 1 <NA> 1
##
## ...
## <29723 more elements>
## -------
## seqinfo: 1870 sequences (1 circular) from dm6 genome
# OrgDb object
orgdb <- org.Dm.eg.db## OrgDb object:
## | DBSCHEMAVERSION: 2.1
## | Db type: OrgDb
## | Supporting package: AnnotationDbi
## | DBSCHEMA: FLY_DB
## | ORGANISM: Drosophila melanogaster
## | SPECIES: Fly
## | EGSOURCEDATE: 2017-Nov6
## | EGSOURCENAME: Entrez Gene
## | EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
## | CENTRALID: EG
## | TAXID: 7227
## | GOSOURCENAME: Gene Ontology
## | GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
## | GOSOURCEDATE: 2017-Nov01
## | GOEGSOURCEDATE: 2017-Nov6
## | GOEGSOURCENAME: Entrez Gene
## | GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
## | KEGGSOURCENAME: KEGG GENOME
## | KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
## | KEGGSOURCEDATE: 2011-Mar15
## | GPSOURCENAME: UCSC Genome Bioinformatics (Drosophila melanogaster)
## | GPSOURCEURL:
## | GPSOURCEDATE: 2014-Dec12
## | FBSOURCEDATE: 2017-Feb01
## | FBSOURCENAME: Flybase
## | FBSOURCEURL: ftp://ftp.flybase.net/releases/current/precomputed_files/genes/
## | ENSOURCEDATE: 2017-Aug23
## | ENSOURCENAME: Ensembl
## | ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
# columns
columns(orgdb)## [1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS" "ENTREZID" "ENZYME" "EVIDENCE" "EVIDENCEALL" "FLYBASE" "FLYBASECG" "FLYBASEPROT" "GENENAME" "GO" "GOALL" "MAP" "ONTOLOGY" "ONTOLOGYALL" "PATH" "PMID" "REFSEQ" "SYMBOL" "UNIGENE" "UNIPROT"
# mapping gene ids
favorite_gene <- "roX2"
mapIds(orgdb,
keys = favorite_gene,
keytype = "SYMBOL",
column = "FLYBASE",
multiVals = "first")## roX2
## "FBgn0019660"
# update gene ranges
fly_genes$symbol <- mapIds(orgdb,
keys = fly_genes$gene_id,
keytype = "FLYBASE",
column = "SYMBOL",
multiVals = "first")## GRanges object with 17522 ranges and 2 metadata columns:
## seqnames ranges strand | gene_id symbol
## <Rle> <IRanges> <Rle> | <character> <character>
## FBgn0000003 chr3R [ 6822498, 6822796] + | FBgn0000003 7SLRNA:CR32864
## FBgn0000008 chr2R [22136968, 22172834] + | FBgn0000008 a
## FBgn0000014 chr3R [16807214, 16830049] - | FBgn0000014 abd-A
## FBgn0000015 chr3R [16927210, 16972236] - | FBgn0000015 Abd-B
## FBgn0000017 chr3L [16615866, 16647882] - | FBgn0000017 Abl
## ... ... ... ... . ... ...
## FBgn0267791 chr2R [20587551, 20606854] + | FBgn0267791 HnRNP-K
## FBgn0267792 chr2R [ 8600415, 8612295] + | FBgn0267792 rgr
## FBgn0267793 chr2R [16297449, 16306695] - | FBgn0267793 CR45232
## FBgn0267794 chr3L [17934032, 17946114] + | FBgn0267794 CR43174
## FBgn0267795 chr3L [14053215, 14071583] + | FBgn0267795 Frl
## -------
## seqinfo: 1870 sequences (1 circular) from dm6 genome
# GO
favorite_gene_GO <- mapIds(orgdb,
keys = favorite_gene,
keytype = "SYMBOL",
column = "GO",
multiVals = "list")## $roX2
## [1] "GO:0000805" "GO:0000805" "GO:0005515" "GO:0007549" "GO:0007549" "GO:0009047" "GO:0016456" "GO:0016457" "GO:0031936" "GO:0035613" "GO:0072487"
# GODb object
GO.db## GODb object:
## | GOSOURCENAME: Gene Ontology
## | GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
## | GOSOURCEDATE: 2017-Nov01
## | Db type: GODb
## | package: AnnotationDbi
## | DBSCHEMA: GO_DB
## | GOEGSOURCEDATE: 2017-Nov6
## | GOEGSOURCENAME: Entrez Gene
## | GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
## | DBSCHEMAVERSION: 2.1
# convert ids
select(GO.db, favorite_gene_GO[[1]], "TERM", "GOID")## GOID TERM
## 1 GO:0000805 X chromosome
## 2 GO:0000805 X chromosome
## 3 GO:0005515 protein binding
## 4 GO:0007549 dosage compensation
## 5 GO:0007549 dosage compensation
## 6 GO:0009047 dosage compensation by hyperactivation of X chromosome
## 7 GO:0016456 X chromosome located dosage compensation complex, transcription activating
## 8 GO:0016457 dosage compensation complex assembly involved in dosage compensation by hyperactivation of X chromosome
## 9 GO:0031936 negative regulation of chromatin silencing
## 10 GO:0035613 RNA stem-loop binding
## 11 GO:0072487 MSL complex
# genome objects
fly_genome <- BSgenome.Dmelanogaster.UCSC.dm6##
## Fly genome:
## # organism: Drosophila melanogaster (Fly)
## # provider: UCSC
## # provider version: dm6
## # release date: Aug. 2014
## # release name: BDGP Release 6 + ISO1 MT
## # 1870 sequences:
## # chr2L chr2R chr3L chr3R chr4 chrX chrY chrM chrX_CP007103v1_random chrX_CP007104v1_random chrX_DS483648v1_random chrX_DS483655v1_random chrX_DS483660v1_random chrX_DS483665v1_random chrX_DS483666v1_random chrX_DS483669v1_random chrX_DS483685v1_random chrX_DS483698v1_random chrX_DS483745v1_random chrX_DS483784v1_random chrX_DS483789v1_random chrX_DS483795v1_random chrX_DS483803v1_random chrX_DS483809v1_random chrX_DS483818v1_random chrX_DS483821v1_random chrX_DS483843v1_random chrX_DS483851v1_random chrX_DS483885v1_random chrX_DS483888v1_random chrX_DS483892v1_random chrX_DS483893v1_random chrX_DS483897v1_random chrX_DS483903v1_random chrX_DS483905v1_random chrX_DS483907v1_random chrX_DS483909v1_random chrX_DS483923v1_random chrX_DS483926v1_random chrX_DS483928v1_random chrX_DS483946v1_random chrX_DS483948v1_random chrX_DS483950v1_random
# seqinfo
seqinfo(fly_genome)## Seqinfo object with 1870 sequences (1 circular) from dm6 genome:
## seqnames seqlengths isCircular genome
## chr2L 23513712 FALSE dm6
## chr2R 25286936 FALSE dm6
## chr3L 28110227 FALSE dm6
## chr3R 32079331 FALSE dm6
## chr4 1348131 FALSE dm6
## ... ... ... ...
## chrUn_DS485998v1 1003 FALSE dm6
## chrUn_DS486002v1 1001 FALSE dm6
## chrUn_DS486004v1 1001 FALSE dm6
## chrUn_DS486005v1 1001 FALSE dm6
## chrUn_DS486008v1 1001 FALSE dm6
# extract sequemce
favorite_gene_ranges <- fly_genes[grep(favorite_gene, fly_genes$symbol)]
getSeq(fly_genome, favorite_gene_ranges)## A DNAStringSet instance of length 1
## width seq names
## [1] 1368 ATTCGCGGCCTGGTCACACTAAGCTAGGGCTACTTTTTATATCATAAGTCGAGCGTTTAGGTAAGCGAAACAAAAAGAGCTTTAGTTAGAGGTATTAGTTTGGTTGCTATTATTTCTAAATTGAAAACTTCACTTCCTTTGATCCAAAAGACACTGAAAAGACACGTTTGCAGTTGAGTTCATTATTTTCTGGTATACATACACACTGATTACTCATTCAATTGGCATTTTGCTCTTGTTTTTCTCCGATTGCCTTGCACTCGCATAAATTTAACACAAAAAAGAAGTTCGGGGTGTTTAGAATCCATCCACTTGGTACAGTTCCCATCGAGCTGGTGAGTACTCCGCGCAGTGCAACGTATACACACTTGAACTCGAATTCTGGCAGCAAAATGGTGGTGACCTATTAATAACACCCGCTCAATTTTCCCTCGCTTTTCCATTCAGTCTCCAACTAGCTGCAAGTGAGTACGTTACTTCCGA...ACAATACAATACAAGACAAAAAAATGTGTCTTGGAACGCAACATTGTACAAGTCGCAATGCAAACTGAAGTCTTAAAAGACGTGTAAAATGTTGCAAATTAAGCAAATATATATGCATATATGGGTAACGTTTTACGCGCCTTAACCAGTCAAAATACAAAATAAATTGGTAAATTTCATATAACTAGTGAAATGTTATACGAAACTTAACAATTGCCAAATAATACAGATCGATTTAGAGCGAGATGACAATAGAGAGGCGATCTCTCTCGTATACGAGTCTTGAAAAGAAAGAGAAGGCGAACGGTGCTGGCTTAGAGAGAGATGGCAATACTAATTAACTGCAAATACATTTCCGCCATTTTGTTGGCGCTAAAAGTAACGGAAATTCGAGATGCTTTTAGGGCTGCCACCTTGGTTTCCAGGGTGACCAGAACTGACACTTAAATTACATATGACAAATAAAGACTTATCTGCTATTGC FBgn0019660
# TxDb from GTF
txdb <- makeTxDbFromGFF("dmel-all-r6.17.gtf", format = "gtf")## TxDb object:
## # Db type: TxDb
## # Supporting package: GenomicFeatures
## # Data source: dmel-all-r6.17.gtf
## # Organism: NA
## # Taxonomy ID: NA
## # miRBase build ID: NA
## # Genome: NA
## # transcript_nrow: 34990
## # exon_nrow: 83728
## # cds_nrow: 62778
## # Db created by: GenomicFeatures package from Bioconductor
## # Creation time: 2018-02-23 13:19:27 +0100 (Fri, 23 Feb 2018)
## # GenomicFeatures version at creation time: 1.30.3
## # RSQLite version at creation time: 2.0
## # DBSCHEMAVERSION: 1.2
# extract genes
genes(txdb)## GRanges object with 17736 ranges and 1 metadata column:
## seqnames ranges strand | gene_id
## <Rle> <IRanges> <Rle> | <character>
## FBgn0000003 3R [ 6822498, 6822796] + | FBgn0000003
## FBgn0000008 2R [22136968, 22172834] + | FBgn0000008
## FBgn0000014 3R [16807214, 16830049] - | FBgn0000014
## FBgn0000015 3R [16927212, 16972236] - | FBgn0000015
## FBgn0000017 3L [16615866, 16647882] - | FBgn0000017
## ... ... ... ... . ...
## FBgn0285994 3L [21576460, 21576661] - | FBgn0285994
## FBgn0286004 X [19558607, 19558693] + | FBgn0286004
## FBgn0286005 2R [18180151, 18180205] - | FBgn0286005
## FBgn0286006 2R [12170383, 12170449] - | FBgn0286006
## FBgn0286007 2R [12170163, 12170230] - | FBgn0286007
## -------
## seqinfo: 25 sequences from an unspecified genome; no seqlengths
# GRanges from GTF
fly_gtf <- import.gff("dmel-all-r6.17.gtf")## GRanges object with 541808 ranges and 9 metadata columns:
## seqnames ranges strand | source type score phase gene_id gene_symbol transcript_id transcript_symbol #
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer> <character> <character> <character> <character> <character>
## [1] X [19961297, 19969323] + | FlyBase gene <NA> <NA> FBgn0031081 Nep3 <NA> <NA> <NA>
## [2] X [19961689, 19968479] + | FlyBase mRNA <NA> <NA> FBgn0031081 Nep3 FBtr0070000 Nep3-RA <NA>
## [3] X [19961689, 19961845] + | FlyBase 5UTR <NA> <NA> FBgn0031081 Nep3 FBtr0070000 Nep3-RA <NA>
## [4] X [19961689, 19961845] + | FlyBase exon <NA> <NA> FBgn0031081 Nep3 FBtr0070000 Nep3-RA <NA>
## [5] X [19963955, 19964071] + | FlyBase exon <NA> <NA> FBgn0031081 Nep3 FBtr0070000 Nep3-RA <NA>
## ... ... ... ... . ... ... ... ... ... ... ... ... ...
## [541804] 2L [779173, 779655] + | FlyBase exon <NA> <NA> FBgn0031277 CG13947 FBtr0078005 CG13947-RA <NA>
## [541805] 2L [779204, 779206] + | FlyBase start_codon <NA> 0 FBgn0031277 CG13947 FBtr0078005 CG13947-RA <NA>
## [541806] 2L [779204, 779560] + | FlyBase CDS <NA> 0 FBgn0031277 CG13947 FBtr0078005 CG13947-RA <NA>
## [541807] 2L [779561, 779563] + | FlyBase stop_codon <NA> 0 FBgn0031277 CG13947 FBtr0078005 CG13947-RA <NA>
## [541808] 2L [779564, 779655] + | FlyBase 3UTR <NA> <NA> FBgn0031277 CG13947 FBtr0078005 CG13947-RA <NA>
## -------
## seqinfo: 25 sequences from an unspecified genome; no seqlengths
# extract by type
fly_genes <- fly_gtf[fly_gtf$type == "gene"]
fly_cds <- fly_gtf[fly_gtf$type == "CDS"]## GRanges object with 17737 ranges and 9 metadata columns:
## seqnames ranges strand | source type score phase gene_id gene_symbol transcript_id transcript_symbol #
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer> <character> <character> <character> <character> <character>
## [1] X [19961297, 19969323] + | FlyBase gene <NA> <NA> FBgn0031081 Nep3 <NA> <NA> <NA>
## [2] X [20025099, 20025170] + | FlyBase gene <NA> <NA> FBgn0052826 tRNA:Pro-CGG-1-1 <NA> <NA> <NA>
## [3] X [20051294, 20052519] + | FlyBase gene <NA> <NA> FBgn0031085 CG9570 <NA> <NA> <NA>
## [4] X [20094398, 20095767] + | FlyBase gene <NA> <NA> FBgn0062565 Or19b <NA> <NA> <NA>
## [5] X [20133579, 20138878] + | FlyBase gene <NA> <NA> FBgn0031088 CG15322 <NA> <NA> <NA>
## ... ... ... ... . ... ... ... ... ... ... ... ... ...
## [17733] 2L [728362, 730564] + | FlyBase gene <NA> <NA> FBgn0011244 Hsp60B <NA> <NA> <NA>
## [17734] 2L [749945, 762399] + | FlyBase gene <NA> <NA> FBgn0031275 GABA-B-R3 <NA> <NA> <NA>
## [17735] 2L [773547, 774017] + | FlyBase gene <NA> <NA> FBgn0031276 CG12506 <NA> <NA> <NA>
## [17736] 2L [776536, 776941] + | FlyBase gene <NA> <NA> FBgn0040725 CG13946 <NA> <NA> <NA>
## [17737] 2L [779173, 779655] + | FlyBase gene <NA> <NA> FBgn0031277 CG13947 <NA> <NA> <NA>
## -------
## seqinfo: 25 sequences from an unspecified genome; no seqlengths
## GRanges object with 160894 ranges and 9 metadata columns:
## seqnames ranges strand | source type score phase gene_id gene_symbol transcript_id transcript_symbol #
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer> <character> <character> <character> <character> <character>
## [1] X [19963955, 19964071] + | FlyBase CDS <NA> 0 FBgn0031081 Nep3 FBtr0070000 Nep3-RA <NA>
## [2] X [19964782, 19964944] + | FlyBase CDS <NA> 0 FBgn0031081 Nep3 FBtr0070000 Nep3-RA <NA>
## [3] X [19965006, 19965126] + | FlyBase CDS <NA> 2 FBgn0031081 Nep3 FBtr0070000 Nep3-RA <NA>
## [4] X [19965197, 19965511] + | FlyBase CDS <NA> 1 FBgn0031081 Nep3 FBtr0070000 Nep3-RA <NA>
## [5] X [19965577, 19966071] + | FlyBase CDS <NA> 1 FBgn0031081 Nep3 FBtr0070000 Nep3-RA <NA>
## ... ... ... ... . ... ... ... ... ... ... ... ... ...
## [160890] 2L [759231, 759549] + | FlyBase CDS <NA> 0 FBgn0031275 GABA-B-R3 FBtr0343787 GABA-B-R3-RG <NA>
## [160891] 2L [759679, 760910] + | FlyBase CDS <NA> 2 FBgn0031275 GABA-B-R3 FBtr0343787 GABA-B-R3-RG <NA>
## [160892] 2L [773595, 773915] + | FlyBase CDS <NA> 0 FBgn0031276 CG12506 FBtr0078003 CG12506-RA <NA>
## [160893] 2L [776542, 776838] + | FlyBase CDS <NA> 0 FBgn0040725 CG13946 FBtr0078004 CG13946-RA <NA>
## [160894] 2L [779204, 779560] + | FlyBase CDS <NA> 0 FBgn0031277 CG13947 FBtr0078005 CG13947-RA <NA>
## -------
## seqinfo: 25 sequences from an unspecified genome; no seqlengths
# extract by gene symbol
fly_rRNA <- fly_gtf[grep("rRNA", fly_gtf$gene_symbol)]## GRanges object with 416 ranges and 9 metadata columns:
## seqnames ranges strand | source type score phase gene_id gene_symbol transcript_id transcript_symbol #
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer> <character> <character> <character> <character> <character>
## [1] 2R [19766144, 19766278] - | FlyBase gene <NA> <NA> FBgn0053353 5SrRNA:CR33353 <NA> <NA> <NA>
## [2] 2R [19766144, 19766278] - | FlyBase rRNA <NA> <NA> FBgn0053353 5SrRNA:CR33353 FBtr0086345 5SrRNA:CR33353-RA <NA>
## [3] 2R [19766144, 19766278] - | FlyBase exon <NA> <NA> FBgn0053353 5SrRNA:CR33353 FBtr0086345 5SrRNA:CR33353-RA <NA>
## [4] 2R [19765775, 19765909] - | FlyBase gene <NA> <NA> FBgn0053354 5SrRNA:CR33354 <NA> <NA> <NA>
## [5] 2R [19765775, 19765909] - | FlyBase rRNA <NA> <NA> FBgn0053354 5SrRNA:CR33354 FBtr0086346 5SrRNA:CR33354-RA <NA>
## ... ... ... ... . ... ... ... ... ... ... ... ... ...
## [412] X [23291549, 23291671] + | FlyBase pseudogene <NA> <NA> FBgn0267523 5.8SrRNA-Psi:CR45863 FBtr0346897 5.8SrRNA-Psi:CR45863-RA <NA>
## [413] X [23291549, 23291671] + | FlyBase exon <NA> <NA> FBgn0267523 5.8SrRNA-Psi:CR45863 FBtr0346897 5.8SrRNA-Psi:CR45863-RA <NA>
## [414] X [23291700, 23291729] + | FlyBase gene <NA> <NA> FBgn0267524 2SrRNA:CR45864 <NA> <NA> <NA>
## [415] X [23291700, 23291729] + | FlyBase rRNA <NA> <NA> FBgn0267524 2SrRNA:CR45864 FBtr0346898 2SrRNA:CR45864-RA <NA>
## [416] X [23291700, 23291729] + | FlyBase exon <NA> <NA> FBgn0267524 2SrRNA:CR45864 FBtr0346898 2SrRNA:CR45864-RA <NA>
## -------
## seqinfo: 25 sequences from an unspecified genome; no seqlengths