Question: Comprehensive gene annotation for drosophila melanogaster
0
gravatar for newscient
20 months ago by
newscient20
European Union
newscient20 wrote:

Is there a trustworthy and so-called comprehensive annotation for drosophila melanogaster of all genomic regions in order to construct a TSS (transcription start site) database? Is it UCSC (by quering), modENCODE, flybase or ensembl that i should search for it? I am looking for something like the Gencode annotation for human/mouse preferably in gtf format (gencode.v19.annotation.gtf) which looks like this:

##description: evidence-based annotation of the human genome (GRCh37), version 19 (Ensembl 74)
##provider: GENCODE
##contact: gencode@sanger.ac.uk
##format: gtf
##date: 2013-12-05
chr1    HAVANA  gene    11869   14412   .   +   .   gene_id "ENSG00000223972.4"; transcript_id "ENSG00000223972.4"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1    HAVANA  transcript  11869   14409   .   +   .   gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    11869   12227   .   +   .   gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    12613   12721   .   +   .   gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    13221   14409   .   +   .   gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";

Thanks for your suggestions!

genome • 863 views
ADD COMMENTlink modified 20 months ago by Jean-Karim Heriche18k • written 20 months ago by newscient20
4
gravatar for genomax
20 months ago by
genomax63k
United States
genomax63k wrote:

Flybase should be authoritative resource for all things Drosophila.

ADD COMMENTlink written 20 months ago by genomax63k
1

Also flyDIVaS

ADD REPLYlink written 20 months ago by st.ph.n2.4k
1
gravatar for Jean-Karim Heriche
20 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

EnsEMBL has an annotated Drosophila genome.
gtf files (and others) are available on the ftp site

ADD COMMENTlink modified 20 months ago • written 20 months ago by Jean-Karim Heriche18k
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