hg19 exon, intron, UTR region

Question

[9521ljh]

where to get the file of hg19 exon, intron, UTR region ?

I read lots of post in biostar. However it's been a long time post.

Answer 1

[ATpoint]

Get the respective GTF (annotation) file for your genome. Once you have this you can basically follow A: how to get intronic and intergenic sequences based on gff file? to get the respective features. GTFs can be found at NCBI, Ensembl or GENCODE.

Answer 2

[i.sudbery]

Be aware that UTRs are part of exons. So when you get UTR regions from a GTF/GFF, they will overlap with the regions annotated as exons in the GTF. Perhaps what you want is not things annotated as exons, but things annotated as CDS?

Answer 3

[Pierre Lindenbaum]

using bioalcidaejdk : http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

$ wget  -q -O - "ftp://ftp.ensemblgenomes.org/pub/release-45/metazoa/gtf/apis_mellifera/Apis_mellifera.Amel_4.5.45.gtf.gz" |\
gunzip -c |\
java -jar dist/bioalcidaejdk.jar -F GTF -f biostar.code  

(...)
6   4682136 4682216 +   GB52198-RA.Intron16
6   4682387 4682473 +   GB52198-RA.Intron17
6   4682696 4682760 +   GB52198-RA.Intron18
6   4682905 4682967 +   GB52198-RA.Intron19
6   4676837 4677042 +   5' UTR of GB52198-RA
6   4683076 4683853 +   3' UTR of GB52198-RA
6   4691339 4691384 +   GB52199-RA.Exon1
6   4692448 4692491 +   GB52199-RA.Exon2
6   4693914 4694249 +   GB52199-RA.Exon3
6   4691384 4692448 +   GB52199-RA.Intron1
6   4692491 4693914 +   GB52199-RA.Intron2
6   4691339 4691339 +   5' UTR of GB52199-RA
(...)

with biostar.code:

stream().
    flatMap(GENE->GENE.getTranscripts().stream()).
    flatMap(TRANSCRIPT->{
        final List<Interval> L = new ArrayList<>();
        TRANSCRIPT.getExons().stream().forEach(E->L.add(E.toInterval()));
        TRANSCRIPT.getIntrons().stream().forEach(I->L.add(I.toInterval()));
        TRANSCRIPT.getUTRs().stream().forEach(U->L.add(U.toInterval()));
        return L.stream();
        }).forEach(R->println(R.getContig()+"\t"+(R.getStart()-1)+"\t"+R.getEnd()+"\t"+R.getStrand()+"\t"+R.getName()));

Answer 4

[WouterDeCoster]

Search for gtf/gff files, these should contain the information you are looking for. Make sure the chromosome notation matches with your reference fasta genome.