How to get the genomic coordinates of a transcripts in EntrezDirect ?

Question

[Manuel]

I have learnt how to get the coding coordinates of a transcripts here Easy way to compare the co-ordenates between RefSeq transcripts. I was wondering how to get the genomics coordinates

[ATpoint]

Download the suitable GTF file, it is all annotated in there. Since splicing comes into play there won't be a single interval unless it is an intronless gene.

[Manuel]

Thanks for your help. I have found this https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/

The file hg19.ncbiRefSeq.gtf.gz shown the transcripts but only the last version. I want to search across different versions. I cannot find a file with old versions

[jv]

Hg19 is also known as GRCh37, data from past Hg19 versions, aka releases, are available at http://ftp.ensembl.org/pub/grch37/

Answer 1

[GenoMax]

$ esearch -db nuccore -query NM_002734.5 | elink -target gene | esummary | xtract -pattern DocumentSummary -element AssemblyAccVer,ChrAccVer,ChrStart,ChrStop
GCF_000001405.40        GCF_009914755.1 GCF_000001405.39        GCF_000001405.39        GCF_000001405.39        GCF_000001405.39        GCF_000001405.39        GCF_000001405.39        GCF_000001405.39        GCF_000001405.39     GCF_000001405.39 GCF_000001405.39        GCF_000001405.38        GCF_000001405.25        GCF_000001405.25        GCF_000001405.25        GCF_000002125.1 GCF_000306695.2 NC_000017.11    NC_000017.11    NC_060941.1     NC_000017.11 NC_000017.11     NC_000017.11    NC_000017.11    NC_000017.11    NC_000017.11    NC_000017.11    NC_000017.11    NC_000017.11    NC_000017.11    NC_000017.11    NC_000017.10    NC_000017.10    NC_000017.10    AC_000149.1     NC_018928.2   68413622        68413622        68413622        69290145        68413622        68413622        68413622        68413622        68413622        68413622        68413622        68413622        68413622        68413622     68413622 66409763        66409763        66507920        61893654        66572676        68551315        68551315        69428168        68551315        68551315        68551315        68551315        68551315        68551315     68551315 68551315        68551315        68551315        68551315        66547456        66547456        66547456        61933190        66612183

Above is bit messy but this would be concise (only works for the latest accession).

$ esearch -db nuccore -query NM_002734.5 | elink -target gene | esummary | xtract -pattern GenomicInfo -element ChrAccVer,ChrStart,ChrStop 
NC_000017.11    68413622        68551315

[Manuel]

Thanks!! This is not the coordinate of the exons, only the start and end of the transcript, right?