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Easy way to compare the co-ordenates between RefSeq transcripts

Working in a clinical lab, we have a list of RefSeq transcripts used to targeted our analysis. My colleagues who carry out the variant interpretation are using a variant interpretation tool that having a variant, ask them to select in which transcripts you are working on. This tools is updating the versions of the transcripts (e.g. we have in our targeted transcripts list this NM_002734.4, however that version is not available in the program and now its show us this NM_002734.5). The program doesn't not allow you to type the transcripts you are working and (not sure) this may affect subsequence analysis.

I have been asked

  • 1 Different transcript versions have different coordinates. I mean, could it be possible to find transcripts with different version and these have exons in different locations for example?? I would say no but I am not sure

  • To check that, is there a easy to check this?

refseq
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written by Manuel • Manuel

1 answer

You can find revision history of GenBank accession numbers using a special URL. For the accession you mention above you can see that information by going to https://www.ncbi.nlm.nih.gov/nuccore/NM_002734?report=girevhist

From there you can select appropriate buttons to see the differences between any two accession revisions: https://www.ncbi.nlm.nih.gov/sviewer/girevhist-diff/girevhist-diff.cgi?tool=portal&db=nuccore&frst=1779521771_4_432481692_Jun%209,%202022%2002:44%20AM_5_1&scnd=443497962_47_133370799_Sep%2025,%202019%2001:48%20AM_4_1&history_fmt=gb

BTW these two versions are rather different

Accession   Gi  Update Date
NM_002734.5 1779521771  Jun 9, 2022 02:44 AM
NM_002734.4 443497962   Sep 25, 2019 01:48 AM

LOCUS       NM_002734               4253 bp    mRNA    linear   PRI 09-JUN-2022
LOCUS       NM_002734               4325 bp    mRNA    linear   PRI 25-SEP-2019
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written by GenoMax GenoMax

Many thanks!

Any way to do this in a more automatic way. I have 70 transcripts to check

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written by Manuel • Manuel

Use EntrezDirect and compare results:

$ esearch -db nuccore -query NM_002734.5 | efetch -format ft | grep -w -e exon -e gene
1       4253    gene
                        gene    PRKAR1A
1       119     exon
120     302     exon
303     473     exon
474     565     exon
566     627     exon
628     674     exon
675     833     exon
834     894     exon
895     1016    exon
1017    1098    exon
1099    4253    exon

$ esearch -db nuccore -query NM_002734.4 | efetch -format ft | grep -w -e exon -e gene

1       4325    gene
                        gene    PRKAR1A
1       170     exon
171     353     exon
354     524     exon
525     616     exon
617     678     exon
679     725     exon
726     884     exon
885     945     exon
946     1067    exon
1068    1149    exon
1150    4304    exon
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written by GenoMax GenoMax

Many thanks for your answer. Do you know how can I take the genomic coordinates?

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written by Manuel • Manuel

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