Transcript location?

[neofit]

Hello,
Sorry for the newbie question but I fail to understand how to locate on the reference genome the transcripts of a gene found e.g. in NCBI Genbank.

Here for instance the description of a transcript for IDH2:

http://www.ncbi.nlm.nih.gov/nuccore/588282795?report=genbank&to=1818

The IDH2 gene is 25499 bases long on chr15. The transcript is 1818 bases long. So how/where do I find the location(s) of this transcript in the gene?

Thanks a lot for your help.

[GenoMax]

You can go to the "gene" record for this transcript which can be found in "related information" --> "gene" section (right column). http://www.ncbi.nlm.nih.gov/gene?Lin..._uid=588282795

From there you can select to see the "Genbank" format entry where you will find the location of the transcript in the gene (excerpted below from Genbank record).

gene               2775..21273
                     /gene="IDH2"
                     /gene_synonym="D2HGA2; ICD-M; IDH; IDHM; IDP; IDPM;
                     mNADP-IDH"
                     /note="isocitrate dehydrogenase 2 (NADP+), mitochondrial;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefSeq."
                     /db_xref="GeneID:3418"
                     /db_xref="HGNC:5383"
                     /db_xref="HPRD:00973"
                     /db_xref="MIM:147650"
     mRNA            join(2775..2975,13607..13698,14607..14772,16504..16664,
                     16749..16892,17676..17812,17988..18139,19864..19976,
                     20153..20250,20343..20435,20898..21273)
                     /gene="IDH2"
                     /gene_synonym="D2HGA2; ICD-M; IDH; IDHM; IDP; IDPM;
                     mNADP-IDH"
                     /product="isocitrate dehydrogenase 2 (NADP+),
                     mitochondrial"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefSeq."
                     /transcript_id="NM_002168.2"
                     /db_xref="GI:28178831"
                     /db_xref="GeneID:3418"
                     /db_xref="HGNC:5383"
                     /db_xref="HPRD:00973"
                     /db_xref="MIM:147650"
     CDS             join(2861..2975,13607..13698,14607..14772,16504..16664,
                     16749..16892,17676..17812,17988..18139,19864..19976,
                     20153..20250,20343..20435,20898..20985)
                     /gene="IDH2"

To see the gene in genomic context, use the linkout to UCSC (found under "link to other resources" in gene record): http://genome.ucsc.edu/cgi-bin/hgTra...27211-90645786 or Ensembl: http://www.ensembl.org/Homo_sapiens/...26277-90645736

[neofit]

Hi GenoMax, thanks a lot for your reply. A few questions though:

You can go to the "gene" record for this transcript which can be found in "related information" --> "gene" section (right column). http://www.ncbi.nlm.nih.gov/gene?Lin..._uid=588282795

From there you can select to see the "Genbank" format entry where you will find the location of the transcript in the gene (excerpted below from Genbank record).

Where is the link to GenBank? When I click on the link under the section "Genomic regions, transcripts, and products" it doesn't show the same genomic region for the gene as the one you pasted.

gene               2775..21273
                     /gene="IDH2"
                     /gene_synonym="D2HGA2; ICD-M; IDH; IDHM; IDP; IDPM;
                     mNADP-IDH"
                     /note="isocitrate dehydrogenase 2 (NADP+), mitochondrial;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefSeq."
                     /db_xref="GeneID:3418"
                     /db_xref="HGNC:5383"
                     /db_xref="HPRD:00973"
                     /db_xref="MIM:147650"
     mRNA            join(2775..2975,13607..13698,14607..14772,16504..16664,
                     16749..16892,17676..17812,17988..18139,19864..19976,
                     20153..20250,20343..20435,20898..21273)
                     /gene="IDH2"
                     /gene_synonym="D2HGA2; ICD-M; IDH; IDHM; IDP; IDPM;
                     mNADP-IDH"
                     /product="isocitrate dehydrogenase 2 (NADP+),
                     mitochondrial"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefSeq."
                     /transcript_id="NM_002168.2"
                     /db_xref="GI:28178831"
                     /db_xref="GeneID:3418"
                     /db_xref="HGNC:5383"
                     /db_xref="HPRD:00973"
                     /db_xref="MIM:147650"
     CDS             join(2861..2975,13607..13698,14607..14772,16504..16664,
                     16749..16892,17676..17812,17988..18139,19864..19976,
                     20153..20250,20343..20435,20898..20985)
                     /gene="IDH2"

Ok, so the length of the gene is here 21273-2775+1=18499 bp. The position of the gene (2775..21273) and transcripts is relative to the region NG_023302, right? I am looking now for the mapping to an absolute position of the form chr15:N1-N2.

To see the gene in genomic context, use the linkout to UCSC (found under "link to other resources" in gene record): http://genome.ucsc.edu/cgi-bin/hgTra...27211-90645786

Cool, but I see a region which is 90645786-90627211+1=18576 bp long.

or Ensembl: http://www.ensembl.org/Homo_sapiens/...26277-90645736

Here the region is 90645736-90626277+1=19460 bp long.

So how do I know exactly where does the (2775..21273) map? Can't I get immediately the absolute position chr15:N1-N2 with the correct length?

[GenoMax]

Where is the link to GenBank? When I click on the link under the section "Genomic regions, transcripts, and products" it doesn't show the same genomic region for the gene as the one you pasted.

You need a couple of steps to get to the GenBank entry.

You will have to scroll down the page a ways to get to the sections I am attaching screenshots for both steps. Click on the highlighted links.

[GenoMax]

Ok, so the length of the gene is here 21273-2775+1=18499 bp. The position of the gene (2775..21273) and transcripts is relative to the region NG_023302, right? I am looking now for the mapping to an absolute position of the form chr15:N1-N2.

Based on the gene record the location of this gene for GRCh38 assembly is Chromosome15 - NC_000015.10 (90083978..90102476, complement)

That said there is a warning about the RefSeqGene records in the attached image.

The latest RefSeqGene record version is NG_023302.1 (note the .1) where as the one in the genome build is NG_023302.

[neofit]

Thanks, this is much clearer now. What is still don't get though is why the following sequence :
ggcatgaggtagtaattggagtctccagtaagggtttgtttttccccagg....
http://genome.ucsc.edu/cgi-bin/das/h...3389,208257979

does not correspond to the one shown under "FASTA" in ncbi (see screenshot below), although the locations seem to be the same.

I guess is has something to do with complement/reverse strand (?) but I don't manage to find how to convert one sequence to the other. Any hint?

[GenoMax]

Thanks, this is much clearer now. What is still don't get though is why the following sequence :
ggcatgaggtagtaattggagtctccagtaagggtttgtttttccccagg....
http://genome.ucsc.edu/cgi-bin/das/h...3389,208257979

does not correspond to the one shown under "FASTA" in ncbi (see screenshot below), although the locations seem to be the same.

I guess is has something to do with complement/reverse strand (?) but I don't manage to find how to convert one sequence to the other. Any hint?

Are you sure this is the same genome build at UCSC and NCBI?

If I take the sequence (I randomly selected a few hundred bases from the start) from UCSC record link you included it seems to be hitting the following location in GRCh38 at NCBI using blast:

Range 1: 207368665 to 207371264GenBankGraphics Next Match Previous Match
Alignment statistics for match #1 Score	Expect	Identities	Gaps	Strand
4802 bits(2600) 	0.0 	2600/2600(100%) 	0/2600(0%) 	Plus/Plus

Query  1          GGCATGAGGTAGTAATTGGAGTCTCCAGTAAGGGTTTGTTTttccccagggctgttataa  60
                  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  207368665  GGCATGAGGTAGTAATTGGAGTCTCCAGTAAGGGTTTGTTTTTCCCCAGGGCTGTTATAA  207368724

Query  61         ccaattatctcaaatttggtggcttaaaataacagaaatgtattctcttgcagttctgga  120
                  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  207368725  CCAATTATCTCAAATTTGGTGGCTTAAAATAACAGAAATGTATTCTCTTGCAGTTCTGGA  207368784

Query  121        tattgtggaggaaaagtctgaaatcaaggtgttggcgtggccacactttctccaaaagtt  180
                  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  207368785  TATTGTGGAGGAAAAGTCTGAAATCAAGGTGTTGGCGTGGCCACACTTTCTCCAAAAGTT  207368844

Query  181        ccaggggaatattcttccttcactcttttggcttctagtggctccagctgcttcttggct  240
                  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  207368845  CCAGGGGAATATTCTTCCTTCACTCTTTTGGCTTCTAGTGGCTCCAGCTGCTTCTTGGCT  207368904

Query  241        tatggcagcctgactccaatgtctgcctctgtcttcacgtggccttctcgcagtgtagct  300
                  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  207368905  TATGGCAGCCTGACTCCAATGTCTGCCTCTGTCTTCACGTGGCCTTCTCGCAGTGTAGCT  207368964

Query  301        ctgtgtctcaaatctctttctcttttctcttataagaacaccagtcattggattaaggat  360
                  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  207368965  CTGTGTCTCAAATCTCTTTCTCTTTTCTCTTATAAGAACACCAGTCATTGGATTAAGGAT  207369024

Query  361        ctgccctaaatccacgatgacctcatcttgaaatcattaacttaattacatctattaaga  420
                  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  207369025  CTGCCCTAAATCCACGATGACCTCATCTTGAAATCATTAACTTAATTACATCTATTAAGA  207369084

Query  421        ccctctttccaaataagatcacattcacaggtaccagaggttaggacttagatgtatttt  480
                  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  207369085  CCCTCTTTCCAAATAAGATCACATTCACAGGTACCAGAGGTTAGGACTTAGATGTATTTT  207369144

But a blat search against the GRCh37 at UCSC seems to point to the location marked in your screenshot even though the FASTA header says GRCh38 assembly in that screenshot.

   ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
---------------------------------------------------------------------------------------------------
browser details YourSeq         2500     1  2500  2500 100.0%     2   +  208233389 208235888   2500
browser details YourSeq          148    70   511  2500  79.1%    20   -   38193407  38193817    411

A blat search against the GRCh38 at UCSC matches the blast results at NCBI.

   ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
---------------------------------------------------------------------------------------------------
browser details YourSeq         2500     1  2500  2500 100.0%     2   +  207368665 207371164   2500
browser details YourSeq          139   111   507  2500  74.8%    12   +    6320367   6320758    392

Something is odd here.