[Genome] ABL2 inconsistency

[Rachel Harte]

Dear Mathias,

I have taken a look at this problem. When I try your mySQL command for
hg18 I get the following results:
name      | chrom | strand | txStart   | cdsStart  | cdsEnd    |
exonStarts  | exonEnds
 NM_005158 | chr1  | -      | 177343379 | 177343475 | 177378802 |
177343379,177346039,177348066,177350635,177353089,177354344,177355947,177357352,177362134,177367068,177378690,
|
177345199,177346213,177348156,177350788,177353274,177354522,177356032,177357625,177362430,177367239,177378808,
|

The position that you see on the Known Genes details page for ABL2 is
consistent with this result. txStart is 177343379 and txEnd is 177378808.
The starts in the table are 0-based so base 1 is represented by 0
therefore the txStart is really 177343380 which gives a position of
chr1:177343380-177378808 for ABL2 (NM_005158). This is consistent with the
position given on the Known Genes details page for the ABL2 transcript for
hg18 (March 2006 assembly).

If I then do the same mySQL query for hg17 known Genes, then I get the
following result:

name      | chrom | strand | txStart   | cdsStart  | cdsEnd    |
exonStarts
| exonEnds
|
+-----------+-------+--------+-----------+-----------+-----------+----------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| NM_005158 | chr1  | -      | 175808413 | 175808509 | 175843836 |
175808413,175811073,175813100,175815669,175818123,175819378,175820981,175822386,175827168,175832102,175843724,
|
175810233,175811247,175813190,175815822,175818308,175819556,175821066,175822659,175827464,175832273,175843842,
|

This looks to be the same as the result from your mySQL query. Please
check again for hg18 and let us know if you still find that there is an
inconsistency. Please let us know if you have further questions.

Rachel

 Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Thu, 28 Dec 2006, Mathias Ehrich wrote:

> Dear Genome Browser Team,
>
> I am trying to retrieve the transcription start sites for a number of
> genes. I have managed to implement the database query using MySQL.
> Everything appeared to be working fine, but when I started checking the
> results I found a small inconsistency between the website results and
> the results obtained by the SQL query. The location of the ABL2 gene
> (NM_005158) differs by approximately 2M bp. I'm not sure that I used the
> correct versions, but I used 'hg18' for the SQL query and the assembly
> 'March 2006' for the website. I have attached both results for your
> review.
>
> Do you know where this inconsistency is might come from.
>
> Thanks for your help.
>
>
>
> Best regards
>
> Mathias Ehrich
>
>
>
> Results from MySQL Query
>
> Schema: hg18
>
> Query:
>
> SELECT k.name, k.chrom, k.strand, k.txStart ,k.cdsStart, k.cdsEnd,
> k.exonStarts, k.exonEnds
>
> FROM knownGene k
>
> WHERE k.chrom =  'chr1' AND k.strand = '-' AND k.name = 'NM_005158'
>
>
>
> Results:
>
> Name, chrom, strand, txStart, cdsStart, cdsEnd
>
> 'NM_005158', 'chr1', '-', 175808413, 175808509, 175843836, '', ''
>
>
>
>
>
> Results from GenomeBrowser Website
>
> Assembly: March 2006
>
>
>
> Description: v-abl Abelson murine leukemia viral oncogene
> Alternate Gene Symbols: RP11-177A2.3-002
> Representative Refseq: NM_005158
> <http://genome.ucsc.edu/cgi-bin/hgc?hgsid=83437299&g=refGene&i=NM_005158
> &c=chr1&o=177343379&l=177343379&r=177378808&db=hg18>     Protein: Q5W0C5
> <http://www.expasy.org/cgi-bin/niceprot.pl?Q5W0C5>
> RefSeq Summary: ABL2 is a cytoplasmic tyrosine kinase which is closely
> related to but distinct from ABL1. The similarity of the proteins
> includes the tyrosine kinase domains and extends amino-terminal to
> include the SH2 and SH3 domains. ABL2 is expressed in both normal and
> tumor cells. The ABL2 gene product is expressed as two variants bearing
> different amino termini, both approximately 12-kb in length.
> Position: chr1:177343380-177378808
> Strand: -
> Genomic Size: 35429
> Exon Count: 11
>
> _______________________________________________
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>