Hello Christophe,
Perhaps the assembly versions between the text download file and the browser
display are being mixed up? An initial guess is that the file is based on
GRCh37 (hg19) and the browser used for comparison based on hg18.
In the Human GRCh37 Assembly (hg19) browser, after entering uc001bcu.2 into the
position/search query box, the transcript uc001bcu.2 is returned as part of the
UCSC Gene's track.
Using just gene symbol name "PLA2G2A" in either the Human GRCh37 Assembly
(hg19) or Human Mar. 2006 (hg18) Assembly brings up the gene location, but the
number of variants is different (this agrees with the information at NCBI - see
analysis below).
Results of a PLA2G2A search in hg19:
UCSC Genes
PLA2G2A (uc010odb.1) at chr1:20301925-20306932 - phospholipase A2, group IIA
precursor
PLA2G2A (uc010oda.1) at chr1:20301925-20306932 - phospholipase A2, group IIA
precursor
PLA2G2A (uc001bcv.2) at chr1:20301925-20306932 - phospholipase A2, group IIA
precursor
PLA2G2A (uc001bcu.2) at chr1:20301925-20306152 - phospholipase A2, group IIA
precursor
PLA2R1 (uc002ubf.2) at chr2:160802327-160919121 - phospholipase A2 receptor 1
isoform 2 precursor
PLA2R1 (uc010zcp.1) at chr2:160798012-160919121 - phospholipase A2 receptor 1
isoform 2 precursor
PLA2R1 (uc002ube.1) at chr2:160798012-160919121 - phospholipase A2 receptor 1
isoform 1 precursor
[..... more in other tracks ......]
Results of a PLA2G2A search in hg18:
UCSC Genes
PLA2G2A (uc001bcv.1) at chr1:20174518-20179496 - phospholipase A2, group IIA
PLA2G2A (uc001bcu.1) at chr1:20174518-20178770 - phospholipase A2, group IIA
PLA2R1 (uc002ube.1) at chr2:160506258-160627367 - phospholipase A2 receptor 1
isoform 1 precursor
[..... more in other tracks ......]
Using the "Convert" tool in hg19 (top blue navigation bar) when the genome is
positioned to cover the transcript uc001bcu.2's genomic position gives the
following results (but this is not the complete explanation for the differences
between the two assemblies, as new transcript variants are involved).
Human GRCh37 chr1:20301925-20306152 to Human Mar. 2006
chr1:20174512-20178739 (100.0% of bases, 100.0% of span)
Using the mRna sequence for uc001bcu.2 from hg19, a BLAT versus
hg18 places it at this location:
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START
END SPAN
---------------------------------------------------------------------------------------------------
browser details uc001bcu.2 919 1 923 940 100.0% 1 -
20174511 20178739 4229
Clicking on "browser" link from these results reveals that same location that
the position/search results give when the gene symbol PLA2G2A is used
(chr1:20174511-20178739), with some slight differences in the intron/exon
structure from the existing transcripts for the gene (CDS is not annotated, as
the query was just a transcript with no specified coding region - this is as
expected for a web-based BLAT).
The RefSeq sequence that this transcript is based on, NM_001161729, was
published at NCBI on 20-DEC-2009. This date is after the UCSC Gene track's
build for hg18, but before the build for hg19. Reading the Genbank data sheet
(specifically the Summary contained in the field "COMMENT")
http://www.ncbi.nlm.nih.gov/nuccore/239915990?report=genbank
provides the data I used to determine that the transcript is new and gives
details about what features exactly were considered when constructing the new
variant for the gene (named there as "variant 4". Overall, it appears that two
new transcript variants have been recently added to RefSeq for this gene
PLA2G2A (and the gene PLA2R1). This correlates with the representation of the
gene's variants in the browser when comparing the UCSC Gene track's results
from hg18 to hg19.
We hope this helps to clarify the data, but if your question has been
misinterpreted or you would like to follow up concerning any of this
information, please reply and we would he happy to offer more assistance,
Have a nice weekend,
Jennifer
------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group
----- "hfth fhfghfgh" <[email protected]> wrote:
> From: "hfth fhfghfgh" <[email protected]>
> To: [email protected]
> Cc: [email protected]
> Sent: Sunday, January 17, 2010 6:02:00 AM GMT -08:00 US/Canada Pacific
> Subject: [Genome] Gene present in knowngene.txt dump but NOT SHOWN im
> browser: why ?
>
> Hello,
>
> in the last knowngene.txt, there is the following entry:
> uc001bcu.2 chr1 - 20301924 20306152 20302193
> 20305266 5 20301924,20304507,20304872,20305226,20306072,
> 20302336,20304614,20305017,20305404,20306152, A8K5I7 uc001bcu.2
>
>
> Why is this gene (PLA2G2A) not shown in the genome browser (It is
> shown in the NCBI browser) ?
>
> thank you very much,
>
> Christophe Andreoli
>
>
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