Luvina,
Thank you for your help.
Could you please help me to know why NR_000137 and NR_000138 are on
the same region? I attach two related records again. As you can see,
these two records are same except names.
#bin name chrom strand txStart txEnd cdsStart cdsEnd
exonCount exonStarts exonEnds score name2 cdsStartStat
cdsEndStat exonFrames
677 NR_000137 chrI + 12144973 12145160
12145160 12145160 1 12144973, 12145160, 0
unk unk -1,
677 NR_000138 chrI + 12144973 12145160
12145160 12145160 1 12144973, 12145160, 0
unk unk -1,
In human genome (Hg18), I can find the description I need. It is field
"type" on track "RNA Genes". For example, "snRNA" tells me the gene is
a snRNA gene. But I can't find a similar field in the genome of
C.elegans. Could you please give me some hints?
Again, thank you very much for your help.
Yingfeng
On Fri, Mar 16, 2012 at 6:31 PM, Luvina Guruvadoo <[email protected]> wrote:
> Hi Yingfeng,
>
> If you BLAT the sequence from NR_000137, you will find that this region is
> an inverted repeat. Details for each nnRNA can be retrieved using the Table
> Browser. Click on "Tables" on the blue bar on the top of the main page and
> make the following selections:
>
> clade: Mammal
> genome: Human
> assembly: hg19
> group: Genes and Gene Prediction Tracks
> track: RefSeqGenes
> table: refGene
> region: genome
> filter: click 'create' then in the 'name DOES match' field type: NR_*
> output format: select fields from primary and related tables output file: if
> you would rather have the results saved to a file instead of displaying in
> the browser window, enter the name you would like the output file to have,
> otherwise, leave blank
> file type returned: plain text
>
> Click "get output". From here, select the appropriate fields then click "get
> output".
>
> I hope this helps. Feel free to contact us again at [email protected] if
> you have further questions.
>
> ---
> Luvina Guruvadoo
> UCSC Genome Bioinformatics Group
>
>
> On 3/15/2012 9:10 AM, Yingfeng Wang wrote:
>>
>> Hello,
>>
>> I meet a problem in genome browser when I use RefSeq Genes track.
>>
>> Here are the first three ncRNA genes I got in a Celegans segment (
>> WS220/ce10, chrI:12140001-12340000 ),
>>
>> #filter: refGene.name like 'NR\_%'
>> #bin name chrom strand txStart txEnd cdsStart cdsEnd
>> exonCount exonStarts exonEnds score name2
>> cdsStartStat cdsEndStat exonFrames
>> 677 NR_000137 chrI + 12144973 12145160
>> 12145160 12145160 1 12144973, 12145160,
>> 0 unk unk -1,
>> 677 NR_000138 chrI + 12144973 12145160
>> 12145160 12145160 1 12144973, 12145160,
>> 0 unk unk -1,
>> 677 NR_000137 chrI - 12149569 12149756
>> 12149756 12149756 1 12149569, 12149756,
>> 0 unk unk -1,
>>
>>
>> All three have the same bin; the 1st and 2nd genes are on the same
>> region with different names; the 1st and 3rd genes have the same name
>> but on the different regions.
>>
>> Could you please explain a little about it?
>>
>> By the way, could you please let me know how to retrieve the
>> description of each ncRNA gene on this track, e.g., the type of a
>> ncRNA gene?
>>
>> Thank you very much!
>>
>> Yingfeng
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
>
_______________________________________________
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https://lists.soe.ucsc.edu/mailman/listinfo/genome
