Genomic features for several mRNA types in UCSC Browser

[Gundala Viswanath]

I'm interested in obtaining the coordinate of the following
genomic features (mRNA types):

1. Mature miRNA *
2.precursor miRNA
3. piRNA
4. lincRNA *
5. human Ribosomal RNA
6. snoRNA *
7. human5S rDNA
8. snRNA

I know that by default UCSC browser provide no.1,4,6 (*) above.
Is there a way I can obtain the annotation for other types?

Best,
G.V.

[Matthew Speir]

Hi Gundala,

Thank you for your question about obtaining the coordinates for
various RNA types. We do have coordinates for all of the RNA types
that you listed, but unfortunately, they are scattered throughout a
few different Gene Prediction tracks. This information can be
retrieved using the Table Browser
(http://genome.ucsc.edu/cgi-bin/hgTables). For more information on
using the Table Browser, please refer to our help documentation here:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.

The GENCODE v19 track,
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV19,
contains genomic coordinates for human ribosomal RNA, snRNA, and 5S
ribosomal RNA. You can use the following steps to access this
information, and get the output in BED format:

1. Navigate to the table browser, http://genome.ucsc.edu/cgi-bin/hgTables.

2. Select your assembly and tracks

clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions Tracks
track: GENCODE Genes V19
table: Basic (wgEncodeGencodeBasicV19)
output: BED - browser extensible data
output file: enter a file name to save your results to a file, or
leave blank to display results in your browser

3. Click 'Filter'.

4. Select the wgEncodeGencodeAttrsV19 from the 'Linked Tables' section

5. Click 'allow filtering using fields in checked tables'.

6. This step will change depending on whether you want the coordinates
for the rRNA or snRNA genes.
6.1 For rRNA, type 'rRNA' in the 'geneType' and 'transciptType'
fields of the hg19.wgEncodeGencodeAttrsV19 based filters section.
The "geneType" line should read: geneType does match rRNA
The "transcriptType" line should read: transcriptType does match rRNA
6.2 For snRNA, type 'snRNA' in the 'geneType' and 'transciptType'
fields of the hg19.wgEncodeGencodeAttrsV19 based filters section.
The "geneType" line should read: geneType does match snRNA
The "transcriptType" line should read: transcriptType does match snRNA

7. Click 'Submit'.

8. After you return to the main Table Browser page, click 'get output'.

Many of the 5S rRNA positions in this table are pseudogenes, and you
may need to try different filtering parameters to exclude these from
the output.

The coordinates for piRNA are contained in the UCSC Genes track,
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene. You can
get this information from the Table Browser using steps similar to
those I previously described:

1. Select your assembly and tracks

clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions Tracks
track: UCSC Genes
table: knownGene
output: BED - browser extensible data
output file: enter a file name to save your results to a file, or
leave blank to display results in the browser

2. Click 'Filter'.

3. Type '*piRNA*' in the 'description' field of the hg19.kgXref based
filters section.
The "description" line should read: description does match *piRNA*

4. Click 'Submit'.

5. After you return to the main Table Browser page, click 'get output'.

Lastly, precursor miRNA coordinates can be found in the sno/miRNA
track, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgRna.
Again, you can get this information using the Table Browser and steps
similar to those I previously described:

1. Select your assembly and tracks

clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions Tracks
track: sno/miRNA
table: wgRna
output: BED - browser extensible data
output file: enter a file name to save your results to a file, or
leave blank to display results in the browser

2. Click 'Filter'.

3. Enter 'miRNA' into the type field.
The "type" line should read: type does match *miRNA*

4. Click 'Submit'.

5. After you return to the main Table Browser page, click 'get output'.

I hope this is helpful. If you have any further questions, please
reply to gen...@soe.ucsc.edu. All messages sent to that address are
archived on a publicly-accessible Google Groups forum. If your
question includes sensitive data, you may send it instead to
genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

> --
>

[Gundala Viswanath]

Dear Matt,

Thanks so much for the comprehensive reply.
I really appreciate that.

> Lastly, precursor miRNA coordinates can be found in the sno/miRNA
> track, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgRna.

But for the point above, I always thought that wgRNA is for "mature miRNA".
If what you suggest above for "precursor miRNA", how can I find mature miRNA?

Thanks and hope to hear from you again.

Best,
G.V.

[Luvina Guruvadoo]

Hi Gundala,

Unfortunately, we do not have any tracks of mature miRNAs. Please see
this previously answered question for details:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/RP6FYeeFm48/F8-RO431lkgJ

If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible

forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.

- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group