LncRNA Seq. Query!
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Sikandar Azam
May 14, 2015, 10:35:37 AM5/14/15
to gen...@soe.ucsc.edu
Respected Sir/ Mam,
Warm Regards,I am searching lncRNA discovered by a recently published paper (The landscape of long noncoding RNAs in the human transcriptome) (Nat Genet. 2015 Mar;47(3):199-208. doi: 10.1038/ng.3192). They developed a transcriptome assembly (http://mitranscriptome.org) (UCSC Genome Browser on Human Feb. 2009 (GRCh37/hg19) Assembly) for lncRNAs. I am trying to find the post-transcriptionaly modified lncRNA sequence, but i could'nt. Although the transcript size and transcript genomic sequence is given. Would you like to help me please! I will be very gratful to you.
Sikandar Azam (PhD Scholar)
Institute of Cancer Stem Cell (ICSC)
Dalian Medical University, China
E-mail: saza...@gmail.com
Tel: 0086 13130029411
Matthew Speir
May 14, 2015, 2:53:11 PM5/14/15
to Sikandar Azam, gen...@soe.ucsc.edu
Hi Sikandar,
Thank you for your question about getting the post-transcriptional sequence for these lncRNAs. I'm assuming what you mean by "post-transcriptional sequence" is the sequence of the gene without any intronic sequence. If so, you can use the following steps to get the sequence for the items you are interested in from the Table Browser:
1. Navigate to the Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables.
2. Make the following selections:
clade: Mammal
genome: Human
assembly: hg19
group: Custom Tracks
track: MiTranscriptome
table: ct_MiTranscriptome_
region: genome, or if you know the positions, you can click "define regions"
output format: sequence
output file: enter a file name to save your results to a file, or leave blank to display results in your browser
3. Click "get output".
4. Under the "Sequence Retrieval Region Options" section, unck the box next to "Introns".
5. Choose any other sequence formatting options.
6. Click "get sequence".
Please note that these steps assumed that you have loaded the " MiTranscriptome" custom track by navigating to http://mitranscriptome.org/ and clicking on the link to the position of at least one of the lncRNAs. If you want more information on using the Table Browser, please refer to our help documentation: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
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
Thank you for your question about getting the post-transcriptional sequence for these lncRNAs. I'm assuming what you mean by "post-transcriptional sequence" is the sequence of the gene without any intronic sequence. If so, you can use the following steps to get the sequence for the items you are interested in from the Table Browser:
1. Navigate to the Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables.
2. Make the following selections:
clade: Mammal
genome: Human
assembly: hg19
group: Custom Tracks
track: MiTranscriptome
table: ct_MiTranscriptome_
region: genome, or if you know the positions, you can click "define regions"
output format: sequence
output file: enter a file name to save your results to a file, or leave blank to display results in your browser
3. Click "get output".
4. Under the "Sequence Retrieval Region Options" section, unck the box next to "Introns".
5. Choose any other sequence formatting options.
6. Click "get sequence".
Please note that these steps assumed that you have loaded the " MiTranscriptome" custom track by navigating to http://mitranscriptome.org/ and clicking on the link to the position of at least one of the lncRNAs. If you want more information on using the Table Browser, please refer to our help documentation: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
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
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Matthew Speir
May 15, 2015, 2:22:16 PM5/15/15
to Sikandar Azam, gen...@soe.ucsc.edu
Hi Sikandar,
Please note that the instructions I provided yesterday will only give you the sequence of a particular item without the intronic sequence. They will not include any other post-transcriptional modifications, like poly-A tails. If you would like the true post-transcriptionally modified sequence of the lncRNAs you are interested in, I would contact the authors of the MiTranscriptome site: https://groups.google.com/forum/#!forum/mitranscriptome.
Please note that the instructions I provided yesterday will only give you the sequence of a particular item without the intronic sequence. They will not include any other post-transcriptional modifications, like poly-A tails. If you would like the true post-transcriptionally modified sequence of the lncRNAs you are interested in, I would contact the authors of the MiTranscriptome site: https://groups.google.com/forum/#!forum/mitranscriptome.
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
On 5/14/15 5:07 AM, 'Sikandar Azam' via
UCSC Genome Browser discussion list wrote:
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