how to get first exon in bed file

[yujin kim]

Dear UCSC Genome Browser team,

Thank you for a great browser.

I have one question.

How can I get the first exon of the gene (e.g., PSMB9) through Table Broswer?'

I want to know their genomic range.

Many thanks,

Yujin Kim

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

If you are unfamiliar with using the Table Browser, you may find the following user guides useful:

Genome Browser training page: https://genome.ucsc.edu/training/
Table Browser user guide: https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

There is also a video tutorial for obtaining coordinates and sequences of gene exons:

https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#codonSeq

You can following these steps to get the coordinates for the first exon in PSMB9 using the NCBI RefSeq track for hg19:

Example Table Browser Steps:

1. Configure the Table Browser

clade: Mammal
organism: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions
track: NCBI RefSeq
table: RefSeq All (ncbiRefSeq)
region: genome
output format: BED - browser extensible data

2. Filter for the gene symbol

Next to the identifiers (names/accessions): setting, click the paste list button, and you will be taken to a new page. on the new page, you can then enter the "PSMB9" gene symbol.

Next, click submit

3. Get output

After creating the filter, you can create a BED file from the results by changing the output format drop-down menu or download the data to a file by adding an output filename.

Once you have configured the output settings, click the get output button. You will be taken to a new page where you can select "Exon plus" to get a BED line for each exon for the transcript. Then, click get BED. Depending on your output choices, you will see the data in your web browser or begin downloading a file.

4. Process the output

You should see the output like the following:

chr6    32821968    32822066    NM_002800.5_exon_0_0_chr6_32821969_f    0    +
chr6    32823914    32823982    NM_002800.5_exon_1_0_chr6_32823915_f    0    +
chr6    32825039    32825171    NM_002800.5_exon_2_0_chr6_32825040_f    0    +
...
chr6_ssto_hap7    4256554    4256684    NM_002800.5_exon_3_0_chr6_ssto_hap7_4256555_f    0    +
chr6_ssto_hap7    4256913    4257055    NM_002800.5_exon_4_0_chr6_ssto_hap7_4256914_f    0    +
chr6_ssto_hap7    4257954    4258398    NM_002800.5_exon_5_0_chr6_ssto_hap7_4257955_f    0    +

For most purposes, you can ignore the haplotype sequences (_hap). In the fourth column, the name field contains the exon number, with the first exon having an item name of "NM_002800.5_exon_0_0_chr6_32821969_f". So the first exon coordinates for the PSMB9 gene is:
"chr6 32821968 32822066"

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.

Jairo Navarro
UCSC Genome Browser

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