Exon locations missing

[Munazah Andrabi]

Dear Browser Staff,

I'm facing a problem retrieving the exon locations using table browser feature.

I'm trying to collect all the exon and intron locations for all transcripts of hg19 in gencode database. The problem that I'm facing is that
for some transcripts there were no entries for exon locations but the intron locations could be retrieved for the same transcript, although there is proper annotation for its exons.

For e.g. for the gene A2ML1 the transcript ENST00000536789.1 has 3 exons but when I try to retrieve the exon locations using the
steps listed below there is no exon information for this transcript but the intron locations could be retrieved.

I use the following steps to retrieve exon locations:

Make a bedfile for exons only:
I) Choose the Parameters:
clade: Mammal; genome:Human; assembly:hg19
group: Genes and Gene Predictions; track:GENCODE Genes V19;
table: Comprehensive(wgEncodeGencodeCompV19)
output format: BED - browser extensible data
Press get output

II) Select Fields:
Exons plus: 0 bases at each end
Press getBED >"exons_gencode_comprehensive_hg19.bed"



Could you lease look into this matter and let me know whether there I'm missing something here.

Many thanks & best regards,
Munazah

-----------------------------------------------------------------------
Munazah Andrabi
Post Doctoral Research Associate
Sharrocks and Bobola Labs
Faculty of Life Sciences
Michael Smith Building (Level 2)
The University of Manchester
Manchester M13 9PT

[Cath Tyner]

Hello Munazah,

Thank you for contacting the UCSC Genome Browser support team and inquiring about your hg19 Table Browser query. I replicated your steps according to the settings that you provided (thank you for those details), with the exception that I added "ENST00000536789.1" as an identifier. I received the following output from the Table Browser:

chr12    8997549    8997902    ENST00000536789.1_exon_0_0_chr12_8997550_f    0    +
chr12    8998037    8998098    ENST00000536789.1_exon_1_0_chr12_8998038_f    0    +
chr12    8998672    8998720    ENST00000536789.1_exon_2_0_chr12_8998673_f    0    +

I then added th

​at output as a​

bed file

​to a​

 custom track in hg19. As you can see in this session, the bed regions do indeed intersect exons only for transcript ENST00000536789.1.

​It's possible that you have a different configuration that what I used, causing the issue. ​

Can you try to reset to defaults by going to the top blue horizontal menu:

Genome Browser > Reset All User Settings

Once you reset, can you try the query again? You can click the "paste list" button for "identifiers (names/accessions)" and add the example transcript, ENST00000536789.1. If you still do not get the same results that I did, would you mind sending me a session so that I can see all of your settings?

Thank you for contacting the UCSC Genome Browser support team. 

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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