[BioMart Users] Problem with Zebrafish Database

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[BioMart Users] Problem with Zebrafish Database

Gulhan Saracaydin


Hello BioMart developers,

I have tried to generate a list of all Danio Rerio miRNA-coding genes that
are located on chromosome 3, between base-pairs 500,000-1,000,000.
However, I think there is a problem in Zebrafish database since I got the
miRNA-coding genes without any selection but when I select the region, I
got nothing. Also, I used miRBase to confirm that there are miRNAs in
Danio Rerio in selected region.

I wonder whether there is a problem with Zebrafish Gene Database in
Ensembl and BioMart. If you give me an answer about this question, I would
be glad.

Hoping to hear from you,

Kind regards,

Gulhan Saracaydin


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Re: [BioMart Users] Problem with Zebrafish Database

Elena Rivkin
Gulhan,
I have tried various queries - and yes, while I get no results from
500,000-1,000,000bp, if I set the filters to for ex. 10,000,000-60,000,000
I get 27 miRNA back. Which means that this is most likely related to the
data and not the filters.
In this case, I would recommend contacting Ensembl help desk, they are
very good at helping with these kinds of questions.

Good luck,
Elena

On 11-03-25 5:06 AM, "Gulhan Saracaydin" <[hidden email]>
wrote:

>
>
>Hello BioMart developers,
>
>I have tried to generate a list of all Danio Rerio miRNA-coding genes that
>are located on chromosome 3, between base-pairs 500,000-1,000,000.
>However, I think there is a problem in Zebrafish database since I got the
>miRNA-coding genes without any selection but when I select the region, I
>got nothing. Also, I used miRBase to confirm that there are miRNAs in
>Danio Rerio in selected region.
>
>I wonder whether there is a problem with Zebrafish Gene Database in
>Ensembl and BioMart. If you give me an answer about this question, I would
>be glad.
>
>Hoping to hear from you,
>
>Kind regards,
>
>Gulhan Saracaydin
>
>
>_______________________________________________
>Users mailing list
>[hidden email]
>https://lists.biomart.org/mailman/listinfo/users

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