Why there are some genes have a same transcription start position?
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7.1 years ago
yinzl2007 ▴ 20

hello biostarters, I downloaded a file from uscs about the genes and gene predictions, the select condition is shown in the first picture.

Every line in the output file represente a gene, however, I found that there are more than one gene have the same txStart(Transcription start position), as shown in the second picture.

Why there are some genes have a same transcription start position? What is the relationship among those genes?

gene transcription start position • 1.8k views
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I can't see any pictures attached with your question, but my guess is they are all different transcripts of the same gene, which you thought were different genes because they have different UCSC IDs. If you also download the corresponding official gene symbol, you will see that they all belong to the same gene.

Of course, this is all my guess and I could be totally wrong. We can answer better once you post the pictures.

Cheers

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where is the second picture? different genes have same txStart on the same strand?

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The line of this file is not a gene exactly, every line represent a transcript of a geneSymbol. You can link the table knownGene and the mm10.kgXref.kgID (via knownGene.name), and you can see the genesymbol in table kgXref.

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7.1 years ago
Can they be different isoforms of the same gene (alternative splicing)?
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7.1 years ago
Chirag Nepal ★ 2.3k

They might be different isoforms of the same gene. If you zoom out and have a look at the intron/exon region, downstream splicing might be different.

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