different positions for a gene

Question

[hamarillo]

Hello, I really don't understand why the same gene has a different number of transcripts, but moreover, a different start position. In this case for example

 entrezgene hgnc_symbol ensembl_gene_id chromosome_name
   2934             ENSG00000283430               9
   2934             ENSG00000283299               9
   2934         GSN ENSG00000148180               9

 start_position end_position strand   gene_biotype
  121300103    121332603      1 protein_coding
  121282452    121332603      1 protein_coding
  121207794    121332843      1 protein_coding

 percentage_gc_content transcript_count
             49.64                1
             50.09                1
             46.87               15

I downloaded all the HUMAN genes with an entrezgene ID using biomaRt, but now I am confused as to why this happes; I've got another couple of examples (but not than many) of multiple start positions for the same gene ID :(

thanks!

Answer 1

[WouterDeCoster]

Just like alternative splicing produces different exons in a gene (and gives rise to multiple isoforms), also alternative start codons exist resulting in multiple start positions for the same gene. And that's normal. You have the same at the other side of the gene with alternative stop codons, alternative poly adenylation signals and alternative UTRs...

The concept of gene is a bit an annoying definition, since it's usually defined as the function unit of a piece of DNA having a certain function or a certain set of functions. However, it turns out that isoforms and different transcripts can have very different functions compared to each other, even completely the opposite. A famous example is the human gene Bcl-x which can be spliced in a short and long isoform. The longer is anti-apoptotic, the shorter promotes apoptosis http://www.ncbi.nlm.nih.gov/pubmed/8358789.

This also reminds me of the following paper: http://www.ncbi.nlm.nih.gov/pubmed/26871637 The authors show that the interactome (set of proteins which interact with a certain protein) is strongly dependent on alternative splicing, so and alternative transcript may have very different interaction partners and as such functions.

[hamarillo]

Right, actually if I download the transcription start site and transcript biotype it becomes evident. Thank you! I really liked the part of "The concept of gene is a bit an annoying definition", it was helpful to remember so.

Answer 2

[natasha.sernova]

See this post:

A: Why a single gene can have multiple locations in chromosome?

There are many isoforms in a human gene you study. There can be alternative splicing, etc.

See also this post:

How To Download The Entire Human Gene List With Their Chromosomal Location