Why a gene in UCSC has different positions?

Question

[Zahra]

Hi all,

I've used the UCSC to get the position of my interest gene in BED format. When I selected my interest gene, I received a BED file with different positions for just one gene and I don't know what it means.

For example all of these positions are the position of DICER1:

chr14   95552564    95572560    uc010avh.1  0   -   95556834    95571447    0   10  4436,76,163,269,889,156,704,176,106,183,    0,4806,4975,7660,9597,13552,17118,18843,19450,19813,
chr14   95552564    95599840    uc021sbc.1  0   -   95556950    95599795    0   25  4436,76,269,889,156,781,176,106,183,154,214,180,140,76,133,155,243,133,473,169,161,135,131,163,189, 0,4806,7660,9597,13552,17118,18843,19450,19813,21380,21652,22096,25089,25944,26864,29439,30225,31394,37968,40352,43244,43830,45281,46287,47087,
chr14   95552564    95603147    uc001ydv.3  0   -   95556834    95599795    0   27  4436,76,163,269,889,156,781,176,106,183,154,214,180,140,76,133,155,243,133,473,169,161,135,131,163,189,188, 0,4806,4975,7660,9597,13552,17118,18843,19450,19813,21380,21652,22096,25089,25944,26864,29439,30225,31394,37968,40352,43244,43830,45281,46287,47087,50395,
chr14   95552564    95608085    uc001ydw.2  0   -   95556834    95599795    0   28  4436,76,163,269,889,156,781,176,106,183,154,214,180,140,76,133,155,243,133,473,169,161,135,131,163,189,101,66,  0,4806,4975,7660,9597,13552,17118,18843,19450,19813,21380,21652,22096,25089,25944,26864,29439,30225,31394,37968,40352,43244,43830,45281,46287,47087,54431,55455,
chr14   95552564    95623759    uc001ydx.2  0   -   95556834    95599795    0   27  4436,76,163,269,889,156,781,176,106,183,154,214,180,140,76,133,155,243,133,473,169,161,135,131,163,189,193, 0,4806,4975,7660,9597,13552,17118,18843,19450,19813,21380,21652,22096,25089,25944,26864,29439,30225,31394,37968,40352,43244,43830,45281,46287,47087,71002,
chr14   95561684    95570386    uc001ydy.1  0   -   95562108    95570288    0   3   1366,156,704,   0,4432,7998,
chr14   95566116    95577787    uc021sbd.1  0   -   95566116    95577745    0   9   156,781,176,106,183,154,214,180,144,    0,3566,5291,5898,6261,7828,8100,8544,11527,
chr14   95598851    95623759    uc001yeb.1  0   -   95598851    95598851    0   5   163,189,101,66,193, 0,800,8144,9168,24715,
chr14   95598851    95623759    uc001ydz.1  0   -   95598851    95598851    0   6   163,189,101,34,66,193,  0,800,8144,8639,9168,24715,
chr14   95598851    95623759    uc001yea.1  0   -   95598851    95598851    0   6   163,189,143,101,66,193, 0,800,1846,8144,9168,24715,
chr14   95599651    95624347    uc001yec.1  0   -   95599651    95599651    0   4   189,101,66,80,  0,7344,8368,24616,
chr14   95604255    95604323    uc021sbe.1  0   -   95604255    95604255    0   1   68, 0,

Thanks for any help.

Answer 1

[Papyrus]

Those are the different isoforms (mRNA variants) of the gene

[i.sudbery]

Here is what DICER1 looks like on the browser:

Each one of those transcripts corresponds to a line in your bed file.

There are several ways to define the location of the "gene", but the most obvious would be to take the the min of the second column of the bed file, and the max of the third column.

[Zahra]

Thanks for your reply. What about the upstream? There are different positions for 200bp upstream. Are they the upstream of different transcripts?