Question: UCSC genome browser
1
gravatar for cv.napping
6.3 years ago by
cv.napping20
United States
cv.napping20 wrote:

Hi.

I'm given an assignment in which I have to use UCSC genome browser to extract the gene (sequence) of LWS (long wav sensitive) opsin in 5-6 mammals. This is my first time using this browser n I'm a beginner in bioinfo so probably thats why I'm experiencing some issues here.

My issues are as follows :

When I hit search by typing the above gene name LWS in the blank area, choose a mammal, say, rabbit, I'm not getting any specific results. The search result page is showing non rabbit genes. I dont understand why when i specifically asked for rabbit. The same happens when I choose a different mammal. Does this mean the lws gene is not present in that particular mammal? I'm giving a link for the results here. Please help me understand what does Non-rabbit ref seq genes and Non-Rabbit Aligned mRNA sequences mean? Why am I not getting the desired result for rabbit?

link: http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=Rabbit&db=oryCun2&position=lws&hgt.positionInput=lws&hgt.suggestTrack=refGene&Submit=submit&hgsid=386006961_uiPIJljYKAYoflaaQehsfbLuB3li

ADD COMMENTlink modified 6.3 years ago by Mary11k • written 6.3 years ago by cv.napping20
1
gravatar for Mary
6.3 years ago by
Mary11k
Boston MA area
Mary11k wrote:

I don't want to do your work for you, but I'll give you 2 suggestions to get you started.

1. First, use the human assembly to begin. It's the best annotated, and find an example of this gene you seek in human. When you find the genomic region, click on the gene in the viewer. That will go to a description page. Scroll down that page a ways to find a place where it shows matches in other species. Back on the viewer, though, you can also look at the species comparisons down lower on the graphic and explore those a bit.

2. Start with a sequence and use BLAT to locate similar sequences in other species.

ADD COMMENTlink written 6.3 years ago by Mary11k
0
gravatar for David Langenberger
6.3 years ago by
Deutschland
David Langenberger9.5k wrote:

The result you get just means that LWS from a non-rabbit species was aligned to that position. Looks like the rabbit annotation does not contain LWS yet. But you get some information from that non-Rabbit RefSeq track: There seems to be a homolog of LWS at that position. If it's a pseudogene, or a functional one, is a different question that has to be answered.

ADD COMMENTlink written 6.3 years ago by David Langenberger9.5k
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