Hello!

This week we used a really cool tool for genome browsing. I typed in my protein name "acidic mammalian chitinase" into the search bar, and was able to see the chromosome my protein is on, the number of base pairs, and its position.

My protein is on Chromosome 1, is 29,713 bp, and stretches between 111,290,851-111,320,563.

I then hid all the stuff that the genome browser had displayed, and just looked at the NCBI RefSeq option. I chose to look at the full display. When I clicked on the heading at the top of the display, it shrunk it down to show a condensed version.

Here is a nice picture of the full display of the NCBI RefSeq track.


When I hovered over my protein's name on the side, it highlights the whole top or bottom section. I clicked on the name, and it took me to a page that showed a brief description about the protein. Clicking on the body seemed to take me to the corresponding CHIA's page as well. At first I thought that there was only one single page for CHIA, but I clicked on a few, and noticed that each one was slightly different. 

This is a picture of the first CHIA in the top section.


This is a picture of the CHIA highlighted in blue, in the bottom section.



Citations

UCSC Genome Browser: Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006. https://genome.cshlp.org/content/12/6/996.abstract

Track Data Hubs: Brian J. Raney, Timothy R. Dreszer, Galt P. Barber, Hiram Clawson, Pauline A. Fujita, Ting Wang, Ngan Nguyen, Benedict Paten, Ann S. Zweig, Donna Karolchik, W. James Kent, Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser, Bioinformatics, Volume 30, Issue 7, 1 April 2014, Pages 1003–1005, https://doi.org/10.1093/bioinformatics/btt637

First screenshot:
UCSC Genome Browser on Human Dec. 2013 (GRCh38/hg38) Assembly. (n.d.). USCS Genome Browser.
Retrieved October 30, 2020. http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=
default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=
chr1%3A111290851-111320563&

Second screenshot:
NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) - NM_0012580002.2. (n.d.). USCS Genome Browser. Retrieved October 30, 2020. http://genome.ucsc.edu/cgi-bin/hgc?hgsid=933386939_UEcV2Ewo9b4lAhWojTqNg33mOQvl&c=chr1&l=111290850&r=111320563&o=111290850&t=111320563&g=ncbiRefSeqCurated&i=NM_001258002.2

Third screenshot:
NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) - NM_0012580002.2. (n.d.). USCS Genome Browser. Retrieved October 30, 2020. http://genome.ucsc.edu/cgi-bin/hgc?hgsid=933386939_UEcV2Ewo9b4lAhWojTqNg33mOQvl&c=chr1&l=111290850&r=111320563&o=111290850&t=111320563&g=refGene&i=NM_001258003


Comments

Post a Comment

Popular posts from this blog

Week 13

Image
Last week of lab. I did another gel today with Jaira which was pretty fun! No results again kinda.... D. rad had a line.... I did take a picture, and noticed a possible second line under row 6... but it’s lower than the ladder, so It’s definitely not in the right spot lol.
Read more

Blog Post 2 -- Spring 2023 -- Professional Identity

 Hello! The second blog post for this semester is about professional identity. My interpretation of professional identity is basically how you want to be viewed as a professional. For example, how much of your authentic-self do you want to show, and how much is appropriate; do you want to be viewed as a leader; do you want to be the type of professional who wants to go to work, do their job, and not have to worry about bossing people around? I think your professional identity varies based on the field you are in in STEM, and what activity you are doing. A biologist might be able to dress fairly casually in the lab, but when they are presenting at a research conference it is important to dress up professionally in order to gain more respect. Engineers tend to dress fairly casually. As a software engineer, my dad would dress in jeans in a collared shirt for work in the office even. He was never working face-to-face with clients or customers, so there was no point in requiring everyon...
Read more

Semester 2 week 4

Image
This week we did a gel on Tuesday, 1/4/2020. I came in late, so they were already in the middle of it. This was for samples 1, 7, 8, and 14. Nothing showed, possibly because the gel was too thin and hardened inconsistently.  We discussed options, and decided Chad would run PCR again and run a gel on the 4 samples again. He succeeded in getting 1, 7, and 8 to show, but not pimensis.  1/7/2020 We did DNA isolation on pimensis. The numbers were low, only 27 ng/micro Liter, so we did DNA isolation on pimensis again on 1/8/2020. We are awaiting to use the nanodrop to get the results for this DNA isolation. 
Read more