work on gene (alpha-catenin) from the home page copy and paste the link(http://w
ID: 132408 • Letter: W
Question
work on gene (alpha-catenin) from the home page copy and paste the link(http://www.genecards.org/ ).)
Current total number of protein coding genes in human genome: ______
How many RNA genes according to this site in human genome? ______
Does your gene or protein have aliases- how many? List a few names that you find surprising.
How many amino acids is the protein your gene encodes for, and what is its proposed molecular weight (in kiloDaltons, kD)?
What is the chromosomal location of your gene?
How many bases does your gene include?
Any orthologs of your gene? If so, provide a few (3-4) specific species and their similarity level.
Does your gene have any paralogs?
Provide a very brief summary of the proposed function of the protein encoded by your gene.
In what tissue is your gene most highly expressed based on RNAseq data?
Are there any SNPs for your gene? If so, choose one and indicate its position, sequence context, and type.
What companies sell ‘CRISPR’ reagents that a researcher could purchase to knock-out the gene from the genome to study its function in cells?
next step log into (: http://www.ncbi.nlm.nih.gov/) and answer these questions :
‘All Databases’ tab, select ‘Genome’ and enter the search term ‘human’.
What organization assembled the current human ‘Reference Genome’ that all genomic data is based on and which ‘version’ are we working with?
Which human chromosome is the largest? Do you notice a pattern to the numbering of the human chromosomes and their relative sizes?
How many proteins are encoded by the human Y chromosome?
next step Back at the top of the http://www.ncbi.nlm.nih.gov/ page, under the ‘All databases’ tab select ‘Gene’ and enter youralpha-catenin into the search tab. Click on the ‘Homo Sapiens’ version of the gene from the list.
In regards to the ‘genomic context’ of your gene. What are the names of genes located in closest proximity to your gene? Are they in the same ‘gene family’ as your gene?
Is it possible for two genes to occupy the same stretch of double-stranded DNA? i.e. could there be a gene encoded on the DNA strand complementary to your gene?
In what orientation is a gene transcribed, i.e. does the gene reading frame run from 5’ to 3’ or 3’ to 5’?
Use the genome viewer under the header ‘Genomic regions, transcripts, and products’ to answer the questions in this section.
How long (in DNA base pairs) is your gene?
How many exons comprise your gene? Are any ‘splice variants’ displayed?
What are the two exons flanking the largest intron?
Center the first exon in the genome browser and zoom in to the ‘sequence’ level using the little ‘ATG’ button next to the zoom control. Find the ATG start site of your gene.
What are the first 20 DNA bases following the ATG start site?
How far into the exon 1 reading frame is the first ‘SNP’ and what base substitutions are possible at this site?
Click on the ‘Tools’ button and highlight the ‘sequence text view’ option. A new window should open with an annotated FASTA format view of the DNA sequences in this region. In my opinion, this is the most practical and useful view of the gene sequence… especially for PCR primer design.
What color is used to highlight the intronic sequences outside of the gene reading frame?
What color is used to highlight exons (coding sequences)?
What are the first 5 amino acids of your protein?
Back at the top of the http://www.ncbi.nlm.nih.gov/ page, under the ‘All databases’ tab select the ‘Homologene’ database and enter alpha-catenin.
How many homologues to your human gene are listed with this tool?
Over what classification level has your gene been conserved? for ex., the gene KRT5 has been conserved since the evolution of tetrapods.
Does your answer to the above question suggest your gene is an ‘ancient’ gene or a more recent addition in our evolutionary history? Give an estimate, in millions of years, when the gene diverged in our ‘common ancestor’ with other species…
What are a few of the more obscure species where your gene has been identified?
Give your impression on the number of amino acids in the protein product of your gene across the different organisms listed. What does this pattern suggest?
Explanation / Answer
Answering any of the 3 sub part questions based on CHEGG rules:
a. There are 21,360 protein coding genes in the human genome.
b.There are 98,609 RNA genes in the human genome.
c.There are 10 aliases to this gene. Some of them are
d) There are 906 amino acids and the molecular weight is 100.071 KDa.
e)Chromosomal location:5q31.2
f)2718 base pairs
Thermo Fisher and Dharmacon sells CRISPR based technolgies for knocking out the gene in a genome.
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