please answer all the questions ansering only one is not helpful. Visualizing th
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Question
please answer all the questions ansering only one is not helpful.
Visualizing the structure of your specific gene. Back at the top of the http://www.ncbi.nlm.nih.gov/ page, under the ‘All databases’ tab select ‘Gene’ and enter your gene of interest into the search tab which is (CTNNA1) alpha-catenin). Click on the ‘Homo Sapiens’ version of the gene from the list.
1.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?
2. 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?
3. In what orientation is a gene transcribed, i.e. does the gene reading frame run from 5’ to 3’ or 3’ to 5’?
4. Use the genome viewer under the header ‘Genomic regions, transcripts, and products’ to answer the questions in this section.
5. How long (in DNA base pairs) is your gene?
6. How many exons comprise your gene? Are any ‘splice variants’ displayed?
7. What are the two exons flanking the largest intron?
8. 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.
9. What are the first 20 DNA bases following the ATG start site?
10. 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?
Explanation / Answer
1. In regards to the genomic context of 'CTNNA1(alpha-catenin), the genes present in the closest proximity are as follows: LRRTM2(leucine rich repeat transmembrane neuronal 2), RNA5SP194, RPL12P21, SIL1(SIL1 nucleotide exchange factor), LOC105379194. No, they do not share the same gene family with my gene of interest.
2. Yes, it is possible for two genes to occupy same stretch of double stranded DNA . i.e., the sense and antisense strand can encode for two different genes.
3. During DNA transcription the open reading frame runs from 3' to 5' , whereas the orientation of the gene transcribed by RNA polymerase is from 5' to 3'.
5. CTNNA1(alpha-catenin) is 181649 basepairs long in length.
11. The usually the intronic sequences are outside of the gene reading frame are highlighted with green color.
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