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Jan 9, 2024

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AS.410.633.84 Assignment #1 The ACC number that I have chosen to do my research on is NM_000492.4. This ACC number is a mRNA sequence that codes for the CFTR (Cystic Fibrosis Transmembrane conductance Regulator) gene. This gene results in the production of the CFTR protein. The CFTR protein functions as a chloride channel that regulates the traffic between chloride ions and water concentration in epithelial tissues. If mutations of this gene arise and affect the production of this protein, this can lead to the organism (human) developing Cystic Fibrosis. One symptom of someone that has the Cystic Fibrosis disease is having lung damage/difficulty breathing. This is due to the fact that the CFTR protein is not doing its intended job. Since the CFTR protein is lacking, the result is improper mucus balance where the imbalance of chloride ions and water lead to the buildup of mucus covering the cellular surface. Overall, Cystic Fibrosis affects mucus, sweat, and digestive juice production. If someone is positive for Cystic Fibrosis, their life expectancy used to be around 30 years old. But thanks to modern medicine, that life expectancy is increasing more and more. When analyzing the Gene database for my sequence, there are four sequence genes; Chromosome 7 Reference GRCh38.p14 Primary Assembly, RefSeqGene, Chromosome 7 Alternate T2T-CHM13v2.0, and Chromosome 7 Reference GRCh37.p13 Primary Assembly whose ACC numbers are, respectively, NC_000007.14 (version 14), NG_016465, NC_060931.1 (version 1), and NC_000007.13 (version 13). To find the chromosome location of our sequence, I navigated to the Ensembl database. Once the database is loaded, the location of the chromosome is located towards the top of the screen. According to Ensembl, this mRNA sequence is located at Chromosome 7 at regions 117287120 to 117715971. After analyzing my sequence’s Ensembl chart, there are 22 unique features within my sequence. Those features are splice acceptor variant, slice donor variant, stop gained, frameshift variant, stop lost, start lost, inframe insertion, inframe deletion, missense variant, protein altering variant, splice donor 5 th base variant, splice region variant, splice donor region variant, splice polypyrimidine tract variant, incomplete terminal codon variant, stop retained variant, synonymous variant, coding sequence variant, 5 prime UTR variant, 3 prime UTR variant, non-coding transcript exon variant, and intron variant. After searching through the databases for information pertaining to my sequence, I was able to find only one contig at the gene level. This contig is AC002465 which of course, is found in the organism Homo Sapiens, also known as humans. The molecular type of this contig is genomic DNA. The base count of this contif is 155,881 base pairs. After searching through the ENA database for information pertaining to my sequence, I was able to find only one contig at the gene level. This contig is AC002465 which of course, is found in the organism Homo Sapiens, also known as humans. The molecular type of this contig is genomic DNA. The base count of this contif is 155,881 base pairs. To figure out the length of my sequence, I navigated to the right side of the sequence chart and launched the UCSC database. Per this database, the length of this gene is 428,852 base pairs. When searching this gene through the NIH database, if we were to find the most recent article using PubMed, this article talks about CFTR mutations in two brothers and the correlation between CFTR mutation and male infertility (Shengjia, S., 2023). If we were to find the most recent article using PubMed Central, this article talks about CFTR- modulating drugs that can possibly overcome defect and restore function of the CFTR gene (Stefania, L., 2023)
AS.410.633.84 References: https://www.ncbi.nlm.nih.gov/gene/?term=NM_000492.4 https://www.cff.org/research-clinical-trials/basics-cftr-protein https://pubmed.ncbi.nlm.nih.gov/7733303/#:~:text=The%20most%20common%20mutation %20in,traffic%20to%20the%20plasma%20membrane https://www.ncbi.nlm.nih.gov/gene/?term=NM_000492.4#bibliography http://useast.ensembl.org/Homo_sapiens/Location/View? g=ENSG00000001626;r=7:117287120-117715971 https://www.ebi.ac.uk/ena/browser/view/AC002465 http://genome.ucsc.edu/cgi-bin/hgTracks? db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode =0&nonVirtPosition=&position=chr7%3A117287120%2D117715971&hgsid=1712066662_MhDa DHTUvcHDlQPXA8ikAydeivAw Shengjia, S. (2023 Jul 24). Compound heterozygous variants in CFTR with potentially reducing ATP-binding ability identified in Chinese infertile brothers with isolated congenital bilateral absence of vas deferens . https://pubmed.ncbi.nlm.nih.gov/37489040/ Stefania, L. (2023 Sept 6 ). L1077P CFTR pathogenic variant function rescue by Elexacaftor– Tezacaftor–Ivacaftor in cystic fibrosis patient-derived air–liquid interface (ALI) cultures and organoids: in vitro guided personalized therapy of non-F508del patients. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10483775/
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