Weeks 9 and 10

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Rutgers University *

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MISC

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Biology

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Apr 3, 2024

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Kaitlyn Kasauskas - Assignment Weeks 9 & 10 Question 1 (6 points) A. (2 points) Are there any Evolutionary Conserved Regions (ECRs) between the genomic sequence for Mouse “FASL” and those for Rat and Human ? To answer, use the sequences found in the week 9 course module in conjunction with “multi-zPicture” ( http://zpicture.dcode.org/multiz.php ) with the Mouse sequence entered as your reference (i.e., “SEQUENCE 1”), the Rat sequence entered as “SEQUENCE 2”, and the Human sequence entered as “SEQUENCE 3”. Copy/paste the resulting “Dynamic Visualization” as your answer. B. (2 points) How many ECRs exist between Rat and Mouse FASL (Hint: click on list of ECRs for “seq 2” in the Output files results section)? 4 ECRS C. (2 points) How many ECRs exist between Human and Mouse FASL (Hint: click on list of ECRs for “seq 3” in the Output files results section)? 14 ECRS Question 2 (7 points) A. (1 point) Using miRBase ( http://www.mirbase.org ), what is the accession number for “mmu-mir-223”? MI0000703 B. (1 point) Looking at the record provided as your answer to Question 2A, what Gene Family does “mmu-mir-223” belong to? MIPF0000067; mir-223 C. (1 point) What genome assembly does “mmu-mir-223” fall within? chrX
D. (1 point) What type of nucleic acid feature or structure does “mmu-mir- 223” show? A stem-loop E. (1 point) What is the genomic position, or coordinates, for “mmu-mir-223”? chrX: 96242817-96242926 [+] F. (1 point) What is the nucleic acid sequence for “mmu-mir-223”? ucuggccaucugcagugucacgcuc CGUGUAUUUGACAAGCUGAGUUG gaca cucugugugguagag UGUCAGUUUGUCAAAUACCCCA aguguggcucaugc cuaucag G. (1 point) What is the 5p Mature sequence for “mmu-mir-223”? 26 - CGUGUAUUUGACAAGCUGAGUUG – 48 Question 3 (3 points) Given the following RNA Stem-Loop sequence: CGGGGUUGGUUGUUAUCUUUGGUUAUCUAGCUGUAUGAGUGGUGUGGAGUCUUCAU AAAGCUAGAUAACCGAAAGUAAAAAUAACCCCA A. (1 point) What am I? What miRNA family does the miRBase Search feature ( http://www.mirbase.org/search.shtml ) say it is likely a member of? To answer, review the search results, explore the recorded family entries in the corresponding records, report the consensus entry as your answer. hsa-mir-9-1 B. (1 point) Using the same RNA Stem-Loop sequence in Question 3, what miRNA family does the Rfam Search feature ( http://rfam.xfam.org ) say it is likely a member of? mir-9/mir-79 microRNA precursor family C. (1 point) Per your answers to Questions 3A and 3B, would you say Rfam and miRBase provide similar or different results? Similar, if not identical, results.
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