Question

please answer questions with the following BLAST results

For your GenBank assignment due at 12 noon on Thursday May 23rd (don't forget, I will not accept late papers): 1. Dr. Monsen-Collar will tell you the number of a sequence posted on Canvas. Copy the entire sequence and use it in a BLAST search to determine what gene the sequence is. Answer the following questions: A. What gene is your unknown sequence likely to be? How do you know it's a good hit? B. From what organism was this gene sequenced? C. Is your sequence conserved or not conserved among other species? A conserved sequence is one that shows little to no sequence difference among different species. How did you arrive at the answer to this question? D. How do you think your results would change if you used a longer sequence? What about a shorter sequence? Explain your answers. MAKE SURE YOU INCLUDE THE # OF THE SEQUENCE YOU USED IN BLAST! 0 土Download GenBank Graphics Next Sida crystallina 18S rRNA gene, isolated in Belgium 1 6 2 Sequence ID: AM490294.1 Length: 2179 Number of Matches: 1 Range 1: 241 to 610 GenBank Graphics Score Gaps Expect Identities St 733 bits(370 0.0 37O/370( 100%) 0/370 (0% Pl Query 1 TCGGGGGGCTCGCTCCCCGTCCTTTTTGGTGACTCTGAATAA Sbjct 241 TCGGGGGGCTCGCTCCCCGTCCTTTTTGGTGACTCTGAATAA Query 61 GCCTTGGAGCCGGCGACGCATCTTTCAAATGTCTGCCTTATC TITIIIITIITTITITI1 Sbjct 301 GCCTTGGAGCCGGCGACGCATCTTTCAAATGTCTGCCTTATC Query 121 ATGCGCCTACCATGGTTGCAACGGGTAACGGGGAATCGGGGT Sbjct 361 ATGCGCCTACCATGGTTGCAACGGGTAACGGGGAATCGGGGT Query 181 CCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCG Sbjct 421 CCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCG Query 241 CACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCTTC Sbjct 481 CACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCTTC 1 Query 301 ATGAGTACACTTTAAATCCTTTAACGAGGACCTATTGGAGGG Sbjct 541 ATGAGTACACTTTAAATCCTTTAACGAGGACCTATTGGAGGG Query 361 CCGCGGTAAC 370 Sbjct 601 CCGCGGTAAC 610

Answer 1

A. The gene is likely to be 18s RNA gene. It is a good hit because E value is 0 and identity is 100 percent.

B. This gene have sequenced from sida crystallina.

Sida crystallina 18S rRNA gene, isolated in Belgium GenBank: AM490294.1 FASTA Graphics Go to: 2179 bp DNA linear INV 11-SEP-2007 LOCUS AM490294 DEFINITION Sida crystallina 18S rRNA gene, isolated in Belgium. ACCESSION AM490294 VERSION AM490294.1 KEYWORDS 18S ribosomal RNA; 18S rRNA gene SOURCE Sida crystallina ORGANISM Sida crystallina Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Crustacea; Branchiopoda; Diplostraca; Cladocera; Ctenopoda; Sididae; Sida. REFERENCE 1 AUTHORS Van Damme,K., Shiel,R.J. and Dumont,H.J TITLE Notothrix halsei gen. n., sp. n., representative of a new family offreshwater cladocerans (Branchiopoda, Anomopoda) from SW Australia, with a discussion of ancestral traits and a preliminary molecular phylogeny of the order JOURNAL Zool Scr. 36 (5), 465-487 (2007) REFERENCE 2 (bases 1 to 2179) AUTHORS Van Damme,K.P.S. TITLE Direct Submission JOURNAL Submitted (30-JAN-2007) Van Damme K.P.S., Belgium, Ghent University, K.L. Ledeganckstr. 35, Ghent, B-9000, BELGIUM Location/Qualifiers FEATURES ce 1..2179 organism-"Sida crystallina" mol type- "genomic DNA" /db xref-"taxon:77656 /sex-"parthenogenesis female" country- "Belgium collection date-"1997" collected by-"H.J. Dumont" source gene1..2179 gene-"18S rRNA" 1..2179 gene-"18S rRNA" /product-"18S ribosomal RNA" TRNA ORIGIN 1 tacctggttg atcctgccag tagcatatgc ttgtctcaaa gattaagcca tgcatgtcta 61 agtacgagcc gtcttgtcgg cgaaaccgcg aatggctcaa taaatcagtt atggttcctt 121 agatcttacc atcctacttg gataactgtg gtaattctag agctaataca cgcactcaag 181 ccccgactct cgccgtctcg gcggcgggca ggaggggtgc ttttattaga tcaaaaccaa 241 tcggggggct cgctccccgt cctttttggt gactctgaat aacttttegc cgatcgcacg 301 gccttggagc cggcgacgca tctttcaaat gtctgcctta tcaactttcg atggtaggtt 361 atgcgcctac catggttgca acgggtaacg gggaatcggg gttcgattcc ggagagggag 421 cctgagaaac ggctaccaca tccaaggaag gcagcaggcg cgcaaattac ccactcccgg 481 cacggggagg tagt gacgaa aaataacgat acgggactct tccgaggccc cgt gattgga 541 atgagtacar tttaaatcct ttaacgagga cctatt ggag gecaaotctg ot arcagrag

C. To give this answer please take this gene sequence from another organisms also and perform multiple sequence alignment. If the result of it is good, then the sequence will be conserved.

D. If we used longer sequence, then our result will be not good because BLAST aim to find shorter stretch of sequence matching with query sequence. If we use shorter sequence we will get better results.