Here is the combination of the CCDS and DNA Gene sequences and the results are a
ID: 163112 • Letter: H
Question
Here is the combination of the CCDS and DNA Gene sequences and the results are at the bottom. The program will give back alignments of the two sequences, showing how they match, and indicating the start and end position in the sequence that matches. Note that the program will look for matches in both the “top” strand and in the “bottom” strand, so the sequence you see in the alignment may not be the sequence you entered, but the reverse complement, to show the match. Recall that CCDS sequences are DNA sequences that correspond to the coding sequences that end up in mature mRNA, and they are listed in a 5’ to 3’ orientation with respect to the gene product (starting with ATG, ending with stop), whereas the genomic DNA is listed as it sits relative to the whole chromosome. In addition, the expectation is that all of the CCDS sequence (from 1 to the end) will be represented exactly once in the genomic sequence, but that it will be broken into pieces that correspond to the exons (which will be interspersed with introns). Use this knowledge to help you answer the following questions.
1. With respect to the genomic DNA as it is listed, does the RNA polymerase move from left to right or right to left along the DNA to produce the RNA product? What is the observation or result that you use answer this question/support your conclusion?
2. How many coding exons are present in the transcript represented by your CCDS? What is the observation or result that you use answer this question/support your conclusion?
3. Draw a “gene model” for your gene, based on your interpretations above. This is an illustration of where the gene is and how it is transcribed from the genomic DNA. While it may be hard to be precise, it should be relatively to-scale. You can draw it by hand (graph paper can be very useful to establish the scale), or use a computer drawing program. An example of a gene model is below. Note that the genomic DNA is indicated at the top, and that the transcript is indicated to scale below, with the exons as boxes, the introns lines, and the direction of transcription is indicated with an arrow at the end of the gene. The figure also includes a scale bar.
Range 1: 485 to 690Graphics Next Match Previous Match First Match
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Range 2: 314 to 493Graphics Next Match Previous Match First Match
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Range 3: 195 to 315Graphics Next Match Previous Match First Match
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Range 4: 1 to 120Graphics Next Match Previous Match First Match
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Range 5: 690 to 795Graphics Next Match Previous Match First Match
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Range 6: 117 to 195Graphics Next Match Previous Match First Match
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Range 7: 149 to 160Graphics Next Match Previous Match First Match
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Range 8: 333 to 343Graphics Next Match Previous Match First Match
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Range 9: 726 to 736Graphics Next Match Previous Match First Match
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Range 10: 744 to 754Graphics Next Match Previous Match First Match
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>gene 2 genomic sequence
AACGCGGGAAGCAGGGGCGGGGCCTCTGGTGGCGGTCGGGAACTCGGTGGGAGGCGGCAA CATTGTTTCAAGTTGGCCAAATTGACAAGAGCGAGAGGTATACTGCGTTCCATCCCGACC CGGGGCCACGGTACTGGGCCCTGTTTCCCCCTCCTCGGCCCCCGAGAGCCAGGGTCCGCC TTCTGCAGGGTTCCCAGGCCCCCGCTCCAGGGCCGGGCTGACCCGACTCGCTGGCGCTTC ATGGAGAACTTCCAAAAGGTGGAAAAGATCGGAGAGGGCACGTACGGAGTTGTGTACAAA GCCAGAAACAAGTTGACGGGAGAGGTGGTGGCGCTTAAGAAAATCCGCCTGGACACGTGA GTGGCCTCTGTACCCGGGACTCCTAACTGGGGACCTCCTTGATTGTCCCCCCCAACCCCC CACGGGCGGGTAGCCGTCCAGGGACCGGAAGAGAGCAGGGAGGGACTTCTTTAGAAGTGG AGAGGTGGGTTGGGGGCCAGTAGAAGGTGAAGAGTATACTTATACTCCCTGGGGAGAGTA TAGGGTGGTGTGGAATCCATGGAAAACTTTCTTCCCAAACTGAGCCGGATCGTGCCCCCA AATGTGCGACTACAGACTCGGGGAGAGAAAGGAGGTCTCTGAGATGAGGTCCAAGACTCT CCATGGAGTGGAGTTATGTGGGAACCGGCGAGAATCGCCTTTCTGAATGAAGAGCCCTCT TCACTGCCCCACCCTCACCTTAGAATTCTCTCCTCTTTCCAAAGAATGGCAGTTGAACCT CACTGGCCCCTCTGGGGAGGCTGGGGGCTACTCCTGCATTTTTTCCCCTCCATTACAGTC TCCCTGCTTCACCTTCACCAGGCGGCTTTACTTACCTACCCCTGGGAAAAGAGGAGATAA TGGCCTTAATATATCCAAAAACCACACCCTGACTACCCAAGAATTAGCTCTTACCATCAC CCTTTCTCTTCTCTCACTTTCCTAGGGGGTGCTGGGTGGTGTCTCCTTGGGGGAAAGAAA TGACTAGGTGGGGGGGAAAGGAATATTTGTAACCATATTCCCATCTCTGCTTTCCCAACC TCTCCAAGTGAGACTGAGGGTGTGCCCAGTACTGCCATCCGAGAGATCTCTCTGCTTAAG GAGCTTAACCATCCTAATATTGTCAAGTAAGTATGCGTCTGAGAGGTGATCCAGCTGGAA AGGAGGATAAGTTCTGTCTGTACAGTGTGGGCATTTCTCTCTCTCACACACCTCCATTTC CTCAAACTTTCCTTCTCTAGGCTGCTGGATGTCATTCACACAGAAAATAAACTCTACCTG GTTTTTGAATTTCTGCACCAAGATCTCAAGAAATTCATGGATGCCTCTGCTCTCACTGGC ATTCCTCTTCCCCTCATCAAGGTAATGCTTCTCATCAGCTCCTCTCATCATGGGCATGTC TTGGGGGACTGGTGGCAGGCAATTCAGGGTGATATTTTATGATTTTGGCCTCCTTCTGAG CCCTCATCTCCTATACACACACACTCCCCTTCTTTTTGTGTCTCCTTCCCTGCTCATTAT ATTCATTAACCCTAGGGTTGGACTGAACAATCAAAGTTGAAACTCTAGTGAGTCAACCTA GCAACTCAGGTGGGAGGTCAGATGAAACTCAGATAAACGGGATTTGAGAGCACTTGGTAA ATTCCTCCAAAAAGCCCTTCCATTTGGTGGAAGACCTAGCTAGTGAGTCCCTATTGTCTA TTTTAGGGCTGGATTCTTCACTCCCAGAGCTACTTTCAATCTATTAACAAACATTTTTTC AATGCACAGGATGTAGAAAAGGGATGGAAAATTGAGTAAGACTTGGTCCTTATCCTCTCT GGGCTGACAGTCCATTGGGAGAAATAGCTTGTAAATATGTAACTATAATCCAACATAATA AAGGCTTTAGTAGAGTTTTAGGGGCACAGAGCAAACCCAGTCTGCTCACTGTAATGGAGA AACACAGTCCTCTCTTTCTCCTTTGTCAGAGCTATCTGTTCCAGCTGCTCCAGGGCCTAG CTTTCTGCCATTCTCATCGGGTCCTCCACCGAGACCTTAAACCTCAGAATCTGCTTATTA ACACAGAGGGGGCCATCAAGCTAGCAGACTTTGGACTAGCCAGAGCTTTTGGAGTCCCTG TTCGTACTTACACCCATGAGGTGAGTCCCTTTATGTCTTTTTTCTCTGAGCTTCCCAAGA GGTGTTAACTAGGGTATTCACAAAGTTACTAAAAATATCTGGCTAACAGTTTCTTACTAG GTAGAAATAATCTCTTGACATCCTAAAGAGTCTTAGGGTATGCATGGAATTCATACTGTG TTGCTAACTGGGCCCACACCTGTAATACCAATACTTTGGGAGGCTGAGGTGGGAGGATCA CTTGAGCCCAGGAGTTCGAGACCATCATGGGCAACATAGCGAGACCCCATCTCTACAAAT CTACAAAAAGAAAAAATTTAGAAATAAAATTATGACCAATTTGTCTCAAGTTTTTCCAGG AAGATCTCAAATTAGGGGTTCAGTCCAGAACTATGGACTGGAAATCAGTGGGAGGGGAAA GATGATGGAGGGAAGGAAACTGCTTGTTAAGAGGCCAAGAGTAAGCAGAGTAGTGTTGAG GAACTGAGATGCGGGAATTTCCATACCCTATAAACCACCCCGCCCCTCCCTATTCCCGTC CCTCAGGTGGTGACCCTGTGGTACCGAGCTCCTGAAATCCTCCTGGGCTGCAAATATTAT TCCACAGCTGTGGACATCTGGAGCCTGGGCTGCATCTTTGCTGAGATGGTATGGAGGCTT GCCCAAGTTCCACCCAGCCCCCTCCCTCTCCTCCCCACATCCAAGAACAACAGAACTGCT TCTTGGCCCAGACCTATGGCCCTTCTATCACAGGGTTCTCTCTCTAAAGTAGCACCAAGG GGAATGGTGGGAAAGGATGCAACTGTTGCCCTGATATCAACCACAGTGTTAGGATATCCT CAAACAGCCTTAGTACCTGGTATACATCTCTTATCCCTGAAATAAGTTAAAGCATTTCTG CAGCTGTTTTAGCTGTAGTCTGCATATATTTGGGAGAATGATTCCATTTAGTGCCTCTTT TATTTCAGGCCTTCATTTCAAGGCTTGTAGACCTTGTTGTATGGTGCCAGCAATGTAGTG AAGACAACTGTGGTCACTTTACCCACACCTTTCATTTAAACTGCAGATTTAGGCAGGGTG CAGTGGCTCACACCTATAATACCAGCACTTTGGGAGGCTGAGGTAGGTGGATCACCTGAG GTCAGGAGTTTGAGACCAGCCTGGCCAACATGTTAAAACCCTGTCTCTACTAAAAATACA AAAATTAGCCAGGTGTGGCTACTTGGGATTACACACCTGTAATCCCAGCTACTTGGGAGG CCAAGGCAGGAGAATCGGTTGAACCCGGGAGATGGAGGTTGCAGTGACCAAGATTGCACC ACTGCACTCCAGCCTGGGCGACAGAATGAGATTCCATCTCAAAAAAAAAAAAAAAAAAAA AAAAAAAAAGATTTAGATCATGTTCCCCTTCAACCTCTGGCTTTTCAGACTGAAGGATCC TTGAAGCCTGGCTTTATGTAGAAGCTCCCATCTCCTTTAATATAACAGTACAGTGGTGCA GTAGGCTGTCTTCAAATCAGCAATATGTTTTATTGTCTTTTATCTTGGTTGTAACCAAGA GCTTAAAGACCATTAGCCTATACATATGTAATGTGCATTTATCCCCCCAGTGCATTACCT TACAATTGTCCGTATTCCTCTCTCAATTCATCAAAAAATATTTGTTAAGCACCTAGTGGG TACCCAGCACCATGCTAGGTGCTGTGGGGAACACAGAAGAAATGGAAGACAGAGTCTCTG CCCGCTGTGCTCGTATCTAGAAGTGGCTGCATCACAAGGTTGGGGGATGACCGCAGTGTC TACCCCCTACCCCGTGAGTGGCTTGGGATACCTTTGCTACATGTCAGTGGCACCCCAGAC ATTCACCCCCTCCCAGACCCACCCAGCCTTGGGGATCTGCAAAGCCATGGTTGGGGGAAG GAAGGAGGGGGCGAGGAGACAGATGAAGGAACTTCATTGTCTCAGGTTCTGTGTGACTGA CCCCATGAAAGGCCCTGGGGAGGGAGTCATGGGGCCCTGCTGACCTTTTACTGTCTGTGG GAACTCCTTTGTATAGAGGAGAGTTTTGACTGACGTCAACGTGGGTCTTGGTATTTCCTC TTTCCCCATTTTCAGGTGACTCGCCGGGCCCTATTCCCTGGAGATTCTGAGATTGACCAG CTCTTCCGGATCTTTCGGACTCTGGGGACCCCAGATGAGGTGGTGTGGCCAGGAGTTACT TCTATGCCTGATTACAAGCCAAGTTTCCCCAAGTGGGCCCGGCAAGATTTTAGTAAAGTT GTACCTCCCCTGGATGAAGATGGACGGAGCTTGTTATCGGTGAGAGTGGGCACCTGTTTT CCCTCATTCATTTCTCCCAGGGAAGGGCTTTTCCAGGATGAAGGAAGGATGAGACCCTGA AATCTGGGCCTCAGTGTTTCATTTCCCTGGTTCCTGCTCTCCCTGTTGGCACACTGATTC AGCTATGGGAGGATGGAAGTGAGAATTCTGCCTTGGGTAGAAGGAGTTCTGGTTTCCTGA TTTCTGGGAACACCTGCTGCCCATTTAGTCCACTATCACATCATTGAAGTCAACATGCAT CTCTCCCTCTAGCAAATGCTGCACTACGACCCTAACAAGCGGATTTCGGCCAAGGCAGCC CTGGCTCACCCTTTCTTCCAGGATGTGACCAAGCCAGTACCCCATCTTCGACTCTGATAG CCTTCTTGAAGCCCCCAGCCCTAATCTCACCCTCTCCTCCAGTGTGGGCTTGACCAGGCT TGGCCTTGGGCTATTTGGACTCAGGTGGGCCCTCTGAACTTGCCTTAAACACTCACCTTC TAGTCTTGGCCAGCCAACTCTGGGAATACAGGGGTGAAAGGGGGGAACCAGTGAAAATGA AAGGAAGTTTCAGTATTAGATGCACTTAAGTTAGCCTCCACCACCCTTTCCCCCTTCTCT TAGTTATTGCTGAAGAGGGTTGGTATAAAAATAATTTTAAAAAAGCCTTCCTACACGTTA GATTTGCCGTACCAATCTCTGAATGCCCCATAATTATTATTTCCAGTGTTTGGGATGACC AGGATCCCAAGCCTCCTGCTGCCACAATGTTTATAAAGGCCAAATGATAGCGGGGGCTAA GTTGGTGCTTTTGAGAACCAAGTAAAACAAAACCACTGGGAGGAGTCTATTTTAAAGAAT TCGGTTGAAAAAATAGATCCAATCAGTTTATACCCTAGTTAGTGTTTTGCCTCACCTAAT AGGCTGGGAGACTGAAGACTCAGCCCGGGTGGGGCTGCAGAAAAATGATTGGCCCCAGTC CCCTTGTTTGTCCCTTCTACAGGCATGAGGAATCTGGGAGGCCCTGAGACAGGGATTGTG CTTCATTCCAATCTATTGCTTCACCATGGCCTTATGAGGCAGGTGAGAGATGTTTGAATT TTTCTCTTCCTTTTAGTATTCTTAGTTGTTCAGTTGCCAAGGATCCCTGATCCCATTTTC CTCTGACGTCCACCTCCTACCCCATAGGAGTTAGAAGTTAGGGTTTAGGCATCATTTTGA GAATGCTGACACTTTTTCAGGGCTGTGATTGAGTGAGGGCATGGGTAAAAATATTTCTTT AAAAGAAGGATGAACAATTATATTTATATTTCAGGTTATATCCAATAGTAGAGTTGGCTT TTTTTTTTTTTTTTTGGTCATAGTGGGTGGATTTGTTGCCATGTGCACCTTGGGGTTTTG TAATGACAGTGCTAAAAAAAAAAAGCATTTTTTTTTTATGATTTGTCTCTGTCACCCTTG TCCTTGAGTGCTCTTGCTATTAACGTTATTTGTAATTTAGTTTGTAGCTCATTAAAAAAA TGTGCCTAGTTTTATA
>gene 2 CCDS
Alignment statistics for match #1 Score Expect Identities Gaps Strand Frame 372 bits(412) 3e-106() 206/206(100%) 0/206(0%) Plus/Plus 5 kbp H 14950k. Cbr-sur-2 (CBG19759) protein coding 14960KExplanation / Answer
The RNA polymerase moves from right to left not from left to right.This is because the strands usually move from 3' to 5'(left to right) where as in this case the strand is from 5' to 3' which is the opposite order to the normal 3'-5'.This is from right to left not from left to right