Gene Sequence AACGCGGGAAGCAGGGGCGGGGCCTCTGGTGGCGGTCGGGAACTCGGTGGGAGGCGGCAA CATTG
ID: 163005 • Letter: G
Question
Gene 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
ATGGAGAACTTCCAAAAGGTGGAAAAGATCGGAGAGGGCACGTACGGAGTTGTGTACAAAGCCAGAAACA
AGTTGACGGGAGAGGTGGTGGCGCTTAAGAAAATCCGCCTGGACACTGAGACTGAGGGTGTGCCCAGTAC
TGCCATCCGAGAGATCTCTCTGCTTAAGGAGCTTAACCATCCTAATATTGTCAAGCTGCTGGATGTCATT
CACACAGAAAATAAACTCTACCTGGTTTTTGAATTTCTGCACCAAGATCTCAAGAAATTCATGGATGCCT
CTGCTCTCACTGGCATTCCTCTTCCCCTCATCAAGAGCTATCTGTTCCAGCTGCTCCAGGGCCTAGCTTT
CTGCCATTCTCATCGGGTCCTCCACCGAGACCTTAAACCTCAGAATCTGCTTATTAACACAGAGGGGGCC
ATCAAGCTAGCAGACTTTGGACTAGCCAGAGCTTTTGGAGTCCCTGTTCGTACTTACACCCATGAGGTGA
CTCGCCGGGCCCTATTCCCTGGAGATTCTGAGATTGACCAGCTCTTCCGGATCTTTCGGACTCTGGGGAC
CCCAGATGAGGTGGTGTGGCCAGGAGTTACTTCTATGCCTGATTACAAGCCAAGTTTCCCCAAGTGGGCC
CGGCAAGATTTTAGTAAAGTTGTACCTCCCCTGGATGAAGATGGACGGAGCTTGTTATCGCAAATGCTGC
ACTACGACCCTAACAAGCGGATTTCGGCCAAGGCAGCCCTGGCTCACCCTTTCTTCCAGGATGTGACCAA
GCCAGTACCCCATCTTCGACTCTGA
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?
Below is the gene sequence from the program.
Range 1: 485 to 690Graphics Next Match Previous Match First Match
Features:
Range 2: 314 to 493Graphics Next Match Previous Match First Match
Features:
Range 3: 195 to 315Graphics Next Match Previous Match First Match
Features:
Range 4: 1 to 120Graphics Next Match Previous Match First Match
Features:
Range 5: 690 to 795Graphics Next Match Previous Match First Match
Features:
Range 6: 117 to 195Graphics Next Match Previous Match First Match
Features:
Range 7: 149 to 160Graphics Next Match Previous Match First Match
Features:
Range 8: 333 to 343Graphics Next Match Previous Match First Match
Features:
Range 9: 726 to 736Graphics Next Match Previous Match First Match
Features:
Range 10: 744 to 754Graphics Next Match Previous Match First Match
Features:
Alignment statistics for match #1 Score Expect Identities Gaps Strand Frame 372 bits(412) 3e-106() 206/206(100%) 0/206(0%) Plus/PlusExplanation / Answer
1) With respect to genomic DNA, the RNA polymerase will read the protein from right to left. The CCDS and the genomic DNA are in the same orientation 5'-3' and the CCDS sequence is same as the genomic DNA and not complementary to it. This indicates that the other strand of the genomic DNA is translated is used as template to transcribe into mRNA. Thus this will produce the CCDS sequence given in the question.
2) It has 6 exons
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