OPEN READING FRAMES

Open reading frames (ORFs) are potentially protein encoding segments of DNA. They consist of all potential codons bound by a start codon and a stop
codon. Analyze the given example then complete the required tasks.

EXAMPLE

Sample DNA Sequence: By convention, single-stranded DNA sequences are written in the 5’ to 3’ direction. Double-stranded DNA sequences are written
with the top strand oriented in the 5’ to 3’ direction and the bottom strand oriented in the 3’ to 5’ direction. (The given is a single-stranded DNA sequence.)

CAGAATCCCTGACCGCCCTGATGTTAACTCACGCCAAGGGTTCCACCTTAACTGAGAAAA
GCATTACTTGTCGATGAAAACATGGGAGATTTTAAACTGGTACCTTGTTAGTAATCGACC
GCTGACAGGTTACCTACTTATGTACTTGCGGTGTGATTGCATGTACTGGCACCTTAGAGA
AAACCGAGTGATTTTTGCGTTAAATGCCTGTCTGAGCCTCTGGAAAAGGTGCGTCACCAC
GGTGTAGAAGCCCACCAGGGGATGCCGGTAGAGGTCAGAAGCAACGGAACGCCCGAGAAC
CGGTAGGGTGTGCGATAGGGCGGGTAAAGAGATTTTCCGACTAAGATGCGTAGCGGAACC
ATGAGAGTTCCTGCTCTGTTAGAGGTTACGAATCCTAGAAGGTACGTAAACAGTTTTATT
TCTTTAGCATGCCCGGCTTTCTCCGGAGCTAAAAGAGTGTCTGGTTTAATCCATTCATGC
ATCCACTGAGGACCGGAAGTATCGAGATTCGATGTCCTAGACATTAACTATCCCGTAAAA
CAACGACTTGTAGTCCTTCTATTTCCCAAGGATCAGCCGTAAGCGTAGGGTGCACCAGAA
TGAGGGTACTGGTGCTATATAGCATGAACGGTAGTTACCGCATTGCGGGCCAACTCAGCA
CATAATAAGTTAAGAGAAGCACACGAGAAAGTGAATAGCCCAAAAAGTTTGGGGTTTGAC
ATAATAGGTCGGTCTCAGGTTAGGCAAACGAGTGTAGAGGTCCAGGAAACACTTGATCTT
TGCCCGTCTGTGGTCCAAGACAACACTCTCCCTGAAGCTGCAGGTGTAAAGACGCAGCAG
CGTTGTCCGTATCAGCATCACAGCCCCAGTCGGATCGCGGACCTGGCGCGGAGTAGGACC
GAATCCTGTTGACATTCCATAATCTCTTGTCAGCGGTCTTCCTGGTCCCACGCATCACGA
TCTCAACCCGTTAGTGGATTGCGCTAGGTCACCGCGCACC

Open Reading Frames: ORFs are systematically determined in a given DNA sequence by locating a start codon from:
1) the first reading frame in the left-to-right direction (spans the first, second, and third nucleotide as they appear in the given sequence and in the
given direction and every nucleotide triplet thereafter; denoted as forward or direct reading frame 1 OR reading frame +1);
2) the second reading frame in the left-to-right direction (spans the second, third, and fourth nucleotide as they appear in the given sequence and in
the given direction and every nucleotide triplet thereafter; denoted as forward or direct reading frame 2 OR reading frame +2);
3) the third reading frame in the left-to-right direction (spans the third, fourth, and fifth nucleotide as they appear in the given sequence and in the
given direction and every nucleotide triplet thereafter; denoted as forward or direct reading frame 3 OR reading frame +3);
 4) the first reading frame in the right-to-left direction (spans the first, second, and third nucleotide as they appear in the given sequence and in the
given direction and every nucleotide triplet thereafter; denoted as reverse reading frame 1 OR reading frame -1);
5) the second reading frame in the right-to-left direction (spans the second, third, and fourth nucleotide as they appear in the given sequence and in
the given direction and every nucleotide triplet thereafter; denoted as reverse reading frame 2 OR reading frame -2); and,
6) the third reading frame in the right-to-left direction (spans the third, fourth, and fifth nucleotide as they appear in the given sequence and in the
given direction and every nucleotide triplet thereafter; denoted as reverse reading frame 3 OR reading frame -3).

The table below summarizes the ORFs identified from the sample DNA sequence given. For this activity, only ORFs containing five codons and higher were
included.

Location Span Translation Product

reading frame +1 base 82 to base 111 MGDFKLVPC
reading frame +1 base 262 to base 306 MPVEVRSNGTPENR
reading frame +1 base 346 to base 489 MRSGTMRVPALLEVTNPRRYVNSFISLACPAFSGAKRVSGLIHSCIH
reading frame +2 base 74 to base 247 MKTWEILNWYLVSNRPLTGYLLMYLRCDCMYWHLRENRVIFALNACLSLWKRCVTTV
reading frame +3 base 21 to base 77 MLTHAKGSTLTEKSITCR
reading frame +3 base 429 to base 452 MPGFLRS
reading frame +3 base 477 to base 527 MHPLRTGSIEIRCPRH
reading frame +3 base 600 to base 665 MRVLVLYSMNGSYRIAGQLST
reading frame -1 base 46 to base 261 MRGTRKTADKRLWNVNRIRSYSAPGPRSDWGCDADTDNAAASLHLQLQGECCLGPQTGKD
QVFPGPLHSFA
reading frame -1 base 376 to base 477 MLYSTSTLILVHPTLTADPWEIEGLQVVVLRDS
reading frame -1 base 523 to base 552 MNGLNQTLF
reading frame -1 base 571 to base 585 MLKK
reading frame -1 base 937 to base 972 MLFSVKVEPLA
reading frame -2 base 86 to base 331 MSTGFGPTPRQVRDPTGAVMLIRTTLLRLYTCSFRESVVLDHRRAKIKCFLDLYTRLPNL
RPTYYVKPQTFWAIHFLVCFS
reading frame -2 base 839 to base 871 MQSHRKYISR
reading frame -3 base 81 to base 143 MECQQDSVLLRARSAIRLGL
reading frame -3 base 279 to base 386 MSNPKLFGLFTFSCASLNLLCAELARNAVTTVHAI
reading frame -3 base 477 to base 767 MSRTSNLDTSGPQWMHEWIKPDTLLAPEKAGHAKEIKLFTYLLGFVTSNRAGTLMVPLRI
LVGKSLYPPYRTPYRFSGVPLLLTSTGIPWWASTPW
reading frame -3 base 918 to base 953 MFSSTSNAFLS

GROUP TASKS

1. Evaluate the DNA sequence assigned to your group.

2. Systematically identify the first ORFs containing five codons and higher in the six reading frames (i.e. reading frame +1, +2, +3, -1, -2, and -3).
3. Organize your output in the table provided. Have your output printed out near the end of the period.
4. Turn in your output to your class representative at the end of the period. Class representative, submit your class output at the MolBioLab.
Group 1: __________, __________, __________, __________, __________, __________, __________, __________, __________ Class Code: ____ Sched: ____

CACCGTTGGTAATGAGTCAATCCCGCGGCAAGGCCGCCATGGTCTCAACTCGAGACTAAC
TAACAAGCTACGGCTCGTCGTGATCTCTTCTCACGAATCGAGCTGACTTGCTCGAGAATT
CTGCCCGCTATGAGGCCTGGACCTAGTACTTGAGCCTTAATGCCCATGTAGTGGACTTGA
GATTTGGCGCTTACAGCCTGACCCGGTTTACCAACGAAACATACCTTTTACCTCAACTCG
GAGGCTGTCGGCGCTGAGGGGCAACTAATCTCCGAGAGGTGTCTGGACCTCCCGATCCGA
ATATAAGGGTATCTTGAAAGGGCCTACTCTGGCTAGGCTTAATGGTTGATCCTCGCATCT
CCAGCAGTATAACCATGTGTGACAACCAAAAGGGTGATGTGAAAGTTAGTACGGGCTAGA
GCTACCCTTTCAATTCTCTGTGCGCTCGACGTCATGTGGGAAGGGAAGTCACGTGTCCTG
GTCGTCTGTCTGGGGGAATTCTGGACCGGCCGCCTGTTGGTGAGTAGGGTACTTCACCCC
CCACTTCATAGTGCACGGGGCCCTCACGGGTACGTTATTCCCTTTAGCATTAATACGGCC
CTCACATCCTTTCGAACGACCTGGTACATACGAGCTAGGCCTTTTGGGGGGGAAGACGTA
GAGAGAAAGAGCTGGGAAACCGCGTGCATCACATGAAGGTTGAGGCCCCAGTTGAACGGC
GAAGGTATTGTTGAAGACTTCTAATACGCGATGGACTGATACAATTCCCGAGTGCAATTC
TGTGTAATCCTGACCCGATTGCATAATGCCCGCTTGGAATGCTTAACCCCCAGCCAGCGT
ACGTACCGTTGGCGACTTGGGAAAGAGGGACACTTGAGCGTCTTATAGGTGGTGTGGTCA
GTTGAGAGTCAACTGGATCTAAGGCATTTGTTTCGATTACGTTACGTATAAAGAGTTTGG
CATGATCATATAATTTAGTCGAAGGCTGGTTCAGCGCAAA

Location Span Translation Product

reading frame +1

reading frame +2

reading frame +3

reading frame -1

reading frame -2

reading frame -3
Group 2: __________, __________, __________, __________, __________, __________, __________, __________, __________ Class Code: ____ Sched: ____

TCAGATAACCTGGAGTTTACCTAGCCATGCTGTGCGCATCGCCACGACTGTGGCCGTTAA
GAGCAGTGCGTATGATCACGTGCTGCATATCCAGGTGGAATAAGTAATAGTGAGATAGAG
GAAGGGCGGATCTGCGCGTACCAGGGGGGGTATCGAGCTACCGCCCTGCATCGGACTGGT
AAGGGATTCCGGGCGAGAGCTATAGGCTTAGAGTCTGTTAAAACCTCATTCTAAAAATGC
CTAGAGCATGACGTCTCCGTTTAATTGTTGACTACCAAACAATCGATCACTGTCTAACGC
TTAGGCTTATACCTTATATGAATTGTTATTTGGGTTAGGTCCTATGGAAGGCGCTCTCCG
TATGAAGTGGATGAGCTGCCGGCGATCCATCAACCCAAGAAACAAACGATTTTGTGAAAG
ACGCCTAATTTGCCAGACTCGGGCTCACACCGTAATGAGGAATATGGGGAAAAGGCCTTA
GATCCGTGAACGTAGGATACACCTCCCAGGACGGAAACGTTAACTGAGGTAATCTGTTCC
TCTAAACCGTGCTGGTCTGTTACGGACCACCCAGAGTACGTGAGAGGATCCACATCGACG
TTTCTGCTCGGCCCGGTGACTTAAGGGGGTCCCGCAAGCACCGCAGGGCGTGGATTCTTG
GAAGGAAACAATCGCCCAAGCCATAGCGTGATAAGTCACATTTATGATGATAAAGCGTGC
TACGTCGGCCTGCGGTGAGCGAATTCGAGCGGGGGCACCGTGAGCGAGCCTCTGTACCTT
CAAAGTTTTAGGAAGTCGTGACGGTACCGATGTAGCCCTTGTCTAACTCCGAGCACCAAC
CGCATTATCCTCTTCTGAAGTATATCACTTCAAATGCCGAAGAGCACCGTTCTCCTCTAT
TGGTCTCCGCGATGGAATCAACGGGGACACACCGAATGAAAGTCACCCAAATCTTACAAC
CCGGCTAGATTTCTGCGGGAGCCTCCTCCCGAATGTTGCC

Location Span Translation Product

reading frame +1

reading frame +2

reading frame +3

reading frame -1

reading frame -2

reading frame -3
Group 3: __________, __________, __________, __________, __________, __________, __________, __________, __________ Class Code: ____ Sched: ____

ACACGCATCTGTTAATGCAGGCCGTTTTGGAGCCGGCCACAAGTCACGTCGCCACGCATT
TGAAACCCAAACTTTACACTCTATCCCTATCTTTTCTAGTCCCGACGAGCGCCATATGTT
GCACAGCGCGCATCGATTCATGAGAGGTATTATTTCCTTTTTCAAGTGCTAGTCTAAACA
CTCCAGCGCAGCTCGCTCGGAGGACCACAATGCCGAGGTTTGTGGTTTATTGGTTGTGGG
CTGCCCTGAGTTCCCTAATTCCAGCAGTCGATTCCAGCTAACAACCGGCCCAGCAGAATG
CATTTGTGAGTAGACTCAAAACATACACAGCAAAGAAAAGATGTAAAGAACGACGTGTAG
AGCCTTTGAGCTTTGCAACTGAATATGCTAACCTAAGGAGAAACATATGCAACTAAAGCA
CGTGCTACACTTGCATATGGCGTGCATTGTTCGCGAAACTATCCGAGAAGGGAGGCGTCA
CGCGTCCCGCACACTTAGATTAAGTGTGCTAAGAACTGCAGAGGTCAGTAGCAGCCAGGA
GGGAACGGGATATTCCGTGTGCCCTCTTGTCAGCCTCATGATCGTCAAGGTATAGTTTAC
TGCCTGTCCTGAGCGAGTGCTAATCTGATCGCCACAGGCCGGCAATAGCAAGGTGCCCAA
AATAAATGGTGGGATAGGTACGTTATGTTTATAATTAGTGAAACGGTAATTTGTCGGTGC
CTCCTAAACGGGAAAGGCACATGAAATTGTATGACGACCTGATTCCTTACCGCAAGTACA
GTGGAATCGAGAGGAGCGGGCACGTTTATGACACCCGACTTTCAAGTTAGCACTGGATGA
CAGAGACGAATACTATTACCGGCGCTCGAGGGCTTCCGTCGAGCGATGGTACTGGTAGTA
CTTAAATGACAAGCCGTCCGCAAACTCAGCAAGGGGGCTGAGGGTCGTGCGTCGCCCACC
CGCAAGTATGCTGATGACAGATGTTTGGCGCAGTGCAGGA

Location Span Translation Product

reading frame +1

reading frame +2

reading frame +3

reading frame -1

reading frame -2

reading frame -3
Group 4: __________, __________, __________, __________, __________, __________, __________, __________, __________ Class Code: ____ Sched: ____

AATGACTTAGCTCGGGGGCGTCCGCAAGGATTTCCAGTAAGGCAGCGCATCGTTAGACTG
AACTATAAAGCTAGTTTACATATTCCACATTAGTGGTGGTACAGTAGAAAAGATTTCACG
CTGTTACGGTAAATCGGGGGACAATCGCACTCTTCGCGTTAAGTTAACCATTTTGCTTCC
GGTTACCTAGGCGTCCAAGGTATACCAAACTACCTGTCCTTAATTGCCTACAAAATCCTA
GCTCGAGAAGTATAAGTGACCTATCTGCATGACAACTTTCTGAGTCGGGTGCAGAGCAAG
TTCTAAGTTTACTCTGTCAGCCAGCAGCGTTTTTCTGCAAGTAACCATCAGACAGTCCTG
GTGCCAGCTGGATACTCGTTTTCAAGTATGTGTGCGTATTAGCGTAGTGAAGAACGAGTC
TCAGAGAAGTCCTAAATTGTTTGTCTCAGGCCCATAAGCAACCGATAACAGACGTTATAG
AGACGTAAAGCGGTGCTGAAATATTCTCGACGTATTGCAAGACTGGAGCACCGTTAGGGT
AAAGGGCTTTAATTTCGGCAATAGTTGGGGCACGCCCGGGCATAATTCCTCAGCCAGTAA
CCACAGGGCCCTTAATCAGCCAGAGCGAGCTGACCCCTTACATCGGAGAGTCTGGACGGA
ACCGCCGACTTATTATTGTTCTGTGATTCTAAGCCAGTACGTGGCAACAGTGGTGGGCAG
GACATACGAATTAGCGGCTTGGAGAGGCGCACGGCTGGAATTGTCTTAGGGCAGGGTAAG
CCGGGTTTATATAGGGTAGTCGAATCACCATTACCCTTTGCAGCATCGAAGTTGACTGCG
CAATGGTGAGTCGTGTACGAAGGCGATAATCATAGTATGCATAATGTACTACAGCGTATA
CTATACTCCAACCGGTACTGGGGCTCCTTACTTGAGCGGCCAGGGGGCCATCTATCTTGC
AGATCGTCGCTACTATATTCCCGGTGCTTGACGGGTAATT

Location Span Translation Product

reading frame +1

reading frame +2

reading frame +3

reading frame -1

reading frame -2

reading frame -3
Group 5: __________, __________, __________, __________, __________, __________, __________, __________, __________ Class Code: ____ Sched: ____

TTCAGTACATCTGGCTCCGTAGGCAATTCCGTAGCAAGGAAGCAACCTAACATCCGTGGG
TATAGGCGCAGAAAGCGGAAACGATGCGTCCGAGCCGCACGCCATGGCCTCTTGTCCTGC
CATTTGTCTTCGTAAGTTTGACGCTTAACCGAATAGAAACACGGTCCACGACCAATGACA
TATAAGCGTTATTGACGTCTAGGGTTATTCCTACAGGTAACAGAGGAAGGCATTGCAAGC
CCAAGACTGCCGCTTTATGAACCCCGGTTCGAGTGAGGTGGTGAACTGATTAATTAGACT
TGCCAGACACGCGGGACGCTCCCGCGGCCCCTAAATTATGTCTAGTATTTCGAACGCTTT
TCAGCAGAGGTCGGGGCTTTATCCACTTAGAGGGGCCCCATATTATTCTAGAAAACGAGG
ATTATAAATTCTGTCTTTGATGTTCCTATAAGTAGGGGCTGAAGAAGGTTACGGAACCAT
GCACTCTGCAATCATCATTCGACTACCGTTGGCCTCCCTTATTTCCGCAATGTAGACTCA
ACCAACGTTCCCTCATCCAGGGGTTTTTTGTAGACTATATCGGTTCCTGTGGACAGATCT
AGACGCGGGAAGCCTTCGAGCATCCGTATCCCATATGACCAATGTCAGGGGGTGGCCTTC
CGAAAGGTTAGACTACCAGCGTGTCATAGTGTTAACCAATCACTAGTTGGTTTACAAGTC
CTCGGCCTAGACCGCCACACTCTTGGCGTTCCAGCATAGTTGGCAAATAAAGGAGTTCTA
GTTACATCAAATGGAGTTCTCAGCTTCCCCCCTAATTTGGCGGGTGCTGAGACATAATAT
CTGGCTAGATATGATCATCGGTGGCTGATAGTACAAGGCGCACTGCAATAGTGACTCTGA
CTAGACTCCTGTCACTTAGGGTGATATTTCCCTAGAACTGTATAATGGAGGGGTACTTGT
TACATCATCGAGACTTTCTTAGTGCCTGTACCTGTGATCT

Location Span Translation Product

reading frame +1

reading frame +2

reading frame +3

reading frame -1

reading frame -2

reading frame -3
Group 6: __________, __________, __________, __________, __________, __________, __________, __________, __________ Class Code: ____ Sched: ____

GTTGAAAACTGCTAGATTCAAAATTGCCCCATGGTCGGTGTCGGGCTTGACGCTGCCGAC
CGACATAGGGCGATATTAGAGCCCGTTTAGAGGAACCGGGTGACAATTCGGTAACGCAGA
AAGCTAGACATGCATGAAGAGGTGCCCCGCGTGCACCCCGACGTGTTGGGTTAGTCAACT
CGTACCGCCATTCTCGGGAGCCTTCTTTCGTGGGCTATAGCCCCCGAAGCTTCGATTAGC
CTGCTTGCCATTCCGGCGCAGCAAGGCCCACGACTTGAGGGTTTGCTTCGGCGCCCCTTC
CCGGATTTATTCCTAGACCAACCAGCCCAGTGCCGTCCTCCTCATACGCCATACGAACAC
AACACGATTTACTCGCCTTCAGGATCCGAACAGTCAACCAAACAATAGTTCCAACCCAGT
GTGTGGCGCAGGAAAGGCCGCTAGGATCTCAAACATCAGATGATCTCACTTTTGTGTTCA
GATGGGAGGTACTATACCGCTTAAGCCCTAATTGTTATTATAGAGATAGGCTGACCTGAA
GATTCCAGTTGTGTACCCATGCACAGCGTGAGAGGGGTGTTTAACTTGCTGAGACGAGAT
CTCAAAAGACGTCATAGGCGCCTTAGACAAGGCTTTGTTACATGGGCCATGCCCAGCCGG
TCTCGGACCATTCAAAGTCTCTAGAAGTCGGGCCAGTGGAATCTGAACTCAGATACCAAA
AGGCGTACTATACTGAGTGGGCAAGTCGGCACGGTCTTTCCTACTGCCTGAGCCTGTGCC
GTCACATGCGCCGGTACGTCTGGGGCTTCCCGATCTTATAAAGGTCCCTCTAGAAACCGT
AGGCCAGAAGCAGTCAGTATGCGCCGTAGGAATGGAAGGTACATAGCTGTCCTATGATAG
TCTCGCTAAAGCCCTAGGAATTTTCTTACGCCACCCCTTGATGAATTCAGTCTCGGGACT
TACTGCCTCGTTCTGTCAAGCGAAACGATCGCAGACGCCT

Location Span Translation Product

reading frame +1

reading frame +2

reading frame +3

reading frame -1

reading frame -2

reading frame -3