>October 16 assigned sequence

ATGACCATGATTACGCCAAGCTCGGAATTAACCCTCACTAAAGGGAACAAAAGCTGGAGCTCCACCGCGG

TGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGATATCAAGCTTATCGATACCGTC

GACCTCGAGGGGGGGCCCGGTACCCAATTCGCCCTATAGTGAGTCGTATTACAATTCACTGGCCGTCGTT

GTGAACGGTCAGCAGTCGTCGTCTCCAGCTGAAGAAGGAATTCTTCCAAGTCAGTCAGCGCGCATTGAAG

TCATCGGCGTTGGTGGTGGTGGAAGCAATGCTGTCAATCGCATGATCATCAGCGATCTCGAGGGAGTGAC

CTATCGGGTGCTGAACACCGATGCCCAAGCCCTGATCCAGTCCGCGGCCGTTCATCGTGTTCAACTCGGT

GGGGCAAACCCTCACCCGGGGGCTCGGCGCTGGTGGCAATCCCAGCATCGGCCAGAAAGCAGCAGAAGAA

TCCAGAGCTGATCTTCAGCAAGCCATTCAGGGTTCTGATCTGGTCTTTATCGCCGCAGGCATGGGCGGCG

GAACCGGAACTGGCGCAGCCCCCGTTGTCGCTGAGGTCGCCAAGGAAAGTGGTGCGCTCACAGTCGGCAT

CGTCACCAAACCCTTTGGATTTGAAGGTCGCCGCCGGATGCGTCAAGCCGATGAAGGGATCGCACGTCTT

GCTGAACATGTGGACACGCTGATCGTGATTCCCAATGACAGGCTCAGAGATGCCATTGCAGCAGCTCCTC

TTCAGGAAGCATTCCGCAGTGCCGATGACGTGTTGCGAATGGGTGTGAAGGGAATTTGCGACATCATCAC

TTGCCCAGGCCTTGTCAATGTTGATTTTGCCGACGTGCGTTCGGTGATGACCGAAGCCGGTACAGCTCTG

CTTGGTATCGGCGTCGGATCCGGTCGCTCTCGTGCCATCGAAGCGGCTCAGACTGCGATCAACAGTCCAC

TCCTCGAGGCGGCTCGGATCGATGGTGCCAAGGGATGTGTGATCAACATCAGTGGTGGTCGTGACATGAC

CCTCGAAGACATGACCAGCGCTTCAGAAGTGATCTACGACGTGGTGGATCCTGAAGCGAACATCATCGTG

GGAGCCGTGGTGGACGAAGCTCTCGAAGGGGAAATTCACGTCACTGTGATTGCCACGGGTTTTGAAAGCG

GCCAGCCCTATCGCAGTGAGCGAAGCATTCCAAAACCGGCAGCCATGCCTTATGTGTCCCCTGAACCCAT

GGATGCTGGAGCAAGGATTCCCGAGTTTTTGCGTCAGCGTCAATCCCGCACTGATCAATCAGAATGATTA

CAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCA

GCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATG

GAAATTGTAA

Your assignment:

Learn all you can about this sequence. Make a visual model of the entire sequence. You should account for the entire sequence including vector sequence, introns, protein coding regions, indels, and any other characteristics you find. Aside from the primary homolog of the central gene, can you find a second homolog of this gene?

You should try to work through this assignment entirely on your own (later in the semester you will be given sequences like this as homework. However, if you get stuck, look here for some hints.

You may find the following programs that you have used previously helpful.

blast (you may want to use several flavors)

emacs (ctrl x ctrl s to save and ctrl x ctrl c to close)

needle

water

You may also need the following new programs.

Psi-Blast (NCBI)

transeq (EMBOSS)

If you finish early, try some of the sequences in the homework for 2000.