a. Download a nucleotide sequence from GenBank for a gene of interest. What gene

Question

a. Download a nucleotide sequence from GenBank for a gene of interest. What gene did you download? Was the sequence published? Where, when, and by whom? What format is your nucleotide sequence in? Why is this gene of interest?

b. Perform a BLAST search with your DNA sequence. What does it match to (show the top 10 hits)? Are they from the same study or different studies? Is your sequence protein coding or not? What is the E-value of hit number 10 compared to hit number 1? What is an E-value?

c. Produce a pdf file with a short fragment (no more than 500 bps) of your sequence and the top 5 hits from your BLAST search showing them in FASTA format plus hits from at least 3 different species. What species are included in your data? List the taxonomic hierarchy of these species?

d. How many characters are in your FASTA file? How much space would you need to store a FASTA file of a human genome? A bacterial genome? A viral genome? How did you calculate this?

e. Translate the following sequence to amino acids (assuming the reading frame starts at the first letter):

ccgtcgtagc accgagcctc agcaccacga aagagattga agtagttcct cggaaagttc ttcgactctt ccttgaaaca tgtcttcctg gagcaaccaa cctgccatgg atgattatgg

What does this sequence encode? From what organism does this sequence come? What is the function of this gene? What are the proportions of polar, non-polar, and charged amino acids (attach a link to or copy of the resource you used to help you determine this)?

Explanation / Answer

Gene Name: ARGONAUTE 1 (AGO1), ICU9
Gene ID : AT1G48410
Gene Description: Encodes an RNA Slicer that selectively recruits microRNAs and siRNAs.
>AGO1 genomic sequence 6490 bp
gtaaaatctcatttctttgagttatctcgtttgttcggagttagagagagagagaaagat
atagagagaacacagagaggcgagagcgacgtagggttggtgtttcgtacggattttctc
ggtcaatcttagtttctccggcgagagattgcttttcaggtaaaaatggcggcggttttg
gtgtttgttcttcacttaatctgtgttcgatctgcgtatgaactcgatttttccactcga
ttgggtggatccgcttcgttttggtgttatggttcactgatagtgttgtatgtttagttg
atctttgcgatttcggatctattagcttcgtagctgttttggtgtgtgtgttcgtcttcg
aagatatttaggttttttttttttgttgcttcaaatttcttactgtttcgtgcttgtttt
cttacttcgttttctgtttaggtctttgattgtttcttactaggttttctatgtttgctt
tgggctgttgaatttggttttctatctctctagctaatcactggttttcgtgcttctgag
tcgtttgtttttgaagctagttagggttttcttctgttgcttctatatttcgatagtttt
gtgcttgttttcaatgtttgcttcttattttcaaggataattttaaaatgacccactgtt
tttgggtggttgtgttattttcacaggaatcatcATGGTGAGAAAGAGAAGAACGGATGC
TCCATCTGAAGGAGGTGAAGGCTCTGGGTCTCGTGAAGCTGGTCCAGTCTCAGGTGGTGG
ACGTGGTTCACAGCGAGGTGGTTTCCAGCAGGGAGGAGGACAACACCAAGGTGGAAGGGG
TTATACTCCTCAACCTCAACAGGGAGGTCGTGGTGGTCGTGGATATGGGCAACCACCACA
ACAGCAACAACAGTATGGAGGACCACAAGAGTACCAAGGAAGAGGAAGAGGAGGACCTCC
TCATCAAGGAGGTCGAGGAGGGTATGGCGGTGGCCGTGGAGGTGGACCTTCTTCTGGACC
ACCGCAGAGACAATCAGTTCCCGAGCTGCATCAAGCTACCTCACCTACTTATCAAGCGGT
GTCTTCTCAGCCTACACTGTCTGAGGTGAGTCCTACCCAGGTACCAGAACCTACTGTTCT
GGCTCAGCAATTTGAACAACTCTCTGTTGAACAAGGAGCTCCCAGTCAGGCAATCCAGCC
TATACCTTCTTCTAGCAAGGCTTTCAAGTTTCCAATGAGGCCTGGTAAAGGACAGAGTGG
AAAGCGTTGCATTGTGAAGGCTAACCATTTCTTTGCTGAACTGCCTGATAAGGATTTGCA
CCATTATGATgtgagttttgtgttcccttagtattagctaccatacatctaatgtctatt
tataaatttacctgaccaactgtgttctttctgttagGTTACCATTACTCCGGAAGTTAC
ATCAAGGGGTGTCAATCGTGCTGTGATGAAACAACTTGTTGATAATTATCGTGATTCTCA
CCTTGGAAGTCGTCTTCCAGCGTATGATGGTCGAAAAAGTCTTTACACTGCTGGTCCACT
TCCCTTTAACTCCAAGGAGTTCAGAATCAATCTTCTTGACGAAGAAGTAGGGGCTGGAGG
TCAAAGgtctagttcttatggtttcttgttgatttttttaataaggaagtttcagaataa
taacatctttcctattttacagACGAGAAAGGGAATTTAAAGTTGTGATCAAGCTAGTTG
CACGTGCTGATCTGCATCACCTAGGAATGTTTTTGGAGGGGAAACAATCAGATGCCCCAC
AGGAAGCTCTGCAGGTTCTTGACATTGTTCTTCGTGAGCTGCCGACCTCTAGgtactggt
tactcatcctatggatgtttgcttctttactaccatgcttgtaagtctcagctggtttag
ttttgctaacatgttagAATCAGGTATATTCCGGTGGGCCGGTCCTTTTATTCCCCTGAT
ATAGGAAAAAAACAATCATTGGGGGATGGCTTGGAGAGCTGGCGTGGATTCTACCAAAGC
ATTCGTCCTACACAGATGGGCTTATCACTCAATATTGgtgtgatggcttgctgtattaca
ttcaataatttttgatatctggttctccttgaatgtttaactcatggttgtgctgcaatt
ttgtctgttttgtagATATGTCATCGACAGCCTTCATAGAGGCAAACCCTGTGATTCAGT
TTGTCTGTGATTTGCTTAACCGGGATATTTCTTCTCGACCTTTATCTGATGCTGATCGTG
TTAAGgtatgaatcaattgtcattttctgtagtaagtgaaatgttgtattaatctactct
tctttgcttagtgacttggaatcttcttctgtcaacagATAAAAAAGGCTCTTAGAGGTG
TCAAAGTTGAAGTGACTCATCGAGGAAACATGCGCCGGAAGTACCGCATTTCCGGTTTGA
CTGCTGTGGCCACTCGGGAATTGACgtgcgtatttgttttagatttactactcttatttc
gcgaatgttgaacttgatgaaattaatttttactctctgtttttatccttttcagATTCC
CAGTAGATGAAAGAAATACTCAGAAATCTGTTGTAGAATACTTCCACGAAACATATGGTT
TTCGCATTCAGCACACTCAACTACCATGCTTGCAAGTTGGGAATTCTAATAGGCCTAATT
ACTTACCAATGGAGgtaactttgaaatacgtcatcaggttttattagctcaccagtactt
ccgattctaatgtgttgctgcacagGTATGCAAGATTGTTGAAGGCCAGCGGTATTCCAA
AAGATTGAATGAGAGACAGATCACTGCTTTGCTGAAGGTTACCTGTCAGCGCCCGATAGA
TCGAGAAAAAGATATCTTACAGgtatgtttctttattttcgataactttgttttccttca
cttgaatcaagagtatctttttgtccgcctatcttgatagtcgttttaaataatgtatgc
tggtgataaagcctcattgtggaatagatcattgtaaaatctgtttattcttacttggtt
gcatgtgtttacttgaagtaagtgattttctcaattcatatctaacttgtttttaatcat
ataaacttgtggctgaaaggatgttatggaatgaatggcttaaaaacctgtttcttcttt
acttggatgcatatgtttgcttgaagagagtgatttaccttgagatgatgcctttacttc
ataaatagtgaggcagattaccatcttcagagttgtgctcttaatttagcagcgcgtgtg
tcttctggctgctgttgttgaaaactcaattgtttattgctaacattatacaatattttc
tgatttctagACGGTGCAACTCAATGATTATGCTAAAGATAATTATGCTCAAGAGTTTGG
CATCAAAATAAGTACTTCTCTGGCTTCTGTTGAGGCTCGTATACTGCCTCCTCCATGGgt
atagtaatcgttcccattgtctctttgctattacactttttctctgtatcttaatgactc
aaattagggttccaatctgattttaatgttctgcagCTTAAGTACCACGAGTCTGGAAGG
GAAGGGACTTGTCTGCCACAAGTTGGTCAATGGAACATGATGAATAAGgtaactagacga
aaatgttcctggttttcaactatgcacttacatgtttcttgcttgtgttacctatatata
cctatgctgtcatttttatgtgaatattttgtaaatcatggctgagctgtatatttccag
gtaattggcaagaaaattgtttatttatttgtctgttatgagacatattactctaaaatg
ctattctcttgatatgagtatgggtgtggcacttgactagttgcagagagtattttgttc
atgtagctatgtagatacacactgaatttgtctttgttattttttgaaagtgatcacaac
gttttctgttgtctggctaatatgagtcttctctgcagAAAATGATCAATGGTGGAACGG
TGAATAATTGGATCTGCATCAACTTTTCTAGGCAAGTGCAGGACAATCTAGCGCGTACAT
TTTGTCAGGAACTTGCTCAAATGTGTTACGTATCTGGCATGgtgagtctttggaagcaca
aacttgatcagtttattaacctttcctacactgattccttccctttaattttttatttct
tacctgcagGCATTTAATCCGGAACCAGTCCTCCCACCAGTCAGTGCTCGCCCTGAGCAA
GTAGAGAAGGTCTTGAAGACTAGATATCATGATGCCACATCAAAACTCTCCCAAGGAAAA
GAAATTGATCTGCTTATTGTCATTCTGCCCGATAATAATGGATCATTATACGgtatgagc
catggtctcggatgtttcattgtctacttctgcttaggaacacactctcaacttattttc
cttaataatatccattgcagGTGATTTGAAACGCATATGTGAGACTGAACTCGGCATAGT
CTCTCAATGTTGCCTGACAAAGCATGTCTTTAAGATGAGCAAACAATACATGGCTAATGT
TGCGCTGAAGATTAATGTGAAGGTTGGAGGAAGAAACACAGTGCTTGTTGATGCTCTATC
TAGGCGGATTCCTCTAGTCAGTGATCGACCCACCATTATATTTGGTGCTGATGTTACCCA
CCCTCACCCTGGAGAGGATTCAAGCCCATCTATTGCTGCTgtaagttagcttctccttta
agatctacttctgtatatggatgcttttgtttattttcatggccttaaccttttcaaatt
gtgcttgttttgttgacaacgaaatttttgttttcagGTTGTGGCATCTCAGGATTGGCC
TGAAATCACTAAATATGCTGGATTAGTTTGCGCTCAAGCGCATAGGCAGGAGCTCATTCA
GGATCTGTTCAAAGAGTGGAAGGATCCTCAGAAAGGTGTGGTGACTGGTGGCATGATAAA
gtacgtgtggatgttatttaatattttcgtgattgggttttagctttagcttgctcttaa
gtaacagatctgtacgtttctccccttacttttgaacagGGAGTTGCTCATAGCCTTCCG
TAGATCAACTGGGCATAAACCACTAAGGATCATCTTCTACAGgtattaactcttcttatg
gcacttacttgactaaataactttctgtctttctttctgaaatgtattatatggttattc
tgcacagGGATGGAGTCAGTGAGGGACAATTTTACCAAGTTTTGCTCTATGAACTTGATG
CCATCCGCAAGgtaacagttacttctaacaaatggcttgtgttgcgtgctcgttttcttc
tgtttaatctgattattatttcaactcatttcagGCCTGTGCTTCGCTGGAAGCAGGTTA
TCAACCACCAGTGACATTTGTGGTGGTGCAGAAGCGTCATCACACGAGGCTGTTTGCTCA
GAACCACAATGATCGCCATTCGGTGGACAGAAGTGGGAATATTTTACCTGgtgagacaag
tttggatctttgtcaagctttttgtgcgtagacctaatcagctgaaaatcccttgcattg
gtttttaacccctttgttaattgtagGCACTGTTGTGGACTCTAAAATCTGCCACCCTAC
AGAGTTTGACTTTTACCTCTGTAGTCATGCTGGTATTCAGgtataatttacaatctcaaa
tgagtttgtgggtgagaatttatttgaagtgtttaacaaatcaaaactccattaacagGG
CACTTCTCGACCTGCTCATTACCACGTTCTTTGGGATGAGAACAACTTTACTGCAGATGG
ACTTCAATCTCTGACCAATAACTTATGTTACACgtaagatttcttacctttgtaacatat
tccttgttacaagtgtttgcaagattgcaaggaaaataagagtaacatttaaactacctt
tttgatttgtacagGTATGCAAGATGCACACGCTCAGTTTCAATTGgtaagttttgtgtt
tcccatcccttaatgtcatcttgattttgatataaagaagagagagatttagtattcaat
gttttttttttttgttttgggatattgtagTTCCCCCTGCATATTATGCACATCTAGCAG
CTTTTAGGGCTCGATTCTACATGGAGCCAGAGACATCAGACAGTGGCTCAATGGCTAGTG
GGAGCATGGCACGTGGAGGTGGAATGGCTGGTAGAAGCACACGCGGGCCTAATGTCAATG
CTGCAGTGAGGCCACTCCCAGCTCTGAAAGAGAATGTGAAGCGTGTCATGTTCTACTGCT
GAgttgattcaccctctatctatctttatgacctaaattaatgaagaatatcatgtatgc
tttctaagacttatcgtgtgtttggatatttcatcactctttctctatgagtatgagatg
ctttatgactcttgtttgacaactactaaaatttattattcaaaacagactttgatcctt
tctttaactc

It is published by Arabidopsis genome initiative in 2003.
The gene sequence is in FASTA format.
AGO gene is involved in post transcriptional gene silencing.

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