NCBI Genome Database - Comparing Hemoglobin Genes
Name ________________________________ Period ____________
NCBI (National Center for Biotechnology Information) is a huge database where DNA sequences from labs all over the
world are deposited. It contains an enormous amount of information about many different organisms, including
humans, that is available to anyone at no cost. The database is easily searched using a free program called BLAST (Basic
Local Alignment Search Tool). In this activity, you will learn how to use these databases and BLAST to compare a human
and chimpanzee hemoglobin gene.
Find it:
1. What is hemoglobin? ___________________________________________________________________________
2. What is the HBB gene and on what chromosome can it be found? _______________________________________
_______________________________________________________________________________________________
3. What is an exon and an intron? ___________________________________________________________________
_______________________________________________________________________________________________
4. Describe the relationship between DNA, proteins, and amino acids.______________________________________
_______________________________________________________________________________________________
5. About how long ago did human and chimpanzees share a common ancestor?______________________________
Procedure:
Part I – Human hemoglobin exons and introns
1. Go to ncbi.nlm.nih.gov
BLAST.
This is the NCBI home page through which you can access both the DNA databases and
2. Type HBB homo sapiens in the search box at the top.
3. On the left of the new screen, click on “nucleotide: core subset of nucleotide sequence records”.
4. Scroll down to click on Homo sapiens beta globin region (HBB@); and hemoglobin, beta (HBB); and
hemoglobin, delta (HBD); and hemoglobin, epsilon 1 (HBE1); and hemoglobin, gamma A (HBG1); and
hemoglobin, gamma G (HBG2), RefSeqGene on chromosome 11
5. On the right sidebar, under “Related Information”, click on “Gene”.
6. Scroll down to #7 HBB and click on the HBB.
7. Scroll down a little until you see, in a gray box on the left “Genomic regions, transcripts and products.”
Click on “Reference sequence details”.
8. Click on the word FASTA. You will see a series of 1606 nitrogen base letters that are in the hemoglobin
gene.
9. Copy this sequence and paste it into a Word document. Type your names at the top and give it a title when
you save (click File, Rename)
Part II – Compare to chimpanzee beta hemoglobin
10. Go back to the NCBI home page by clicking on the NCBI logo at the top of the page. At the top and in the
right sidebar under Popular Resources, click on BLAST.
11. Under BLAST Assembled RefSeq Genomes, click on Pan troglodytes (the species name of
chimpanzee).
12. In your Word document, copy the first DNA sequence you pasted (the HBB homo sapiens). You will paste
the sequence in the big, white box of the NCBI BLAST page that says “Enter accession number(s)….” . If
there are any words in the box, delete them first before pasting. This is your query.
13. Scroll to the bottom of the page and click on BLAST. It takes some time for the sequences to come up, so
be patient.
14. Scroll down to see the Human-Chimp DNA comparison for the beta hemoglobin genes. The “Query” is
human beta hemoglobin and the “Subject” is the chimpanzee beta hemoglobin. You will notice that there is a
vertical line between each identical nitrogen base and no line if there is a difference.
15. Copy the entire gene up to where you see this for the “hemoglobin subunit beta”:
stop copying here
See – this is no longer human beta globin.
We don’t want this sequence.
Then paste it into your Word document. SAVE IT. Then print.
Analysis:
18. Look at the copy of the HBB gene on the next page. There are 3 exons and 2 introns. You can identify
the exons because I have made the font slightly bigger, bold face type and highlighted. On your printout,
identify and highlight the 3 exons of the human/query.
19. Using your codon translator, identify the amino acid sequence of one of the exons – you choose! Write it
on your Word document just above the exon sequence.
20. Look carefully at the Human and Chimp sequences. Are the exons identical? ___________ Circle all the
differences you find with a pen. How many differences are there? ______________
21. Despite the differences, would the chimp amino acid sequence be the same? Explain why or why not.
22. Are the introns identical? ______________ Circle all the differences you find with a pencil. How many
differences are there? ____________
23. Mutations occur over the entire genome at the same rate. So how can you think of an explanation for the
results above? Hint: it has to do with evolution/natural selection.
HBB gene:
70501
70561
70621
70681
70741
70801
70861
70921
70981
71041
71101
71161
71221
71281
71341
71401
71461
71521
71581
71641
71701
71761
71821
71881
71941
72001
72061
72121
72181
72241
72301
gccagggctg ggcataaaag tcagggcaga gccatctatt gcttacattt gcttctgaca
caactgtgtt cactagcaac ctcaaacaga caccatggtg catctgactc ctgaggagaa
gtctgccgtt actgccctgt ggggcaaggt gaacgtggat gaagttggtg gtgaggccct
gggcaggttg gtatcaaggt tacaagacag gtttaaggag accaatagaa actgggcatg
tggagacaga gaagactctt gggtttctga taggcactga ctctctctgc ctattggtct
attttcccac ccttaggctg ctggtggtct acccttggac ccagaggttc tttgagtcct
ttggggatct gtccactcct gatgctgtta tgggcaaccc taaggtgaag gctcatggca
agaaagtgct cggtgccttt agtgatggcc tggctcacct ggacaacctc aagggcacct
ttgccacact gagtgagctg cactgtgaca agctgcacgt ggatcctgag aacttcaggg
tgagtctatg
ataggaaggg
cagtgtggaa
tcttttgttt
aatgccttaa
aaaaaaactt
gcatattcat
acatatttat
gtaattttgc
tcttatttct
atgcctcttt
atatctctgc
tgctaatagc
tggattattc
ctcccacagc
ggacgcttga
gataagtaac
gtctcaggat
aattcttgct
cattgtgtat
tacacagtct
aatctcccta
gggttaaagt
atttgtaatt
aatactttcc
gcaccattct
atataaatat
agctacaatc
tgagtccaag
tgttttcttt
agggtacagt
cgttttagtt
ttcttttttt
aacaaaagga
gcctagtaca
ctttattttc
gtaatgtttt
ttaaaaaatg
ctaatctctt
aaagaataac
ttctgcatat
cagctaccat
ctaggccctt
ccccttcttt
ttagaatggg
tcttttattt
ttcttctccg
aatatctctg
ttactatttg
ttttattttt
aatatgtgta
ctttcttctt
tctttcaggg
agtgataatt
aaattgtaac
tctgctttta
ttgctaatca
tctatggtta
aaacagacga
gctgttcata
caatttttac
agatacatta
gaatatatgt
aattgataca
cacatattga
ttaatatact
caataatgat
tctgggttaa
tgatgtaaga
ttttatggtt
tgttcatacc
agttcatgtc
atgattgcat
acaattgttt
tattatactt
agtaacttaa
gtgcttattt
taatcattat
ccaaatcagg
tttttgttta
acaatgtatc
ggcaatagca
ggtttcatat
gggataaggc
tcttatcttc
tcctgggcaa cgtgctggtc tgtgtgctgg cccatcactt tggcaaagaa
ttcaccccac cagtgcaggc tgcctatcag aaagtggtgg ctggtgtggc taatgccctg
gcccacaagt atcactaagc tcgctttctt gctgtccaat ttctattaaa ggttcctttg
ttccctaagt ccaactacta aactggggga tattatgaag ggccttgagc atctggattc
tgcctaataa aaaacattta ttttcattgc aatgatgtat ttaaattatt tctgaatatt
ttactaaaaa gggaatgtgg gaggtcagtg catttaaaac ataaagaaat gaagagctag
ttcaaacctt gggaaaatac actatatctt aaactccatg aaagaaggtg aggctgcaaa
cagctaatgc acattggcaa cagcccctga tgcatatgcc ttattcatcc ctcagaaaag