Question 1: What is the number of entries for Animals, Plants and Fungi in the Genome database?

Animal: 748

Plants: 246

Fungi: 980

Question 2: Why are there so many hits for VIM in the database based on protein sequences?

Because VIM presents in many species and this gene is well studied.

On the GQuery page, there is also a hit in HomoloGene, the database that lists the eukaryotic homology groups. Here
information is shown for the same gene/protein in different species including a direct comparison of the protein sequences
(under Show Multiple Alignment). Open the link Homologene and follow the link to Vimentin with hgid:2538

Question 3: Give the common name for the 9 species that are listed under hgid:2538

H.sapiens, P.troglodytes, C.lupus, B.taurus, M.musculus, R.norvegicus, G.gallus, X.tropicalis, D.rerio

Question 4: What is the size of the vimentin protein in the different vertebrates shown?
Question 5: What part of the protein shows most of the differences resulting in the different sizes of the vimentin proteins
shown?

the first sequences

Follow the link to the human VIM gene. Examine the Gene page that contains very detailed information on the human VIM
gene and numerous links to other databases. Note that this Gene page can also be reached via the Gene hits on the GQuery
output page. Examine the information about genomic regions, transcripts and products.

Based on the NCBI homo sapiens Annotation shown under genomic regions, transcripts and products.:

Question 6: How many different transcripts are shown for VIM and do the transcripts shown code for identical or different
vimentin proteins?

2, they are the same

,

In genbank accessions that start with X*_ are predicted, while those that start with N*_ represent confirmed reference
sequences. (where *=M for mRNAs, *=P for proteins, *=R for non-coding regulatory RNAs and *=C for genomic contigs).

Question 7: What are the accession numbers of the RefSeq mRNA (NM_####) for this gene and the RefSeq protein
(NP_####)?

NM_003380.3, NP_003371.2

Question 8: Based on the RefSeq mRNA, how many exons does the human VIM gene have?

Question 9: Where on the genome is the VIM gene located (chromosome, position in bps)?

chromosome 10, 17,227,935..17,237,593

Question 10: What are the two protein coding genes that are adjacent to the VIM gene?

CUBN, TRDMT, ST8SIA6

Examine the homepage of the UCSC web site at Santa Cruz. Select Genome browser and again search for VIM. Select the
entry based on the NM RefSeq accession number (Question 7) which again takes you to the VIM gene in the genome browser.
The large white box with the detailed information for this gene. Contains several different tracks with different information. At the
lift you will notice small gray vertical bars showing the individual tracks. I you move your mouse over these vertical bars you csn
see what information is shown in each of these different tracks. In the track representing the GenCode annotation
Question 11: How many different transcripts are shown in the track representing the GenCode annotation? Are these identical
or different from the transcripts from the NCBI annotation (question 6)

3, different

Zoom out 10x. Also adjust the size of the image under configure to widen the view of the browser. Take time to examine the
information that is provided in this window. Notice that only a small fraction of the available information is shown. You can use
the drop down menus below the window to add, change or delete tracks displayed in the window. To show how this works, go
to the mRNA and EST tracks and set spliced-ESTs to full and click on refresh.
Question 12: What are the two genes adjacent to the VIM gene?

CUBN, HACD_1

Go to the tab with the link to Ensembl or open a new tab for the Ensembl web site and examine the home page. Open the link
view full list of Ensembl species. This page gives you the list of species that is covered in Ensembl.

From the home page in ensemble search human for VIM and on from the list of results follow the link to the human VIM gene.
There are several tabs. The tab Gene show specific information for the gene itself, while the tab location shows the genomic
location and adjacent genes. Note that you can jump from less detailed to more detailed views in the panels shown. You can
also adjust the images by clicking on configure this page in the left column where you can then open or close tracks.

Now lets briefly compare the human VIM gene to the VIM gene in a few other mammals.

Assuming you still have the VIM in the browser window, click on the tab Gene:VIM. Now in the left column of the window
under Comparative Genomics select Genomic alignments. In the new window, in the box Select an alignment type mouse
and select Mouse reference (Mus musculus) and click Apply and on the new page select View an image of this alignment.

On the horizontal blue bar of the panel showing the alignment, select the button Configure this page and for both human and
mouse under Genes and Transcripts change the GENcode 25 display to Expanded with labels.

Question 13: Compare the structure of the human and the mouse VIM genes. Are the VIM gene and protein structures
conserved between these species? Where do you observe most differences between these genes?

in the first exon of mouse

Lets briefly have a look at a comparison of the VIM gene between multiple species. Click on select another alignment and in
the new box select multiple and then 18 eutherian mammals EPO and Apply. For cow expand the GENcode 25 display to
Expanded with labels.

Question 14: Why do you think there is only 1 transcript identified in cow?

Research about VIM genes in cow is limited so its not annotated

Question 15: Based on the multiple alignment what is the most likely structure of the VIM gene in the eutherian ancestor?

The structures are all the same as the ancestors

Ensembl, NCBI and UCSC provides access to a huge amount of precomputed data and information, and in this first exercise
we only scratched the surface. Furthermore, often you might have research questions that are not covered by the precomputed
data. For example, within the homologene database at NCBI you only obtained information for the vimentin gene in 9
vertebrates, whereas for the multalignment at Ensembl, you used the vimentin gene for 18 mammals. In fact when you would
do a BLAST search against all vertebrates in the nucleotide database you would retrieve vimentin gene sequences for
hundreds of species. Lets explore this a bit further and perform a BLAST search of the vimentin gene against sequences
derived from the the fruitfly (Drosophila melanogaster, taxid:7227). To do so, at the NCBI select BLAST and then
proteinBLAST. For the query sequence use the human NP_ protein reference sequence and for the database choose the non-
redundant protein database. Limit your search to the organism Drosophila melanogaster (taxid:7227).

Question 16: What Drosophila protein (gene) shows significant sequence homology to the human vimentin? Does this protein
share a functional relationship with the vimentin gene found in vertebrates?
Question 17: Does the gene that you have identified also occur in vertebrates (e.g. human)? What does this suggest for the
evolution of these genes in animals?

Yes, lamina c gene is also found in human, chimpanze, rhesus monkey. It has almost the same function as
vimentin so probably in the evolutuion those genes are developed and separated due to some random
chances.