QuBi/modules/biol203-Lab4 - Revision history

imported>Weigang: /* Exercise 2. Explore the structure of human mdm2 gene */

2015-02-11T20:59:37Z

Exercise 2. Explore the structure of human mdm2 gene

← Older revision		Revision as of 20:59, 11 February 2015
Line 74:		Line 74:
	## Align the first 5 bases of all introns. Which bases are conserved near intron start ("donor site")?		## Align the first 5 bases of all introns. Which bases are conserved near intron start ("donor site")?
	## Align the last 5 bases of all introns. Which bases are conserved near intron end ("acceptor site")?		## Align the last 5 bases of all introns. Which bases are conserved near intron end ("acceptor site")?
	## ~~Follow examples and instructions on~~ [http://weblogo.berkeley.edu/ WebLogo] and make a sequence logo for the acceptor site and another sequence logo for the donor site.		## Using [http://weblogo.berkeley.edu/ WebLogo] and make a sequence logo for the acceptor site and another sequence logo for the donor site. To do so, copy & paste individual sequences at the acceptor site into [http://weblogo.threeplusone.com/create.cgi this text box] and click "Create Logo". Save the resulting image file and paste it into your notebook file. Repeat for the donor-site sequences.
	<center>		<center>
	Table 1. ''mdm2'' Exons		Table 1. ''mdm2'' Exons

imported>Weigang: /* Exercise 1. Homology searching using BLAST */

2015-02-11T20:51:45Z

Exercise 1. Homology searching using BLAST

← Older revision		Revision as of 20:51, 11 February 2015
Line 24:		Line 24:
	----		----
	==Exercise 1. Homology searching using BLAST==		==Exercise 1. Homology searching using BLAST==
	# Go to the NCBI-BLAST website at [http://blast.ncbi.nlm.nih.gov/Blast.cgi~~?CMD=Web&%20PAGE_TYPE=BlastHome~~ NCBI/BLAST Home Page]		# Go to the NCBI-BLAST website at [http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI/BLAST Home Page]
	# What is BLAST? Read and copy the expanded answer by clicking on "more"		# What is BLAST? Read and copy the expanded answer by clicking on "more"
	# Since BLAST finds matches between biological sciences, it needs a "query" sequence as input as well as a "database" to search against. To find matches of a sequence in human genome, what would be your "query" sequence and what would be your "database"?		# Since BLAST finds matches between biological sciences, it needs a "query" sequence as input as well as a "database" to search against. To find matches of a sequence in human genome, what would be your "query" sequence and what would be your "database"?
Line 57:		Line 57:
	</ol>		</ol>
	----		----

	==Exercise 2. Explore the structure of human ''mdm2'' gene==		==Exercise 2. Explore the structure of human ''mdm2'' gene==
	# Search [http://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide GenBank] using the accession AF527840. Read the GenBank file and find out from the feature table how many introns and exons this sequence has according to the "mRNA" and "CDS" features.		# Search [http://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide GenBank] using the accession AF527840. Read the GenBank file and find out from the feature table how many introns and exons this sequence has according to the "mRNA" and "CDS" features.

imported>Weigang: /* Discussion Questions */

2015-02-11T15:07:14Z

Discussion Questions

← Older revision		Revision as of 15:07, 11 February 2015
Line 151:		Line 151:

	==Discussion Questions==		==Discussion Questions==
	# Explain the following BLAST terms: “Expect” (e-value) ([http://blast.ncbi.nlm.nih.gov~~%20~~/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect ~~read~~ this FAQ]), “Identities”, “Gap”, “Strand”.		# Explain the following BLAST terms: “Expect” (e-value) [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect Read this FAQ], “Identities”, “Gap”, “Strand”.
	# Which is a statistically more significant match by BLAST, a match with an e-value=1e-5 or a match with an e-value of 1?		# Which is a statistically more significant match by BLAST, a match with an e-value=1e-5 or a match with an e-value of 1?
	# If you want your match to be biologically relevant (and not random, chance matches), should you use the default e-value cutoff of 10?		# If you want your match to be biologically relevant (and not random, chance matches), should you use the default e-value cutoff of 10?

imported>Weigang: /* Exercise 2. Explore the structure of human mdm2 gene */

2015-02-11T13:53:57Z

Exercise 2. Explore the structure of human mdm2 gene

← Older revision		Revision as of 13:53, 11 February 2015
Line 73:		Line 73:
	## Align the first 5 bases of all introns. Which bases are conserved near intron start ("donor site")?		## Align the first 5 bases of all introns. Which bases are conserved near intron start ("donor site")?
	## Align the last 5 bases of all introns. Which bases are conserved near intron end ("acceptor site")?		## Align the last 5 bases of all introns. Which bases are conserved near intron end ("acceptor site")?
	## Follow examples and instructions on [http://weblogo.berkeley.edu/ WebLogo] and make a ~~seqlogo~~ for the acceptor site and another ~~seqlogo~~ for the donor site.		## Follow examples and instructions on [http://weblogo.berkeley.edu/ WebLogo] and make a sequence logo for the acceptor site and another sequence logo for the donor site.
	<center>		<center>
	Table 1. ''mdm2'' Exons		Table 1. ''mdm2'' Exons

imported>Weigang: /* Discussion Questions */

2015-02-11T13:53:27Z

Discussion Questions

← Older revision		Revision as of 13:53, 11 February 2015
Line 154:		Line 154:
	# Which is a statistically more significant match by BLAST, a match with an e-value=1e-5 or a match with an e-value of 1?		# Which is a statistically more significant match by BLAST, a match with an e-value=1e-5 or a match with an e-value of 1?
	# If you want your match to be biologically relevant (and not random, chance matches), should you use the default e-value cutoff of 10?		# If you want your match to be biologically relevant (and not random, chance matches), should you use the default e-value cutoff of 10?
	# List and describe individual elements of a typical human gene based on mdm2. What is the "GT-AG" rule?		# List and describe individual elements of a typical human gene based on mdm2.
			# What is the "GT-AG" rule? Explain how to read the sequence logos. Explain the significance of sequence conservation at exon-intron junctions.
	# Describe biological significance of alternative splicing, using mdm2 gene as an example.		# Describe biological significance of alternative splicing, using mdm2 gene as an example.
	----		----

	==Reference==		==Reference==
	* Arva NC, Talbott KE, Okoro DR, Brekman A, Qiu WG, Bargonetti J. 2008. Disruption of the p53-Mdm2 complex by Nutlin-3 reveals different cancer cell phenotypes. Ethnicity and Disease. 18(S2):1-8. [http://www.ncbi.nlm.nih.gov/pubmed/18646312 PubMed Abstract]		* Arva NC, Talbott KE, Okoro DR, Brekman A, Qiu WG, Bargonetti J. 2008. Disruption of the p53-Mdm2 complex by Nutlin-3 reveals different cancer cell phenotypes. Ethnicity and Disease. 18(S2):1-8. [http://www.ncbi.nlm.nih.gov/pubmed/18646312 PubMed Abstract]
	----		----

imported>Weigang: /* Exercise 2. Explore the structure of human mdm2 gene */

2015-02-11T13:51:19Z

Exercise 2. Explore the structure of human mdm2 gene

← Older revision		Revision as of 13:51, 11 February 2015
Line 73:		Line 73:
	## Align the first 5 bases of all introns. Which bases are conserved near intron start ("donor site")?		## Align the first 5 bases of all introns. Which bases are conserved near intron start ("donor site")?
	## Align the last 5 bases of all introns. Which bases are conserved near intron end ("acceptor site")?		## Align the last 5 bases of all introns. Which bases are conserved near intron end ("acceptor site")?
	## Follow instructions on [http://weblogo.berkeley.edu/ WebLogo] and make a seqlogo for the acceptor site and another seqlogo for the donor site.		## Follow examples and instructions on [http://weblogo.berkeley.edu/ WebLogo] and make a seqlogo for the acceptor site and another seqlogo for the donor site.
	<center>		<center>
	Table 1. ''mdm2'' Exons		Table 1. ''mdm2'' Exons
Line 95:		Line 95:
	\|}		\|}

	* Introns have phases. Phase 0 introns sit between 2 codons, phase 1 ~~intro~~ sit between the 1st codon position and the 2nd codon position, and phase 3 introns sit between the 2nd and 3rd codon position. How would you find out the phase of an intron? [Hint, use Table 3 CDS positions below].		* Introns have phases. Phase 0 introns sit between 2 codons, phase 1 intron sit between the 1st codon position and the 2nd codon position, and phase 3 introns sit between the 2nd and 3rd codon position. How would you find out the phase of an intron? [Hint, use Table 3 CDS positions below].

	Table 3. ''mdm2'' Coding Sequences (CDS)		Table 3. ''mdm2'' Coding Sequences (CDS)

imported>Weigang: /* Exercise 2. Explore the structure of human mdm2 gene */

2015-02-11T13:40:38Z

Exercise 2. Explore the structure of human mdm2 gene

← Older revision		Revision as of 13:40, 11 February 2015
Line 88:		Line 88:
	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! Intro Number !! Start Position !! End Position !! Length !! First 5 bases !! Last 5 bases !! ~~phase~~*		! Intro Number !! Start Position !! End Position !! Length !! First 5 bases !! Last 5 bases !! Phase*
	\|-		\|-
	\| #1 \|\| 2272 \|\| 2987 \|\| 616 \|\| GTACT \|\| TGTAG \|\| ?		\| #1 \|\| 2272 \|\| 2987 \|\| 616 \|\| GTACT \|\| TGTAG \|\| ?

imported>Weigang: /* Exercise 2. Explore the structure of human mdm2 gene */

2015-02-11T13:40:08Z

Exercise 2. Explore the structure of human mdm2 gene

← Older revision		Revision as of 13:40, 11 February 2015
Line 88:		Line 88:
	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! Intro Number !! Start Position !! End Position !! Length !! First 5 bases !! Last 5 bases		! Intro Number !! Start Position !! End Position !! Length !! First 5 bases !! Last 5 bases !! phase*
	\|-		\|-
	\| #1 \|\| 2272 \|\| 2987 \|\| 616 \|\| GTACT \|\| TGTAG		\| #1 \|\| 2272 \|\| 2987 \|\| 616 \|\| GTACT \|\| TGTAG \|\| ?
	\|-		\|-
	\| #2 \|\| ? \|\| ? \|\| ? \|\| ? \|\| ?		\| #2 \|\| ? \|\| ? \|\| ? \|\| ? \|\| ? \|\| ?
	\|}		\|}

			* Introns have phases. Phase 0 introns sit between 2 codons, phase 1 intro sit between the 1st codon position and the 2nd codon position, and phase 3 introns sit between the 2nd and 3rd codon position. How would you find out the phase of an intron? [Hint, use Table 3 CDS positions below].

	Table 3. ''mdm2'' Coding Sequences (CDS)		Table 3. ''mdm2'' Coding Sequences (CDS)

imported>Weigang: /* Exercise 2. Explore the structure of human mdm2 gene */

2015-02-11T13:35:37Z

Exercise 2. Explore the structure of human mdm2 gene

← Older revision		Revision as of 13:35, 11 February 2015
Line 71:		Line 71:
	## What is the total length of exons, introns, and coding sequences of this gene?		## What is the total length of exons, introns, and coding sequences of this gene?
	## Are all exon sequences code for proteins? Which exons are non-coding in mdm2?		## Are all exon sequences code for proteins? Which exons are non-coding in mdm2?
	## Align the first 5 bases of all introns. Which bases are conserved ~~among~~ intron ~~starts~~ ("donor ~~sites~~")?		## Align the first 5 bases of all introns. Which bases are conserved near intron start ("donor site")?
	## Align the last 5 bases of all introns. Which bases are conserved ~~among~~ intron ~~ends~~ ("acceptor ~~sites~~")?		## Align the last 5 bases of all introns. Which bases are conserved near intron end ("acceptor site")?
			## Follow instructions on [http://weblogo.berkeley.edu/ WebLogo] and make a seqlogo for the acceptor site and another seqlogo for the donor site.
	<center>		<center>
	Table 1. ''mdm2'' Exons		Table 1. ''mdm2'' Exons
Line 105:		Line 106:
	</center>		</center>
	----		----

	==Exercise 3. Alternative splicing: Use BLAST to determine which exons are present in an mRNA==		==Exercise 3. Alternative splicing: Use BLAST to determine which exons are present in an mRNA==
	<center>		<center>

imported>Weigang: /* Exercise 3. Alternative splicing: Use BLAST to determine which exons are present in an mRNA */

2015-02-11T02:53:13Z

Exercise 3. Alternative splicing: Use BLAST to determine which exons are present in an mRNA

← Older revision		Revision as of 02:53, 11 February 2015
Line 143:		Line 143:
	\| ? \|\| ? \|\| ? \|\| ? \|\| ? \|\| ?		\| ? \|\| ? \|\| ? \|\| ? \|\| ? \|\| ?
	\|}		\|}
			</center>
	----		----