QuBi/modules/biol302 - Revision history

imported>Weigang: /* Part 2 (Extra Credit Assignment): Identification of mdm2 Splice Variants Using BLAST */

2013-03-23T14:50:53Z

Part 2 (Extra Credit Assignment): Identification of mdm2 Splice Variants Using BLAST

← Older revision		Revision as of 14:50, 23 March 2013
Line 68:		Line 68:

	==[[QuBi/modules/biol302#Part 2: Identification of mdm2 Splice Variants Using BLAST\|Part 2 (Extra Credit Assignment): Identification of mdm2 Splice Variants Using BLAST]]==		==[[QuBi/modules/biol302#Part 2: Identification of mdm2 Splice Variants Using BLAST\|Part 2 (Extra Credit Assignment): Identification of mdm2 Splice Variants Using BLAST]]==
	<div ~~class~~="~~center~~">		<div style="font-family:Monospace;line-height:1;width:800px;border-style:solid;border-width:1px;border-color:#AAAAFF;background-color:#EEEEFF;padding-left:5px;padding-right:5px;padding-top:0px;padding-bottom:0px;">
	[[File:4seq.png\|800px]]		[[File:4seq.png\|800px]]

	''A diagram of the MDM2 gene used in this exercise, along with its splice variants. By the end of this module you will create a similar diagram.''		A diagram of the MDM2 gene used in this exercise, along with its splice variants. By the end of this module you will create a similar diagram. ''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.
	</div>		</div>
	----		----

imported>Weigang: /* Part 2 (Extra Credit Assignment): Identification of mdm2 Splice Variants Using BLAST */

2013-03-23T14:43:07Z

Part 2 (Extra Credit Assignment): Identification of mdm2 Splice Variants Using BLAST

← Older revision		Revision as of 14:43, 23 March 2013
Line 74:		Line 74:
	</div>		</div>
	----		----



	===[[QuBi/modules/biol302#Objectives\|Key Concepts]]===		===[[QuBi/modules/biol302#Objectives\|Key Concepts]]===
	* Use BLAST ('''not Google''') to find matches of DNA and protein sequences		* Use BLAST ('''not Google''') to find matches of DNA and protein sequences

imported>Weigang: /* Key Concepts */

2013-03-23T14:41:59Z

Key Concepts

imported>Weigang: /* Key Concepts */

2013-03-23T14:39:22Z

Key Concepts

← Older revision		Revision as of 14:39, 23 March 2013
Line 81:		Line 81:
	* Alternative splicing and isoforms of a single gene		* Alternative splicing and isoforms of a single gene
	You will use the following table for your exercise:		You will use the following table for your exercise:


	{\| class="wikitable"		{\| class="wikitable"
	! Genbank Accession # !! cDNA Clone !! Description !! Cell Line !! Length (bp)		! Genbank Accession # !! cDNA Clone !! Description !! Cell Line !! Length (bp)

imported>Weigang: /* Exercise */

2013-03-23T14:39:08Z

Exercise

← Older revision		Revision as of 14:39, 23 March 2013
Line 82:		Line 82:
	You will use the following table for your exercise:		You will use the following table for your exercise:

	~~===[[QuBi/modules/biol302#Exercise\|Exercise]]===~~
	{\| class="wikitable"		{\| class="wikitable"
	! Genbank Accession # !! cDNA Clone !! Description !! Cell Line !! Length (bp)		! Genbank Accession # !! cDNA Clone !! Description !! Cell Line !! Length (bp)

imported>Weigang: /* Key Concepts */

2013-03-23T14:38:51Z

Key Concepts

← Older revision		Revision as of 14:38, 23 March 2013
Line 80:		Line 80:
	* Use BLAST ('''not Google''') to find matches of DNA and protein sequences		* Use BLAST ('''not Google''') to find matches of DNA and protein sequences
	* Alternative splicing and isoforms of a single gene		* Alternative splicing and isoforms of a single gene
	~~----~~		You will use the following table for your exercise:

	===[[QuBi/modules/biol302#Exercise\|Exercise]]===		===[[QuBi/modules/biol302#Exercise\|Exercise]]===

imported>Weigang: /* Exit Questions */

2013-03-23T14:37:54Z

Exit Questions

← Older revision		Revision as of 14:37, 23 March 2013
Line 119:		Line 119:
	# Explain the following BLAST terms: “Expect” (e-value), “Identities”, “Gap”, “Strand”		# Explain the following BLAST terms: “Expect” (e-value), “Identities”, “Gap”, “Strand”
	----		----

	~~===[[QuBi/modules/biol302#Exit_Questions\|Exit Questions]]===~~
	~~#Describe essential experimental steps of obtaining cDNA clones of a gene from a cell culture.~~
	~~#Based on the NCBI BLAST documentation, define BLAST. Describe applications of different BLAST tools.~~
	~~#Describe informatics steps of identifying a splice variant using BL2SEQ.~~
	~~# Explain why the following statement is FALSE: The first exon always starts with ATG and the last exon always ends with a stop codon. What are the terms for the untranslated regions of exons?~~

imported>Weigang: /* Key Concepts */

2013-03-23T14:36:12Z

Key Concepts

← Older revision		Revision as of 14:36, 23 March 2013
Line 7:		Line 7:

	===[[QuBi/modules/biol302#Key Concepts2\|Key Concepts]]===		===[[QuBi/modules/biol302#Key Concepts2\|Key Concepts]]===
	*Homology searching using BLAST		*Homology searching using BLAST ('''not Google''')
	*Mammalian gene regulation		*Mammalian gene regulation

imported>Weigang: /* Identify regulatory elements through literature search */

2013-03-23T14:33:19Z

Identify regulatory elements through literature search

← Older revision		Revision as of 14:33, 23 March 2013
Line 56:		Line 56:
	[[File:Zauberman_fig2.png\|800px]]		[[File:Zauberman_fig2.png\|800px]]

	''~~Taken from~~'' Zauberman et al. "A functional p53-responsive intronic promoter is contained within the human mdm2 gene". Nucleic Acids Res. 1995 July 25; 23(14): 2584–2592. ''[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307078/ Pubmed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307078/pdf/nar00014-0022.pdf PDF]''		''Source:'' Zauberman et al. "A functional p53-responsive intronic promoter is contained within the human mdm2 gene". Nucleic Acids Res. 1995 July 25; 23(14): 2584–2592. ''[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307078/ Pubmed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307078/pdf/nar00014-0022.pdf PDF]''
	</div>		</div>
	----		----

imported>Weigang: /* Gene identification using genome BLAST */

2013-03-23T14:31:42Z

Gene identification using genome BLAST

← Older revision		Revision as of 14:31, 23 March 2013
Line 28:		Line 28:
	# Copy and paste the above sequence into the "Enter Query Sequence" box		# Copy and paste the above sequence into the "Enter Query Sequence" box
	# Scroll down to the bottom of the page and click "BLAST"		# Scroll down to the bottom of the page and click "BLAST"
	# Wait for 10-30 seconds for the results to return ('''Be Patient'''). Once the result page is loaded, locate and copy the following information:		# Wait for 10-30 seconds for the results to return ('''Be Patient'''). Once the result page is loaded, locate and copy/write down the following information:
	## Species and strain		## Species and strain
	## Chromosome		## Chromosome
	## Length of your query sequence		## Length of your query sequence
	## Sequence identity, number of matched bases, and number of gaps between the matched sequences		## Sequence identity, number of matched bases, and number of gaps between the matched sequences
	# Click the link for "5' side" ~~gene~~ will bring you a standard GenBank file of this gene. Locate and copy the following structural information about this gene:		# Click the link for "5' side" (next to '''Features''') will bring you a standard GenBank file of this gene. Locate and copy the following structural information about this gene:
	## Gene accession (ID number)		## Gene accession (ID number)
	## Total length of the gene		## Total length of the gene
	## Number of introns		## Number of introns
	## Which is non-template (mRNA analog) strand: the above sequence itself or its reverse complement?		## Which is the non-template (mRNA analog) strand: the above sequence itself or its reverse complement? [Hint: note the word '''complement''' in mRNA and cDNA lines)
	----		----

← Older revision		Revision as of 14:41, 23 March 2013
Line 97:		Line 97:

	----		----
	; Explore the ~~gene annotation for AF527840.~~		===Explore the GenBank file===
	#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.
	# DRAW a diagram of this gene using the information and coordinates listed in the annotation.		# DRAW a diagram of this gene using the information and coordinates listed in the annotation.
Line 104:		Line 104:
	##Draw the diagram mostly to scale. It does NOT have to be perfect, but make a reasonable effort. Put a scale bar and length markers on your drawing.		##Draw the diagram mostly to scale. It does NOT have to be perfect, but make a reasonable effort. Put a scale bar and length markers on your drawing.
	----		----
	; Explore the graphical presentation of the gene ~~to answer the following question.~~		===Explore the graphical presentation of the gene===
	Genbank provides graphical representations of the sequences on its database: click the "Graphics" link below the sequence title, OR click "Display Settings" above the title, and choose "Graphics". Take a few minutes to explore this graphical and compare it with your diagram.		Genbank provides graphical representations of the sequences on its database: click the "Graphics" link below the sequence title, OR click "Display Settings" above the title, and choose "Graphics". Take a few minutes to explore this graphical and compare it with your diagram.
	----		----
	; Use BLAST to determine which exons are used in the mRNA ~~transcripts.~~		===Use BLAST to determine which exons are used in the mRNA transcript===
	This is the most "bioinformatic" part of the assignment. Blast one of the mRNA sequences (EU076746, EU076747, EU076748, EU076749) against the main sequence (AF527840) and use the results to answer the following questions. Suggested procedures:		This is the most "bioinformatic" part of the assignment. Blast one of the mRNA sequences (EU076746, EU076747, EU076748, EU076749) against the main sequence (AF527840) and use the results to answer the following questions. Suggested procedures:
	# Go to the [http://www.ncbi.nlm.nih.gov/BLAST/ NCBI BLAST] website		# Go to the [http://www.ncbi.nlm.nih.gov/BLAST/ NCBI BLAST] website
Line 113:		Line 113:
	# In the “Sequence 1” text box, type “AF527840” (the accession for the genomics). Fill in “from 1” and “to 34088”. In the “Sequence 2” text box, type in "EU076748" (or other cDNA accession in the table). Fill in the “from” box with 1 and the “to” box with 505.		# In the “Sequence 1” text box, type “AF527840” (the accession for the genomics). Fill in “from 1” and “to 34088”. In the “Sequence 2” text box, type in "EU076748" (or other cDNA accession in the table). Fill in the “from” box with 1 and the “to” box with 505.
	# Click “Align”. You should get a “Blast Result” output page.		# Click “Align”. You should get a “Blast Result” output page.
	; Interpret your results:		# Interpret your results:
	# Which exons are present and which ones are absent in EU076746, EU076747, EU076748, EU076749? (Hint: Refer to the mRNA join statement).		## Which exons are present and which ones are absent in EU076746, EU076747, EU076748, EU076749? (Hint: Refer to the mRNA join statement).
	# Explain the following BLAST terms: “Expect” (e-value), “Identities”, “Gap”, “Strand”		## Explain the following BLAST terms: “Expect” (e-value), “Identities”, “Gap”, “Strand”
	----		----