Vargula tsujii - Revision history

Nleung: /* Project Progress */

2011-12-13T22:04:46Z

‎Project Progress

Nleung: /* Project Progress */

2011-12-13T22:04:37Z

‎Project Progress

Nleung: /* Project Progress */

2011-12-13T22:04:13Z

‎Project Progress

Nleung at 22:03, 13 December 2011

2011-12-13T22:03:11Z

Nleung at 22:02, 13 December 2011

2011-12-13T22:02:34Z

Nleung at 22:02, 13 December 2011

2011-12-13T22:02:21Z

Nleung at 22:02, 13 December 2011

2011-12-13T22:02:01Z

Oakley at 23:35, 17 November 2011

2011-11-17T23:35:09Z

Oakley at 23:32, 17 November 2011

2011-11-17T23:32:57Z

Oakley at 10:21, 16 November 2011

2011-11-16T10:21:59Z

@@ Line 17: / Line 17: @@
 Vargular tsujii consensus sequence:
 GCAGTCAGTGTCTTCAGTGATCAGTCGAGAAACGAAACGTGATAATGTGGTTAMAAAAMTTATTWATCTTAGCAGTAGGGATCTGCTTTTGTGCAGCTCAAGATTGTTATGAATCAACATGGGCTTCGAATGATTATCCATCTTCATGTGAGGCTCTAAACGGAAGATGTGTAGACTCTGCGTGCGGCAGCTGTGACGAGGTTCTGTTTGGTGATGGATTGTGTGAAAATGCAGGAGGAGCGTCTCCCAAGTGCTGTAGAGATTGCCCAGAAATCGTCAGATGCAGAGCTTCAGCAGCTGGATACTTCCATACATTCTATGGGCAGAGATTCAATCTCCAGGTACCAGGAACCTATCTCTTGAGTGAAGACTGCGTGGGAGGACTATGGTCTCTATACGTTAACCTGGCGAATATTGAAGGAGAGAAGGGAGCAGTTTTGGATTCCGTCAAGATGGTTGTTGGAGACGTAACTGTCGATATTAAACAGAAAGTTGGAGCTGTTACAGTAAATGGAGGTTCCGTTGAAATCGACAGCAA:CCCGTTCTCTATCGGTGACGTCACYATTGCCATCGTACGCACTCCTAACTTTGACGTCTCCGTCATCGAGTTCCTTAAGCTTGTTACATTCGATATCTTACAAGGCAGAGCTTTCAGACTTGCTCCAGATTTCTTATACGCAGACAGGACCTGTGGTTTATGTGGAGTCATGTCCGATGAACCTACTGATTTTATTGACAATCCAGATCAGCTTGCAATCCARGACCAAATGAACCAGGATGTAGACGGCTGCCCACTCTCTGGAAATCCTTCTGACGTCGAATATTGCSTGAATAAGATGCAGCCATATAAGGACGGGTGTGTTAACAAGAACGATGTCCACTTCGGAACCTACCTKTACGCATGCGCACTGGCYTACTGCATGGGCGGMGACGACAGAGTGGAGGATGTTATCTTTGAATACGCTGAAGCCTGCGTTGAACCCATCGGTAGAGCAACCTGCGTCATGAATGGACACACATACTACGATACMTTCGACAAAACAAGTTATCAGTTCCAGGCACCTTGCAAGGTTCTATTYGCCAAAGACTGTACAGATGACGATTGGGAAGTAACCATTACCCATAAAGCAGTTGGAGAATATACTGAAGTAGAGAAGGTCACCGTCCGGTATTTCCAAACCTTGATTGACCTGATAKCGGAGACTAAGAAAGTTTTCGTTAATGGATCGGAAGTGAGCGTCCCTTACAACTATGGAGATACATCTATATACATGTATGATAACTTAATAACCACAGCAGTTCTACCAGGAGCMGTGGTGGTGAAGTACAACTTCGAGCAGATGTTGGCTCTACACATCAGAGATCCATATGAAGCAGACAGCTGTGGTCTGTGTGGTATCTGGGATTTGGATAAATCTAATGAGGGTCCTGATACCCAGTATGTAGATTGTGAACCAACTCCCAACCCTCCAACATGTACTGCTGACAAAGAGGCTGAAGCTAGAGAACTATGTCAGAATATGTTCCCTGCTTCTCTCGACGACGTATGTAACATCTGCTACAAGGCCGACCGTGTTGAGCGTTGCATGTATGAGTATTGTCTTGGTGGTATGGAAGGCTTCTGTCAACAYGCTGGKACCGTCATCGATGAATGCTTCGTGAGACAYGGAGACGATCTACAGTATCCCCCTCAGTGTAAATAAGACGCCTGAGTGAGCTGTAGCAACTACACTATGGTCCATTGAGCATAAAAATGTGTAYTYCTTAAATWTTATAGTTGAGAAGAATGTTGCTATATACATAAACACGACGTAGCATTCAATGTTACTGATATATAAATTGTTATTYAAAATAWATGTATTGATAATATTATATAATAAAGCATTTTGAAGCAAAAAAGAAAAAAG
 Primers that sit in gene:

@@ Line 16: / Line 16: @@
 ==Project Progress==
 Vargular tsujii consensus sequence:
 GCAGTCAGTGTCTTCAGTGATCAGTCGAGAAACGAAACGTGATAATGTGGTTAMAAAAMTTATTWATCTTAGCAGTAGGGATCTGCTTTTGTGCAGCTCAAGATTGTTATGAATCAACATGGGCTTCGAATGATTATCCATCTTCATGTGAGGCTCTAAACGGAAGATGTGTAGACTCTGCGTGCGGCAGCTGTGACGAGGTTCTGTTTGGTGATGGATTGTGTGAAAATGCAGGAGGAGCGTCTCCCAAGTGCTGTAGAGATTGCCCAGAAATCGTCAGATGCAGAGCTTCAGCAGCTGGATACTTCCATACATTCTATGGGCAGAGATTCAATCTCCAGGTACCAGGAACCTATCTCTTGAGTGAAGACTGCGTGGGAGGACTATGGTCTCTATACGTTAACCTGGCGAATATTGAAGGAGAGAAGGGAGCAGTTTTGGATTCCGTCAAGATGGTTGTTGGAGACGTAACTGTCGATATTAAACAGAAAGTTGGAGCTGTTACAGTAAATGGAGGTTCCGTTGAAATCGACAGCAA:CCCGTTCTCTATCGGTGACGTCACYATTGCCATCGTACGCACTCCTAACTTTGACGTCTCCGTCATCGAGTTCCTTAAGCTTGTTACATTCGATATCTTACAAGGCAGAGCTTTCAGACTTGCTCCAGATTTCTTATACGCAGACAGGACCTGTGGTTTATGTGGAGTCATGTCCGATGAACCTACTGATTTTATTGACAATCCAGATCAGCTTGCAATCCARGACCAAATGAACCAGGATGTAGACGGCTGCCCACTCTCTGGAAATCCTTCTGACGTCGAATATTGCSTGAATAAGATGCAGCCATATAAGGACGGGTGTGTTAACAAGAACGATGTCCACTTCGGAACCTACCTKTACGCATGCGCACTGGCYTACTGCATGGGCGGMGACGACAGAGTGGAGGATGTTATCTTTGAATACGCTGAAGCCTGCGTTGAACCCATCGGTAGAGCAACCTGCGTCATGAATGGACACACATACTACGATACMTTCGACAAAACAAGTTATCAGTTCCAGGCACCTTGCAAGGTTCTATTYGCCAAAGACTGTACAGATGACGATTGGGAAGTAACCATTACCCATAAAGCAGTTGGAGAATATACTGAAGTAGAGAAGGTCACCGTCCGGTATTTCCAAACCTTGATTGACCTGATAKCGGAGACTAAGAAAGTTTTCGTTAATGGATCGGAAGTGAGCGTCCCTTACAACTATGGAGATACATCTATATACATGTATGATAACTTAATAACCACAGCAGTTCTACCAGGAGCMGTGGTGGTGAAGTACAACTTCGAGCAGATGTTGGCTCTACACATCAGAGATCCATATGAAGCAGACAGCTGTGGTCTGTGTGGTATCTGGGATTTGGATAAATCTAATGAGGGTCCTGATACCCAGTATGTAGATTGTGAACCAACTCCCAACCCTCCAACATGTACTGCTGACAAAGAGGCTGAAGCTAGAGAACTATGTCAGAATATGTTCCCTGCTTCTCTCGACGACGTATGTAACATCTGCTACAAGGCCGACCGTGTTGAGCGTTGCATGTATGAGTATTGTCTTGGTGGTATGGAAGGCTTCTGTCAACAYGCTGGKACCGTCATCGATGAATGCTTCGTGAGACAYGGAGACGATCTACAGTATCCCCCTCAGTGTAAATAAGACGCCTGAGTGAGCTGTAGCAACTACACTATGGTCCATTGAGCATAAAAATGTGTAYTYCTTAAATWTTATAGTTGAGAAGAATGTTGCTATATACATAAACACGACGTAGCATTCAATGTTACTGATATATAAATTGTTATTYAAAATAWATGTATTGATAATATTATATAATAAAGCATTTTGAAGCAAAAAAGAAAAAAG

← Older revision		Revision as of 22:04, 13 December 2011
Line 15:		Line 15:

	==Project Progress==		==Project Progress==
		+	Vargular tsujii consensus sequence:
		+	>Vargula tsujii luciferase
		+	GCAGTCAGTGTCTTCAGTGATCAGTCGAGAAACGAAACGTGATAATGTGGTTAMAAAAMTTATTWATCTTAGCAGTAGGGATCTGCTTTTGTGCAGCTCAAGATTGTTATGAATCAACATGGGCTTCGAATGATTATCCATCTTCATGTGAGGCTCTAAACGGAAGATGTGTAGACTCTGCGTGCGGCAGCTGTGACGAGGTTCTGTTTGGTGATGGATTGTGTGAAAATGCAGGAGGAGCGTCTCCCAAGTGCTGTAGAGATTGCCCAGAAATCGTCAGATGCAGAGCTTCAGCAGCTGGATACTTCCATACATTCTATGGGCAGAGATTCAATCTCCAGGTACCAGGAACCTATCTCTTGAGTGAAGACTGCGTGGGAGGACTATGGTCTCTATACGTTAACCTGGCGAATATTGAAGGAGAGAAGGGAGCAGTTTTGGATTCCGTCAAGATGGTTGTTGGAGACGTAACTGTCGATATTAAACAGAAAGTTGGAGCTGTTACAGTAAATGGAGGTTCCGTTGAAATCGACAGCAA:CCCGTTCTCTATCGGTGACGTCACYATTGCCATCGTACGCACTCCTAACTTTGACGTCTCCGTCATCGAGTTCCTTAAGCTTGTTACATTCGATATCTTACAAGGCAGAGCTTTCAGACTTGCTCCAGATTTCTTATACGCAGACAGGACCTGTGGTTTATGTGGAGTCATGTCCGATGAACCTACTGATTTTATTGACAATCCAGATCAGCTTGCAATCCARGACCAAATGAACCAGGATGTAGACGGCTGCCCACTCTCTGGAAATCCTTCTGACGTCGAATATTGCSTGAATAAGATGCAGCCATATAAGGACGGGTGTGTTAACAAGAACGATGTCCACTTCGGAACCTACCTKTACGCATGCGCACTGGCYTACTGCATGGGCGGMGACGACAGAGTGGAGGATGTTATCTTTGAATACGCTGAAGCCTGCGTTGAACCCATCGGTAGAGCAACCTGCGTCATGAATGGACACACATACTACGATACMTTCGACAAAACAAGTTATCAGTTCCAGGCACCTTGCAAGGTTCTATTYGCCAAAGACTGTACAGATGACGATTGGGAAGTAACCATTACCCATAAAGCAGTTGGAGAATATACTGAAGTAGAGAAGGTCACCGTCCGGTATTTCCAAACCTTGATTGACCTGATAKCGGAGACTAAGAAAGTTTTCGTTAATGGATCGGAAGTGAGCGTCCCTTACAACTATGGAGATACATCTATATACATGTATGATAACTTAATAACCACAGCAGTTCTACCAGGAGCMGTGGTGGTGAAGTACAACTTCGAGCAGATGTTGGCTCTACACATCAGAGATCCATATGAAGCAGACAGCTGTGGTCTGTGTGGTATCTGGGATTTGGATAAATCTAATGAGGGTCCTGATACCCAGTATGTAGATTGTGAACCAACTCCCAACCCTCCAACATGTACTGCTGACAAAGAGGCTGAAGCTAGAGAACTATGTCAGAATATGTTCCCTGCTTCTCTCGACGACGTATGTAACATCTGCTACAAGGCCGACCGTGTTGAGCGTTGCATGTATGAGTATTGTCTTGGTGGTATGGAAGGCTTCTGTCAACAYGCTGGKACCGTCATCGATGAATGCTTCGTGAGACAYGGAGACGATCTACAGTATCCCCCTCAGTGTAAATAAGACGCCTGAGTGAGCTGTAGCAACTACACTATGGTCCATTGAGCATAAAAATGTGTAYTYCTTAAATWTTATAGTTGAGAAGAATGTTGCTATATACATAAACACGACGTAGCATTCAATGTTACTGATATATAAATTGTTATTYAAAATAWATGTATTGATAATATTATATAATAAAGCATTTTGAAGCAAAAAAGAAAAAAG
		+
	Primers that sit in gene:		Primers that sit in gene:

@@ Line 15: / Line 15: @@
 ==Project Progress==
-Primers that sit in gene
+Primers that sit in gene:
 F- GGGCTTCGAATGATTATCCA
@@ Line 22: / Line 22: @@
-Primers that amplify the entire fragment
+Primers that amplify the entire fragment:
 UTR FOR- ATCAGTCGAGAAACGAAACGTGATA
 UTR REV- ATAGTGTAGTTGCTACAGCTCACTCA

← Older revision		Revision as of 22:02, 13 December 2011
Line 20:		Line 20:

	6R- AGCCAACATCTGCTCGAAGT		6R- AGCCAACATCTGCTCGAAGT
		+

	Primers that amplify the entire fragment		Primers that amplify the entire fragment

← Older revision		Revision as of 22:02, 13 December 2011
Line 13:		Line 13:
	==Project Notes and Ideas==		==Project Notes and Ideas==
	An interesting result is that a truncated luciferase from ''Vargula hilgendorfii'' produces bioluminescence, suggesting that one VWD domain is sufficient to catalyze the light reaction. [[Maeda 1996]].		An interesting result is that a truncated luciferase from ''Vargula hilgendorfii'' produces bioluminescence, suggesting that one VWD domain is sufficient to catalyze the light reaction. [[Maeda 1996]].
		+
		+	==Project Progress==
		+	Primers that sit in gene
		+	1F- GGGCTTCGAATGATTATCCA
		+	6R- AGCCAACATCTGCTCGAAGT
		+
		+	Primers that amplify the entire fragment
		+	5UTR FOR- ATCAGTCGAGAAACGAAACGTGATA
		+	3UTR REV- ATAGTGTAGTTGCTACAGCTCACTCA

← Older revision		Revision as of 23:35, 17 November 2011
Line 12:		Line 12:

	==Project Notes and Ideas==		==Project Notes and Ideas==
−	An interesting result is that a truncated luciferase from ''Vargula hilgendorfii'' produces bioluminescence, suggesting that one VWD domain is sufficient to catalyze the light reaction.	+	An interesting result is that a truncated luciferase from ''Vargula hilgendorfii'' produces bioluminescence, suggesting that one VWD domain is sufficient to catalyze the light reaction. [[Maeda 1996]].
−
−
−	<ref name="Horne">{{cite journal \|author=D. J. Horne \|url=http://www.cosis.net/abstracts/EGU2007/00093/EGU2007-J-00093.pdf?PHPSESSID=e \|title=A Mutual Temperature Range Method for European Quaternary Nonmarine Ostracoda \|journal=Geophysical Research Abstracts \|volume=9 \|pages=00093 \|year=2007 \|publisher=European Geosciences Union \|format=[[~~Portable Document Format\|PDF~~]]~~}}</ref>~~
−
−
−	~~Maeda1996_JBiochem~~.~~pdf~~

← Older revision		Revision as of 23:32, 17 November 2011
Line 1:		Line 1:
		+	==Project History==
	We conducted 454 sequencing on bodies minus eyes. The specimens were collected from Catalina Island, with specific data available on the phylogeny website.		We conducted 454 sequencing on bodies minus eyes. The specimens were collected from Catalina Island, with specific data available on the phylogeny website.

Line 9:		Line 10:

	There is also similarity to vitellogenein, through the VWD similarity.		There is also similarity to vitellogenein, through the VWD similarity.
		+
		+	==Project Notes and Ideas==
		+	An interesting result is that a truncated luciferase from ''Vargula hilgendorfii'' produces bioluminescence, suggesting that one VWD domain is sufficient to catalyze the light reaction.
		+
		+
		+	<ref name="Horne">{{cite journal \|author=D. J. Horne \|url=http://www.cosis.net/abstracts/EGU2007/00093/EGU2007-J-00093.pdf?PHPSESSID=e \|title=A Mutual Temperature Range Method for European Quaternary Nonmarine Ostracoda \|journal=Geophysical Research Abstracts \|volume=9 \|pages=00093 \|year=2007 \|publisher=European Geosciences Union \|format=[[Portable Document Format\|PDF]]}}</ref>
		+
		+
		+	Maeda1996_JBiochem.pdf

← Older revision		Revision as of 10:21, 16 November 2011
Line 5:		Line 5:

	There are 8 isotigs retrieved with an E-value of 0.001, when blasting the transcriptome with Vargula hilgendorfii luciferase. When blasted back to GenBank, all 8 of these have strong similarity to known ostracod luciferases.		There are 8 isotigs retrieved with an E-value of 0.001, when blasting the transcriptome with Vargula hilgendorfii luciferase. When blasted back to GenBank, all 8 of these have strong similarity to known ostracod luciferases.
		+
		+	These luciferase genes are also similar to kielin/crossveinless, which is involved in development.
		+
		+	There is also similarity to vitellogenein, through the VWD similarity.