Difference between revisions of "Vargula tsujii"
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| + | ==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. | ||
I've made a galaxy history to assemble the transcriptome and look for luciferase genes | I've made a galaxy history to assemble the transcriptome and look for luciferase genes | ||
[http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/vargula-tsujii-454] | [http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/vargula-tsujii-454] | ||
| + | |||
| + | 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. | ||
| + | |||
| + | ==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]]. | ||
| + | |||
| + | ==Project Progress== | ||
| + | Vargular tsujii consensus sequence: | ||
| + | GCAGTCAGTGTCTTCAGTGATCAGTCGAGAAACGAAACGTGATAATGTGGTTAMAAAAMTTATTWATCTTAGCAGTAGGGATCTGCTTTTGTGCAGCTCAAGATTGTTATGAATCAACATGGGCTTCGAATGATTATCCATCTTCATGTGAGGCTCTAAACGGAAGATGTGTAGACTCTGCGTGCGGCAGCTGTGACGAGGTTCTGTTTGGTGATGGATTGTGTGAAAATGCAGGAGGAGCGTCTCCCAAGTGCTGTAGAGATTGCCCAGAAATCGTCAGATGCAGAGCTTCAGCAGCTGGATACTTCCATACATTCTATGGGCAGAGATTCAATCTCCAGGTACCAGGAACCTATCTCTTGAGTGAAGACTGCGTGGGAGGACTATGGTCTCTATACGTTAACCTGGCGAATATTGAAGGAGAGAAGGGAGCAGTTTTGGATTCCGTCAAGATGGTTGTTGGAGACGTAACTGTCGATATTAAACAGAAAGTTGGAGCTGTTACAGTAAATGGAGGTTCCGTTGAAATCGACAGCAA:CCCGTTCTCTATCGGTGACGTCACYATTGCCATCGTACGCACTCCTAACTTTGACGTCTCCGTCATCGAGTTCCTTAAGCTTGTTACATTCGATATCTTACAAGGCAGAGCTTTCAGACTTGCTCCAGATTTCTTATACGCAGACAGGACCTGTGGTTTATGTGGAGTCATGTCCGATGAACCTACTGATTTTATTGACAATCCAGATCAGCTTGCAATCCARGACCAAATGAACCAGGATGTAGACGGCTGCCCACTCTCTGGAAATCCTTCTGACGTCGAATATTGCSTGAATAAGATGCAGCCATATAAGGACGGGTGTGTTAACAAGAACGATGTCCACTTCGGAACCTACCTKTACGCATGCGCACTGGCYTACTGCATGGGCGGMGACGACAGAGTGGAGGATGTTATCTTTGAATACGCTGAAGCCTGCGTTGAACCCATCGGTAGAGCAACCTGCGTCATGAATGGACACACATACTACGATACMTTCGACAAAACAAGTTATCAGTTCCAGGCACCTTGCAAGGTTCTATTYGCCAAAGACTGTACAGATGACGATTGGGAAGTAACCATTACCCATAAAGCAGTTGGAGAATATACTGAAGTAGAGAAGGTCACCGTCCGGTATTTCCAAACCTTGATTGACCTGATAKCGGAGACTAAGAAAGTTTTCGTTAATGGATCGGAAGTGAGCGTCCCTTACAACTATGGAGATACATCTATATACATGTATGATAACTTAATAACCACAGCAGTTCTACCAGGAGCMGTGGTGGTGAAGTACAACTTCGAGCAGATGTTGGCTCTACACATCAGAGATCCATATGAAGCAGACAGCTGTGGTCTGTGTGGTATCTGGGATTTGGATAAATCTAATGAGGGTCCTGATACCCAGTATGTAGATTGTGAACCAACTCCCAACCCTCCAACATGTACTGCTGACAAAGAGGCTGAAGCTAGAGAACTATGTCAGAATATGTTCCCTGCTTCTCTCGACGACGTATGTAACATCTGCTACAAGGCCGACCGTGTTGAGCGTTGCATGTATGAGTATTGTCTTGGTGGTATGGAAGGCTTCTGTCAACAYGCTGGKACCGTCATCGATGAATGCTTCGTGAGACAYGGAGACGATCTACAGTATCCCCCTCAGTGTAAATAAGACGCCTGAGTGAGCTGTAGCAACTACACTATGGTCCATTGAGCATAAAAATGTGTAYTYCTTAAATWTTATAGTTGAGAAGAATGTTGCTATATACATAAACACGACGTAGCATTCAATGTTACTGATATATAAATTGTTATTYAAAATAWATGTATTGATAATATTATATAATAAAGCATTTTGAAGCAAAAAAGAAAAAAG | ||
| + | |||
| + | |||
| + | Primers that sit in gene: | ||
| + | |||
| + | 1F- GGGCTTCGAATGATTATCCA | ||
| + | |||
| + | 6R- AGCCAACATCTGCTCGAAGT | ||
| + | |||
| + | |||
| + | Primers that amplify the entire fragment: | ||
| + | |||
| + | 5UTR FOR- ATCAGTCGAGAAACGAAACGTGATA | ||
| + | |||
| + | 3UTR REV- ATAGTGTAGTTGCTACAGCTCACTCA | ||
Latest revision as of 15:04, 13 December 2011
Project History[edit]
We conducted 454 sequencing on bodies minus eyes. The specimens were collected from Catalina Island, with specific data available on the phylogeny website.
I've made a galaxy history to assemble the transcriptome and look for luciferase genes [1]
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.
Project Notes and Ideas[edit]
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[edit]
Vargular tsujii consensus sequence: GCAGTCAGTGTCTTCAGTGATCAGTCGAGAAACGAAACGTGATAATGTGGTTAMAAAAMTTATTWATCTTAGCAGTAGGGATCTGCTTTTGTGCAGCTCAAGATTGTTATGAATCAACATGGGCTTCGAATGATTATCCATCTTCATGTGAGGCTCTAAACGGAAGATGTGTAGACTCTGCGTGCGGCAGCTGTGACGAGGTTCTGTTTGGTGATGGATTGTGTGAAAATGCAGGAGGAGCGTCTCCCAAGTGCTGTAGAGATTGCCCAGAAATCGTCAGATGCAGAGCTTCAGCAGCTGGATACTTCCATACATTCTATGGGCAGAGATTCAATCTCCAGGTACCAGGAACCTATCTCTTGAGTGAAGACTGCGTGGGAGGACTATGGTCTCTATACGTTAACCTGGCGAATATTGAAGGAGAGAAGGGAGCAGTTTTGGATTCCGTCAAGATGGTTGTTGGAGACGTAACTGTCGATATTAAACAGAAAGTTGGAGCTGTTACAGTAAATGGAGGTTCCGTTGAAATCGACAGCAA:CCCGTTCTCTATCGGTGACGTCACYATTGCCATCGTACGCACTCCTAACTTTGACGTCTCCGTCATCGAGTTCCTTAAGCTTGTTACATTCGATATCTTACAAGGCAGAGCTTTCAGACTTGCTCCAGATTTCTTATACGCAGACAGGACCTGTGGTTTATGTGGAGTCATGTCCGATGAACCTACTGATTTTATTGACAATCCAGATCAGCTTGCAATCCARGACCAAATGAACCAGGATGTAGACGGCTGCCCACTCTCTGGAAATCCTTCTGACGTCGAATATTGCSTGAATAAGATGCAGCCATATAAGGACGGGTGTGTTAACAAGAACGATGTCCACTTCGGAACCTACCTKTACGCATGCGCACTGGCYTACTGCATGGGCGGMGACGACAGAGTGGAGGATGTTATCTTTGAATACGCTGAAGCCTGCGTTGAACCCATCGGTAGAGCAACCTGCGTCATGAATGGACACACATACTACGATACMTTCGACAAAACAAGTTATCAGTTCCAGGCACCTTGCAAGGTTCTATTYGCCAAAGACTGTACAGATGACGATTGGGAAGTAACCATTACCCATAAAGCAGTTGGAGAATATACTGAAGTAGAGAAGGTCACCGTCCGGTATTTCCAAACCTTGATTGACCTGATAKCGGAGACTAAGAAAGTTTTCGTTAATGGATCGGAAGTGAGCGTCCCTTACAACTATGGAGATACATCTATATACATGTATGATAACTTAATAACCACAGCAGTTCTACCAGGAGCMGTGGTGGTGAAGTACAACTTCGAGCAGATGTTGGCTCTACACATCAGAGATCCATATGAAGCAGACAGCTGTGGTCTGTGTGGTATCTGGGATTTGGATAAATCTAATGAGGGTCCTGATACCCAGTATGTAGATTGTGAACCAACTCCCAACCCTCCAACATGTACTGCTGACAAAGAGGCTGAAGCTAGAGAACTATGTCAGAATATGTTCCCTGCTTCTCTCGACGACGTATGTAACATCTGCTACAAGGCCGACCGTGTTGAGCGTTGCATGTATGAGTATTGTCTTGGTGGTATGGAAGGCTTCTGTCAACAYGCTGGKACCGTCATCGATGAATGCTTCGTGAGACAYGGAGACGATCTACAGTATCCCCCTCAGTGTAAATAAGACGCCTGAGTGAGCTGTAGCAACTACACTATGGTCCATTGAGCATAAAAATGTGTAYTYCTTAAATWTTATAGTTGAGAAGAATGTTGCTATATACATAAACACGACGTAGCATTCAATGTTACTGATATATAAATTGTTATTYAAAATAWATGTATTGATAATATTATATAATAAAGCATTTTGAAGCAAAAAAGAAAAAAG
Primers that sit in gene:
1F- GGGCTTCGAATGATTATCCA
6R- AGCCAACATCTGCTCGAAGT
Primers that amplify the entire fragment:
5UTR FOR- ATCAGTCGAGAAACGAAACGTGATA
3UTR REV- ATAGTGTAGTTGCTACAGCTCACTCA
