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Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.

Matthews BB, Dos Santos G, Crosby MA, Emmert DB, St Pierre SE, Gramates LS, Zhou P, Schroeder AJ, Falls K, Strelets V, Russo SM, Gelbart WM, FlyBase Consorti - G3 (Bethesda) (2015)

Bottom Line: FlyBase has adopted a philosophy of excluding low-confidence and low-frequency data from gene model annotations; we also do not attempt to represent all possible permutations for complex and modularly organized genes.The number of identified pseudogenes and mutations in the sequenced strain also increased significantly.We discuss remaining challenges, for instance, identification of functional small polypeptides and detection of alternative translation starts.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138 bmatthew@morgan.harvard.edu.

No MeSH data available.


Related in: MedlinePlus

The two nonoverlapping protein isoforms of klar. A GBrowse2 view of klar is shown, as it exists in R6.03, with nonoverlapping isoforms highlighted in yellow (klar-RC and -RI do not overlap klar-RD and -RH). The C-terminus of the longer, "upstream" isoforms (klar-RD and -RH) is sufficient for targeting proteins to lipid droplets, whereas the "KASH" domain present in the "downstream" isoforms (klar-RC and -RI) is sufficient for targeting to the nuclear envelope (Guo et al. 2005). The "upstream" nonoverlapping isoform is necessary for proper lipid droplet targeting in the embryo. While the KASH domain is necessary for nuclear migration in the embryo and retina, this function is associated with the "full-length" KASH-containing isoforms. The short KASH-containing isoform, which lacks motor interaction domains, is expressed (Western blot, immunofluorescence) and is apparently enriched in nurse cells but is not sufficient to rescue nuclear migration in the retina. See Figure 2 and Figure 3 for GBrowse track descriptions. More information on data presented in GBrowse may be found at http://flybase.org/wiki/FlyBase:GBrowse_Tracks.
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fig7: The two nonoverlapping protein isoforms of klar. A GBrowse2 view of klar is shown, as it exists in R6.03, with nonoverlapping isoforms highlighted in yellow (klar-RC and -RI do not overlap klar-RD and -RH). The C-terminus of the longer, "upstream" isoforms (klar-RD and -RH) is sufficient for targeting proteins to lipid droplets, whereas the "KASH" domain present in the "downstream" isoforms (klar-RC and -RI) is sufficient for targeting to the nuclear envelope (Guo et al. 2005). The "upstream" nonoverlapping isoform is necessary for proper lipid droplet targeting in the embryo. While the KASH domain is necessary for nuclear migration in the embryo and retina, this function is associated with the "full-length" KASH-containing isoforms. The short KASH-containing isoform, which lacks motor interaction domains, is expressed (Western blot, immunofluorescence) and is apparently enriched in nurse cells but is not sufficient to rescue nuclear migration in the retina. See Figure 2 and Figure 3 for GBrowse track descriptions. More information on data presented in GBrowse may be found at http://flybase.org/wiki/FlyBase:GBrowse_Tracks.

Mentions: Six of these cases have been identified in the literature, but in no case has the functional significance of each of the two nonoverlapping isoforms been fully characterized. The best characterized case is the klar gene (Figure 7). The klar protein has been implicated in microtubule-based transport of lipid droplets (Patterson et al. 2004) and nuclei (Guo et al. 2005). The existence of nonoverlapping transcripts encoding nonoverlapping protein isoforms has been characterized by cDNA analysis, RT-PCR, and Western blot (Guo et al. 2005; Kim et al. 2013).


Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.

Matthews BB, Dos Santos G, Crosby MA, Emmert DB, St Pierre SE, Gramates LS, Zhou P, Schroeder AJ, Falls K, Strelets V, Russo SM, Gelbart WM, FlyBase Consorti - G3 (Bethesda) (2015)

The two nonoverlapping protein isoforms of klar. A GBrowse2 view of klar is shown, as it exists in R6.03, with nonoverlapping isoforms highlighted in yellow (klar-RC and -RI do not overlap klar-RD and -RH). The C-terminus of the longer, "upstream" isoforms (klar-RD and -RH) is sufficient for targeting proteins to lipid droplets, whereas the "KASH" domain present in the "downstream" isoforms (klar-RC and -RI) is sufficient for targeting to the nuclear envelope (Guo et al. 2005). The "upstream" nonoverlapping isoform is necessary for proper lipid droplet targeting in the embryo. While the KASH domain is necessary for nuclear migration in the embryo and retina, this function is associated with the "full-length" KASH-containing isoforms. The short KASH-containing isoform, which lacks motor interaction domains, is expressed (Western blot, immunofluorescence) and is apparently enriched in nurse cells but is not sufficient to rescue nuclear migration in the retina. See Figure 2 and Figure 3 for GBrowse track descriptions. More information on data presented in GBrowse may be found at http://flybase.org/wiki/FlyBase:GBrowse_Tracks.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4528329&req=5

fig7: The two nonoverlapping protein isoforms of klar. A GBrowse2 view of klar is shown, as it exists in R6.03, with nonoverlapping isoforms highlighted in yellow (klar-RC and -RI do not overlap klar-RD and -RH). The C-terminus of the longer, "upstream" isoforms (klar-RD and -RH) is sufficient for targeting proteins to lipid droplets, whereas the "KASH" domain present in the "downstream" isoforms (klar-RC and -RI) is sufficient for targeting to the nuclear envelope (Guo et al. 2005). The "upstream" nonoverlapping isoform is necessary for proper lipid droplet targeting in the embryo. While the KASH domain is necessary for nuclear migration in the embryo and retina, this function is associated with the "full-length" KASH-containing isoforms. The short KASH-containing isoform, which lacks motor interaction domains, is expressed (Western blot, immunofluorescence) and is apparently enriched in nurse cells but is not sufficient to rescue nuclear migration in the retina. See Figure 2 and Figure 3 for GBrowse track descriptions. More information on data presented in GBrowse may be found at http://flybase.org/wiki/FlyBase:GBrowse_Tracks.
Mentions: Six of these cases have been identified in the literature, but in no case has the functional significance of each of the two nonoverlapping isoforms been fully characterized. The best characterized case is the klar gene (Figure 7). The klar protein has been implicated in microtubule-based transport of lipid droplets (Patterson et al. 2004) and nuclei (Guo et al. 2005). The existence of nonoverlapping transcripts encoding nonoverlapping protein isoforms has been characterized by cDNA analysis, RT-PCR, and Western blot (Guo et al. 2005; Kim et al. 2013).

Bottom Line: FlyBase has adopted a philosophy of excluding low-confidence and low-frequency data from gene model annotations; we also do not attempt to represent all possible permutations for complex and modularly organized genes.The number of identified pseudogenes and mutations in the sequenced strain also increased significantly.We discuss remaining challenges, for instance, identification of functional small polypeptides and detection of alternative translation starts.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138 bmatthew@morgan.harvard.edu.

No MeSH data available.


Related in: MedlinePlus