Dataset mE_MB8_gene_predictions

General Information
Name	mE_MB8_gene_predictions	Species	D. melanogaster
Dataset type	predicted_gene_model_set	FlyBase ID	FBlc0000285
Source & Content
Consists of	Predicted transcripts and corresponding protein-coding regions. (Graveley et al., 2011)
Created by
Available from
Strain
Stage & tissue

Cell Line
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Description & Members
Description	Genome annotation is done in cycles consisting of gene prediction, target selection and RT-PCR sequencing of the targets. The gene prediction programs used are N-SCAN (Brent Lab) and Contrast (Sam Gross), both of which use conservation and transcription evidence. Before each round of gene prediction, new cDNAs and ESTs are downloaded from GenBank, and are clustered using the PASA pipeline developed by Brian Haas at TIGR. These clusters are then converted to an 'EST evidence track' that can be used by the program. Similarly, a conservation track is created from alignments of 'informant' species to the target genome. Predicted transcripts (models) are classified as 'supported', 'partially supported', and 'novel' based on overlap with transcripts. If all splice sites of a transcript model are present in cDNAs, this transcript is supported. Transcripts with no supported splice sites are novel. Novel and partially supported genes are targeted for PCR on reverse transcribed RNA from one or multiple tissues. Primers are designed around unsupported splices. If a spliced sequence results from the PCR it is submitted to GenBank (whether or not it supports the transcript model) and it becomes part of the EST/cDNA download for the next round of gene predictions. The cycles are numbered and prefixed "DMG". (Graveley et al., 2011)
Parent collections
Component collection(s)
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector
Sample preparation
Collection preparation
Mode of assay
Assay platform
Data analysis
Additional data

Associated files
Additional sites
Synonyms & Secondary IDs
Reported As
Symbol Synonym	MB8 gene models (Graveley et al., 2011) mE_MB8_gene_predictions new transcript models (Graveley et al., 2011)
Secondary FlyBase IDs

References ( 2 )
Research paper	Graveley et al., 2011, Nature 471(7339): 473--479 The developmental transcriptome of Drosophila melanogaster. [FBrf0213330]
Supplementary material	Graveley et al., 2011, Nature 471(7339): Supplementary Table 34: modENCODE transcript models. [FBrf0213556]