FlyBase Sequence Feature Report: Dmel\Dmel:r6:3R:15936340:15944683:+

Umbrella record for 30 collections that differ by developmental stage, from 0-2-hr embryos to 30-day adults. Consists of 76-nt single-end and paired-end reads; RNA junctions identified and characterized (presented in GBrowse and in RNA junction reports). Restricted to uniquely aligned reads.

(Graveley, 2011.1.5)

Additional data

Sample preparation

Collection preparation

Mode of assay

Data analysis

RNA-Seq reads were aligned to databases of predicted splice junctions and to gene models using TopHat, STAR and BLAT. A number of criteria were used to distinguish true splice junctions from false positives. First, only reads with a minimum of 6nt overhang across a junction were considered. Second, an entropy score (which reflects the number of offset reads) was calculated for each splice junction, and only junctions with entropy score >2 in at least two biological samples were considered. The set of junctions was filtered further to exclude junctions when intron length less than 41 nt, junctions that join parologous genes and non-canonical splice junctions not supported by other experimental support.

(Graveley, 2011.1.5)

Cell lines

Observed in

Not observed in

Collection: BCM_1_RNAseq_junctions

Symbol

BCM_1_RNAseq_junctions

Title

Exon junction identification from RNA-Seq assays of D. melanogaster, Canton-S strain, 10 developmental stages.

Source and Progenitors

Species of derivation

D. melanogaster

Strain of derivation

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 4 -- 9

organism

Comment: 2-4 hr, rep1, 75nt reads

(Daines et al., 2011)

embryonic stage 4 -- 16

organism

Comment: 2-16 hr, rep1, 75nt reads

2-16 hr, rep2, 100nt reads

(FlyBase Curators, 2016-, Daines et al., 2011)

embryonic stage 16

organism

Comment: 14-16 hr, rep1, 75nt reads

(Daines et al., 2011)

second instar larval stage -- third instar larval stage

organism

Comment: 48 to 120 hrs post egg-lay, rep1, 75nt reads

(Daines et al., 2011)

late third instar larval stage

organism

Comment: wandering, rep1, 75nt reads

wandering, rep2, 100nt reads

(FlyBase Curators, 2016-, Daines et al., 2011)

pupal stage

organism

Comment: aged 1 to 5 days after collection as third instar larvae, rep1, 75nt reads

(Daines et al., 2011)

pupal stage P6 -- pharate adult stage P10

organism

Comment: aged 72 hrs after collection as third instar larvae, rep1, 75nt reads

(Daines et al., 2011)

adult stage | male

organism

Comment: aged 2-3 days post-eclosion, rep1, 75nt reads

(Daines et al., 2011)

adult stage

organism

Comment: aged 17 days post-eclosion, rep1, 75nt reads

(Daines et al., 2011)

adult stage | female

organism

Comment: aged 2-3 days post-eclosion, rep1, 75nt reads

(Daines et al., 2011)

Vector of progenitor construct

Description

Umbrella record for 12 collections that differ by developmental stage, from embryos to aged adults. RNA junctions identified and characterized (presented in GBrowse and in RNA junction reports).

(Daines et al., 2011.3.30)

Additional data

Sample preparation

Collection preparation

Mode of assay

Data analysis

Cell lines

Observed in

Not observed in

Comments

Splice acceptor site identified as a predicted recursive splice site.

(Duff et al., 2015)

Predicted Alternative Junction Differing in Splice Acceptor Site.

Reviewed, but not incorporated into the FlyBase gene model.

Stocks (0)

External Crossreferences and Linkouts ( 0 )

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

3R(+)11770405 (ratchet point)

(Duff et al., 2015)

3R:11762062-11770404

(Daines et al., 2010.2.8)

Dmel:r5:3R:11762062:11770405:+

(FlyBase, 1992-)

Dmel:r6:3R:15936340:15944683:+

(FlyBase, 1992-)

chr3R_11762063_11770404

(Graveley et al., 2010.3.15)

Secondary FlyBase IDs

References (5)

Report Sections

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