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General Information
Symbol
Dmel\Dmel:r6:3L:7828712:7853183:-
Species
D. melanogaster
Feature type
FlyBase ID
FBsf0000175035
Collection
Associated gene
Genomic Location
Chromosome (arm)
3L
Sequence location

3L:7,828,712..7,853,183 [-]

Sequence Data
Length
Comments

GT..AG

Associated Information
Gene(s) (targeted or local)
    Allele(s)
      Transcripts(s)
        Polypeptide(s)
          Construct
            Experimental Data
            RNA-Seq Read Counts
            Dataset: modENCODE_mRNA-Seq_U_junctions
            Expression stage(s)
            Read Count
            embryonic stage 1 -- 4

            Comment: 0-2 hr AEL

            0
            embryonic stage 4 -- 9

            Comment: 2-4 hr AEL

            0
            embryonic stage 9 -- 11

            Comment: 4-6 hr AEL

            0
            embryonic stage 11 -- 12

            Comment: 6-8 hr AEL

            0
            embryonic stage 12 -- 13

            Comment: 8-10 hr AEL

            1
            embryonic stage 13 -- 15

            Comment: 10-12 hr AEL

            2
            embryonic stage 15 -- 16

            Comment: 12-14 hr AEL

            6
            embryonic stage 16

            Comment: 14-16 hr AEL

            0
            embryonic stage 17(i)

            Comment: 16-18 hr AEL

            9
            embryonic stage 17(ii)

            Comment: 18-20 hr AEL

            2
            embryonic stage 17(iii)

            Comment: 20-22 hr AEL

            7
            embryonic stage 17(iv)

            Comment: 22-24 hr AEL

            3
            first instar larval stage

            Comment: 42-44hr AEL

            0
            second instar larval stage

            Comment: 66-70h AEL

            2
            3
            third instar - uncleared gut stage

            Comment: indicated as puff stage 1-2

            0
            third instar - partially cleared gut stage

            Comment: indicated as puff stage 3-6

            0
            third instar - cleared gut stage

            Comment: indicated as puff stage 7-9

            0
            pupal stage P5

            Comment: aged 12 hrs after collection as white prepupae

            0
            pupal stage P6

            Comment: aged 24 hrs after collection as white prepupae

            0
            pharate adult stage P8

            Comment: aged 2 days after collection as white prepupae

            1
            pharate adult stage P9 -- P10

            Comment: aged 3 days after collection as white prepupae

            0
            pharate adult stage P15

            Comment: aged 4 days after collection as white prepupae

            1
            day 1 of adulthood | female

            Comment: aged 1 day after eclosion

            0
            day 1 of adulthood | male

            Comment: aged 1 day after eclosion

            0
            day 5 of adulthood | female

            Comment: aged 5 days after eclosion

            0
            day 5 of adulthood | male

            Comment: aged 5 days after eclosion

            1
            day 30 of adulthood | female

            Comment: aged 30 days after eclosion

            1
            day 30 of adulthood | male

            Comment: aged 30 days after eclosion

            0

            Total
            41
            Collection Information
            Collection: modENCODE_mRNA-Seq_U_junctions
            Title
            Exon junction identification from RNA-Seq assays of D. melanogaster, iso-1 strain, 30 developmental stages.
            Source and Progenitors
            Species of derivation
            D. melanogaster
            Strain of derivation
            Stage
            Tissue/Position (including subcellular localization)
            Reference
            organism

            Comment: aged 12 hrs after collection as white prepupae

            organism

            Comment: aged 24 hrs after collection as white prepupae

            organism

            Comment: aged 2 days after collection as white prepupae

            organism

            Comment: aged 3 days after collection as white prepupae

            organism

            Comment: aged 4 days after collection as white prepupae

            organism

            Comment: aged 1 day after eclosion

            organism

            Comment: aged 1 day after eclosion

            organism

            Comment: aged 5 days after eclosion

            organism

            Comment: aged 5 days after eclosion

            organism

            Comment: aged 30 days after eclosion

            organism

            Comment: aged 30 days after eclosion

            Vector of progenitor construct
            Description

            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.

            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.

            Cell lines
            Observed in
            Not observed in
            Comments

            Splice acceptor site identified as a predicted recursive splice site.

            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
            3L(-)7821812 (ratchet point)
            Dmel:r5:3L:7821812:7846283:-
            Dmel:r6:3L:7828712:7853183:-
            PAR-domain protein 1 intron 1 site
            chr3L_7821813_7846282
            Secondary FlyBase IDs
              References (5)