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General Information
Symbol
Dmel\Dmel:r6:3R:9420047:9444011:+
Species
D. melanogaster
Feature type
FlyBase ID
FBsf0000114673
Genomic Location
Chromosome (arm)
3R
Sequence location

3R:9,420,047..9,444,011 [+]

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: BCM_1_RNAseq_junctions
            Expression stage(s)
            Read Count
            embryonic stage 4 -- 9

            Comment: 2-4 hr

            0
            embryonic stage 4 -- 16

            Comment: 2-16 hr

            0
            embryonic stage 4 -- 16

            Comment: 2-16 hr

            0
            embryonic stage 16

            Comment: 14-16 hr

            0
            second instar larval stage -- third instar larval stage

            Comment: 48 to 120 hrs post egg-lay

            0
            pupal stage

            Comment: aged 1 to 5 days after collection as third instar larvae

            0
            pupal stage P6 -- pharate adult stage P10

            Comment: aged 72 hrs after collection as third instar larvae

            0
            adult stage

            Comment: aged 17 days post-eclosion

            0
            adult stage | female

            Comment: aged 2-3 days post-eclosion

            0
            adult stage | male

            Comment: aged 2-3 days post-eclosion

            0

            Total
            0
            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

            0
            embryonic stage 13 -- 15

            Comment: 10-12 hr AEL

            0
            embryonic stage 15 -- 16

            Comment: 12-14 hr AEL

            0
            embryonic stage 16

            Comment: 14-16 hr AEL

            0
            embryonic stage 17(i)

            Comment: 16-18 hr AEL

            1
            embryonic stage 17(ii)

            Comment: 18-20 hr AEL

            0
            embryonic stage 17(iii)

            Comment: 20-22 hr AEL

            0
            embryonic stage 17(iv)

            Comment: 22-24 hr AEL

            0
            first instar larval stage

            Comment: 42-44hr AEL

            0
            second instar larval stage

            Comment: 66-70h AEL

            2
            1
            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

            1
            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

            0
            pharate adult stage P9 -- P10

            Comment: aged 3 days after collection as white prepupae

            1
            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

            2
            day 1 of adulthood | male

            Comment: aged 1 day after eclosion

            2
            day 5 of adulthood | female

            Comment: aged 5 days after eclosion

            1
            day 5 of adulthood | male

            Comment: aged 5 days after eclosion

            1
            day 30 of adulthood | female

            Comment: aged 30 days after eclosion

            0
            day 30 of adulthood | male

            Comment: aged 30 days after eclosion

            0

            Total
            13
            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
            Collection: 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
            organism

            Comment: aged 1 to 5 days after collection as third instar larvae

            organism

            Comment: aged 72 hrs after collection as third instar larvae

            organism

            Comment: aged 17 days post-eclosion

            organism

            Comment: aged 2-3 days post-eclosion

            organism

            Comment: aged 2-3 days post-eclosion

            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).

            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.

            Predicted Alternative Junction.

            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:5245769-5269732
            Dmel:r5:3R:5245769:5269733:+
            Dmel:r6:3R:9420047:9444011:+
            chr3R_5245770_5269732
            pasilla intron 1 site
            Secondary FlyBase IDs
              References (5)