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General Information
Symbol
Dmel\Dmel:r6:X:13239225:13256617:-
Species
D. melanogaster
Feature type
FlyBase ID
FBsf0000184451
Collection
Associated gene
Genomic Location
Chromosome (arm)
X
Sequence location

X:13,239,225..13,256,617 [-]

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

          2
          embryonic stage 9 -- 11

          Comment: 4-6 hr AEL

          7
          embryonic stage 11 -- 12

          Comment: 6-8 hr AEL

          0
          embryonic stage 12 -- 13

          Comment: 8-10 hr AEL

          4
          embryonic stage 13 -- 15

          Comment: 10-12 hr AEL

          1
          embryonic stage 15 -- 16

          Comment: 12-14 hr AEL

          2
          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

          1
          embryonic stage 17(iii)

          Comment: 20-22 hr AEL

          1
          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

          1
          0
          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

          7
          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

          0
          day 1 of adulthood | female

          Comment: aged 1 day after eclosion

          1
          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

          0
          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
          31
          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.

          Matches FlyBase Annotated Junction.

          Stocks (0)
          External Crossreferences and Linkouts ( 0 )
          Synonyms and Secondary IDs (4)
          Reported As
          Symbol Synonym
          Dmel:r5:X:13133258:13150650:-
          Dmel:r6:X:13239225:13256617:-
          chrX_13133259_13150649
          multiple edematous wings intron 3 site
          Secondary FlyBase IDs
            References (4)