Open Close
General Information
Symbol
Dmel\Dmel:r6:3R:16710612:16732725:-
Species
D. melanogaster
Feature type
FlyBase ID
FBsf0000141823
Genomic Location
Chromosome (arm)
3R
Sequence location

3R:16,710,612..16,732,725 [-]

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

          12
          embryonic stage 16

          Comment: 14-16 hr

          1
          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
          15
          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

          1
          embryonic stage 9 -- 11

          Comment: 4-6 hr AEL

          15
          embryonic stage 11 -- 12

          Comment: 6-8 hr AEL

          27
          embryonic stage 12 -- 13

          Comment: 8-10 hr AEL

          40
          embryonic stage 13 -- 15

          Comment: 10-12 hr AEL

          63
          embryonic stage 15 -- 16

          Comment: 12-14 hr AEL

          69
          embryonic stage 16

          Comment: 14-16 hr AEL

          47
          embryonic stage 17(i)

          Comment: 16-18 hr AEL

          32
          embryonic stage 17(ii)

          Comment: 18-20 hr AEL

          22
          embryonic stage 17(iii)

          Comment: 20-22 hr AEL

          4
          embryonic stage 17(iv)

          Comment: 22-24 hr AEL

          11
          first instar larval stage

          Comment: 42-44hr AEL

          6
          second instar larval stage

          Comment: 66-70h AEL

          3
          3
          third instar - uncleared gut stage

          Comment: indicated as puff stage 1-2

          4
          third instar - partially cleared gut stage

          Comment: indicated as puff stage 3-6

          2
          third instar - cleared gut stage

          Comment: indicated as puff stage 7-9

          21
          pupal stage P5

          Comment: aged 12 hrs after collection as white prepupae

          9
          pupal stage P6

          Comment: aged 24 hrs after collection as white prepupae

          15
          pharate adult stage P8

          Comment: aged 2 days after collection as white prepupae

          8
          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

          2
          day 1 of adulthood | female

          Comment: aged 1 day after eclosion

          4
          day 1 of adulthood | male

          Comment: aged 1 day after eclosion

          6
          day 5 of adulthood | female

          Comment: aged 5 days after eclosion

          2
          day 5 of adulthood | male

          Comment: aged 5 days after eclosion

          6
          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
          441
          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.

          Matches FlyBase Annotated Junction.

          Stocks (0)
          External Crossreferences and Linkouts ( 0 )
          Synonyms and Secondary IDs (5)
          Reported As
          Symbol Synonym
          3R:12536334-12558446
          Dmel:r5:3R:12536334:12558447:-
          Dmel:r6:3R:16710612:16732725:-
          Ultrabithorax intron 3 site
          chr3R_12536335_12558446
          Secondary FlyBase IDs
            References (5)