Sequence Feature: exon_junction

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General Information
Symbol	Dmel:r5:X:11499111:11499171:+	Species	D. melanogaster
Feature type	exon_junction	FlyBase ID	FBsf0000135787
Collection	BCM_1_RNAseq_junctions modENCODE_mRNA-Seq_U_junctions	Associated gene(s)	rho-4
Genomic Location
Chromosome (arm)	X	Sequence location	X:11,499,111..11,499,171 [+]
Map ( GBrowse )
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Sequence Data
Length
Comments	GT..AG
Sequence
Associated Information
Gene(s) (targeted or local)
Allele(s)
Transcripts(s)
Polypeptide(s)
Construct
Experimental Data
RNA-Seq Read Counts
Library: BCM_1_RNAseq_junctions
BCM_1_RNAseq_junctions	Expression stage(s) Read Count embryonic stage 4 -- 9 Comment:2-4hr 1 embryonic stage 4 -- 16 Comment:2-16 hr 14 embryonic stage 4 -- 16 Comment:2-16 hr 13 embryonic stage 16 Comment:14-16 hr 10 second instar larval stage -- third instar larval stage Comment:48 to 120 hrs post egg-lay 47 late third instar larval stage Comment:wandering 14 late third instar larval stage Comment:wandering 6 pupal stage Comment:aged 1 to 5 days after collection as third instar larvae 22 pupal stage P6 -- pharate adult stage P10 Comment:aged 72 hrs after collection as third instar larvae 28 adult stage Comment:aged 17 days post-eclosion 32 adult stage \| female Comment:aged 2-3 days post-eclosion 13 adult stage \| male Comment:aged 2-3 days post-eclosion 3 Total 203
Library: modENCODE_mRNA-Seq_U_junctions
modENCODE_mRNA-Seq_U_junctions	Expression stage(s) Read Count embryonic stage 1 -- 4 Comment:0-2 hr 252 embryonic stage 4 -- 9 Comment:2-4 hr 397 embryonic stage 9 -- 11 Comment:4-6 hr 744 embryonic stage 11 -- 12 Comment:6-8 hr 348 embryonic stage 12 -- 13 Comment:8-10 hr 270 embryonic stage 13 -- 15 Comment:10-12 hr 277 embryonic stage 15 -- 16 Comment:12-14 hr 374 embryonic stage 16 Comment:14-16 hr 293 embryonic stage 17(i) Comment:16-18 hr 165 embryonic stage 17(ii) Comment:18-20 hr 127 embryonic stage 17(iii) Comment:20-22 hr 218 embryonic stage 17(iv) Comment:22-24 hr 314 first instar larval stage 140 second instar larval stage 270 early third instar larval stage Comment:12 hr post-molt 53 third instar - uncleared gut stage Comment:indicated as puff stage 1-2 89 third instar - partially cleared gut stage Comment:indicated as puff stage 3-6 151 third instar - cleared gut stage Comment:indicated as puff stage 7-9 284 prepupal stage P1 468 pupal stage P5 Comment:aged 12 hrs after collection as white prepupae 275 pupal stage P6 Comment:aged 24 hrs after collection as white prepupae 270 pharate adult stage P8 Comment:aged 2 days after collection as white prepupae 306 pharate adult stage P9 -- P10 Comment:aged 3 days after collection as white prepupae 140 pharate adult stage P15 Comment:aged 4 days after collection as white prepupae 71 day 1 of adulthood \| female Comment:aged 1 day after eclosion 196 day 1 of adulthood \| male Comment:aged 1 day after eclosion 77 day 5 of adulthood \| female Comment:aged 5 days after eclosion 136 day 5 of adulthood \| male Comment:aged 5 days after eclosion 88 day 30 of adulthood \| female Comment:aged 30 days after eclosion 131 day 30 of adulthood \| male Comment:aged 30 days after eclosion 98 Total 7022
Progenitors
PCR template
Primer 1
Primer 2
Comments
Collection Information
Collection: BCM_1_RNAseq_junctions
Symbol	BCM_1_RNAseq_junctions
Source and Progenitors
Species of derivation	D. melanogaster
Strain of derivation

Vector or 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
	See report for BCM_1_RNAseq. (Daines et al., 2011.3.30)
Collection: modENCODE_mRNA-Seq_U_junctions
Symbol	modENCODE_mRNA-Seq_U_junctions
Source and Progenitors
Species of derivation	D. melanogaster
Strain of derivation

Vector or 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. (Graveley, 2011.1.5)
Additional data
	See report for modENCODE_mRNA-Seq_U. (Graveley, 2011.1.5)
Cell lines
Observed in
Not observed in
Comments
	Matches FlyBase Annotated Junction.
Stocks Listed in FlyBase ( 0 )

External Crossreferences & Linkouts

Synonyms & Secondary IDs ( 3 )
Reported As
Symbol Synonym	chrX_11499112_11499170 (Graveley et al., 2010.03.15) Dmel:r5:X:11499111:11499171:+ (FlyBase, 1992-) X:11499111-11499170 (Daines et al., 2010.2.8)
Secondary FlyBase IDs

References ( 4 )
Personal communication to FlyBase	Graveley, 2011.11.3, Total entropy scores for the 67,317 modENCODE junctions. Total entropy scores for the 67,317 modENCODE junctions. [FBrf0216691] Daines et al., 2010.2.8, Drosophila melanogaster mRNA high-throughput sequencing Drosophila melanogaster mRNA high-throughput sequencing [FBrf0210193] Graveley et al., 2010.03.15, The D. melanogaster transcriptome: modENCODE RNA-Seq data The D. melanogaster transcriptome: modENCODE RNA-Seq data [FBrf0210195]
FlyBase analysis	FlyBase, 1992-, FlyBase curation. FlyBase curation. [FBrf0105495]