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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggtttacgtcctccgcaattatgttcttcgactcttattcttctcttatgttgtttatcagctggtgaaatgggaaaattctaatttcctttgttt...

Basic information

species Zea mays
transcript GRMZM5G824600_T02
intron # 6
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148969452|gb|EE020260.2|EE020260
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|149055770|gb|EE156478.2|EE156478
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTACCCCAAA-GAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|60343794|gb|DN210767.1|DN210767
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|74034792|gb|DT535283.1|DT535283
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|78077865|gb|DV506290.1|DV506290
EST:     TGCTTCTCGAGTTATTGGCATTGACATCCACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|149107259|gb|EE189142.2|EE189142
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGAC
EST: gi|149001497|gb|EE038802.2|EE038802
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CCAAGAACTTTGGAGTTACAGATTTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|61119600|gb|DN560561.1|DN560561
EST:     TTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|60349074|gb|DN216047.1|DN216047
EST:     TAAAAAGTTTGATGTTG                         CAAANGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAA
genomic: TAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAA-GAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAA
EST: gi|148930859|gb|EC873272.2|EC873272
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|78120687|gb|DV539071.1|DV539071
EST:     TAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|78077864|gb|DV506289.1|DV506289
EST:     GCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: GCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|211087315|gb|FL378413.1|FL378413
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|148971977|gb|EE022778.2|EE022778
EST:     TGCTTCTCGCGTTATTGGCATTGACATCGACGATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACCAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|71429707|gb|DR810757.1|DR810757
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|31355494|gb|CD439851.1|CD439851
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATTGACAA-
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCAT-GACAAA
EST: gi|78092172|gb|DV520546.1|DV520546
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|60337655|gb|DN204628.1|DN204628
EST:     ATAAAAAGTTTGATGTTG                         CAAAGANACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAA
genomic: ATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGA-ACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAA
EST: gi|31355047|gb|CD439404.1|CD439404
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|31355865|gb|CD440222.1|CD440222
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|30087007|gb|CB885215.1|CB885215
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|211356389|gb|FL426375.1|FL426375
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGG
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGG
EST: gi|60348372|gb|DN215345.1|DN215345
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|211284800|gb|FL428470.1|FL428470
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|149103654|gb|EE289058.2|EE289058
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|60344516|gb|DN211489.1|DN211489
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|110515671|gb|EE020259.1|EE020259
EST:     TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: TGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
EST: gi|110518190|gb|EE022777.1|EE022777
EST:     CGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG                         CAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC
genomic: CGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 414

GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAACCGATACAGCAGGTCCTGGTCGATCTTACAGATGGCGGCGTGGATTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 299

GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAACCGATACAGCAGGTCCTGGTCGATCTTACAGATGGCGGCGTGGATTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAACCGATACAGCAGGTCCTGGTCGATCTTACAGATGGCGGCGTGGATTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 297

GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggttta ... ctgtttgcagCAAAGAACTTTGGAGTTACAGAATTTGTTAACCCAAAAGAGCATGACAAACCGATACAGCAGGTCCTGGTCGATCTTACAGATGGCGGCGTGGATTACAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTGgtatggtttacgtcctccgcaattatgttcttcgactcttattcttctcttatgttgtttatcagctggtgaaatgggaaaattctaatttcctttgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccgc