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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAACCGCCTCTTTGCTCTCTCCCTGTCCCCGCCCTGCCCGCGCCCTGCCTGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccaccgggtgcactccacctgttcgacttaattacgcacaacttaggccatctagtctaccaaagcatagcatagcatagtacaacactcatagcttgtggctttgatccggcag

Basic information

species Zea mays
transcript GRMZM5G896082_T01
intron # 1
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|149051802|gb|EE155929.2|EE155929
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|149070758|gb|EE159171.2|EE159171
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|71325794|gb|DR799576.1|DR799576
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|76293829|gb|DV033397.1|DV033397
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|50329134|gb|CO524260.1|CO524260
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|148959398|gb|EC905432.2|EC905432
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|78092904|gb|DV521278.1|DV521278
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|71449206|gb|DR830256.1|DR830256
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|74239749|gb|DT647663.1|DT647663
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|71435282|gb|DR816332.1|DR816332
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|50328983|gb|CO524109.1|CO524109
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|71773101|gb|DR971019.1|DR971019
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|149097127|gb|EE182939.2|EE182939
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|37426517|gb|CF651015.1|CF651015
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|33467672|gb|CF244721.1|CF244721
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGCGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|211033504|gb|FL333366.1|FL333366
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|149111107|gb|EE294603.2|EE294603
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|149058763|gb|EE156781.2|EE156781
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|71322554|gb|DR797954.1|DR797954
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|148971891|gb|EE022659.2|EE022659
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|78114034|gb|DV532423.1|DV532423
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|71775245|gb|DR973123.1|DR973123
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|89757906|gb|DY687292.1|DY687292
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|211111363|gb|FL325867.1|FL325867
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|149011246|gb|EE042332.2|EE042332
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|78107802|gb|DV526220.1|DV526220
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
EST: gi|148949267|gb|EC894710.2|EC894710
EST:     TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAG                         GCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT
genomic: TGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCT

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: 38 (upstream exon), 49 (downstream exon)
Score: 8

ACAACCGCCTCTTTGCTCTCTCCCTGTCCCCGCCCTGCCCGCGCCCTGCCTGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCTACTGCAGCATCGACAGGAAGCAGAAGAAGACGCTGGGAGAGATGGAGCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 34

ACAACCGCCTCTTTGCTCTCTCCCTGTCCCCGCCCTGCCCGCGCCCTGCCTGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCTACTGCAGCATCGACAGGAAGCAGAAGAAGACGCTGGGAGAGATGGAGCA


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 5

ACAACCGCCTCTTTGCTCTCTCCCTGTCCCCGCCCTGCCCGCGCCCTGCCTGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCTACTGCAGCATCGACAGGAAGCAGAAGAAGACGCTGGGAGAGATGGAGCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 17

ACAACCGCCTCTTTGCTCTCTCCCTGTCCCCGCCCTGCCCGCGCCCTGCCTGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccacc ... gatccggcagGCCAGGTTCAGGAGCAAGATGACGAGGTGGTGGACAGGAACATCCTCCCCTACTGCAGCATCGACAGGAAGCAGAAGAAGACGCTGGGAGAGATGGAGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAACCGCCTCTTTGCTCTCTCCCTGTCCCCGCCCTGCCCGCGCCCTGCCTGTGCTGCGTGTCCGTCGCCGCCGCCGACTTCGCGCCACCGAGCAGCAAGgtcttccaccgggtgcactccacctgttcgacttaattacgcacaacttaggccatctagtctaccaaagcatagcatagcatagtacaacactcatagcttgtggctttgatccggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG