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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctagcctgtgttacttctttgttttatgttacttgttgaactgatcctagcgttacttttcctccttttgtctgtctgtttgtttgtctgtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAGAAT

Basic information

species Zea mays
transcript GRMZM2G049382_T01
intron # 1
splice site 3'
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|78077755|gb|DV506187.1|DV506187
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|74237928|gb|DT645842.1|DT645842
EST:     GCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|94476136|gb|EB705094.1|EB705094
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|211441856|gb|FL182593.1|FL182593
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|78109677|gb|DV528093.1|DV528093
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|93014379|gb|EB639899.1|EB639899
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|71775361|gb|DR973239.1|DR973239
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|93016747|gb|EB642267.1|EB642267
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|30306535|gb|CD001208.1|CD001208
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|71437491|gb|DR818541.1|DR818541
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|71444264|gb|DR825314.1|DR825314
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|17970113|gb|BM276864.1|BM276864
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|32919043|gb|CF023855.1|CF023855
EST:     CCGCCTGCGGGCGCCGCAAGGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: CCGCCTGCGGGCGCCGCAA-GCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|76015982|gb|DT943152.1|DT943152
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|74241229|gb|DT649143.1|DT649143
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|211441853|gb|FL182590.1|FL182590
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|87298772|gb|DY470775.1|DY470775
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|76015122|gb|DT942292.1|DT942292
EST:     GCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|32943700|gb|CF048519.1|CF048519
EST:     CCGCCTGCGGGCGCCGCAAGGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: CCGCCTGCGGGCGCCGCAA-GCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|211441855|gb|FL182592.1|FL182592
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|71437490|gb|DR818540.1|DR818540
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|149081435|gb|EE170555.2|EE170555
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|101389927|gb|EB816894.1|EB816894
EST:     CGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: CGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|22489209|gb|BU049119.1|BU049119
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|32918957|gb|CF023769.1|CF023769
EST:     CCGCCTGCGGGCGCCGCAAGGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGGTCAACAAGACTTAGTCCAACCCTACT
genomic: CCGCCTGCGGGCGCCGCAA-GCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|78109421|gb|DV527837.1|DV527837
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|149015537|gb|EE045415.2|EE045415
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|211441852|gb|FL182589.1|FL182589
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|211441854|gb|FL182591.1|FL182591
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TTTATTTACGGAAG-TTACAATTGATCAACAAGACTTAGTCCAACCCTACT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACT
EST: gi|76286587|gb|DV026155.1|DV026155
EST:     CGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: CGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt
EST: gi|50330365|gb|CO525491.1|CO525491
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGTAG                       
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-T-Ggtaactgctc ... gtggcagt

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: 24

ACTCGGAGTCTTCCCCCACCCCCATAACGTCCTCTTCCGTGCTCTGCGTTGCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 21

ACTCGGAGTCTTCCCCCACCCCCATAACGTCCTCTTCCGTGCTCTGCGTTGCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAGAAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 10

ACTCGGAGTCTTCCCCCACCCCCATAACGTCCTCTTCCGTGCTCTGCGTTGCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 14

ACTCGGAGTCTTCCCCCACCCCCATAACGTCCTCTTCCGTGCTCTGCGTTGCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... gtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctagcgttacttttcctccttttgtctgtctgtttgtttgtctgtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAGAAT
        ttactttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctagcctgtgttacttctttgttttatgttacttgttgaactgatcctagcgttacttttcctccttttgtctgtctgtttgtttgtctgtggcagtagTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG