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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagctacgctacgacgtgggcgtggcgttcagttcccacagcagtgtgtgctctgtctgaaagctttcttgtgtgcttcattcag

Basic information

species Zea mays
transcript GRMZM2G024887_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024887_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g45010.1 (Oryza sativa), 5'ss of exon 2
ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagctacgctacgacgtgggcgtggcgttcagttcc-cacagcagtgtgtgctctgtctgaaagctttcttgtgtgcttcattcag
|||||||||||||| ||||||||||| || || ||||||||||||||||| |||||||||||||||||||| ||||||||||||||||| ||| ||||||||||||||  |   || ||    ||  | |  |||  ||| |  |    |  |  |  |   |||  |   |||  |||||   |   ||||
ATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAGgtaatgtaa-tgtactgcg----ggtagagaggtttggtttcatatcaaaaaggcttattgatcttgacagtttactgtgttacttgatcag

upper sequence: GRMZM2G024887_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G01780.1 (Arabidopsis thaliana), 5'ss of exon 2
ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgta-atgtagctacg-ctacgacgtgggcgtggcgttcagttcccacagcagtgtgtgctctgtctgaaagctttcttgtgtgcttcattcag
||| ||| ||| || ||||||||||| ||  ||||||||||||| || || ||||| |||||||||||  | || |  |||  ||| |||||    ||||||   | |    |   ||  ||| | |        |  |  |  || | ||   ||  |      | | |  | ||||   |   |||     
ATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAGgttcgtattataaaatctctgacatcgaatc--tctctatctttcaaatcatcatgatca-----taacaagtctctttcttttctcag----
















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|211391775|gb|FL355251.1|FL355251
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|211455531|gb|FL349675.1|FL349675
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|21480972|gb|BQ577655.1|BQ577655
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|211378105|gb|FL329996.1|FL329996
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|32869494|gb|CF009176.1|CF009176
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|32870818|gb|CF010500.1|CF010500
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|211331555|gb|FL357939.1|FL357939
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|211007496|gb|FL346568.1|FL346568
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|18661649|gb|BM501509.1|BM501509
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|21480781|gb|BQ577464.1|BQ577464
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|211134068|gb|FL308365.1|FL308365
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTGACAAGGG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTGACAAGGG
EST: gi|211267283|gb|FL319971.1|FL319971
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTSTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|26455128|gb|CA826711.1|CA826711
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|21330893|gb|BQ486274.1|BQ486274
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|21480794|gb|BQ577477.1|BQ577477
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|116819068|gb|EC862153.1|EC862153
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCGAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|32868868|gb|CF008550.1|CF008550
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|21330183|gb|BQ485564.1|BQ485564
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|9743144|gb|BE519292.1|BE519292
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|32869353|gb|CF009035.1|CF009035
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|21330046|gb|BQ485441.1|BQ485441
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|21330759|gb|BQ486140.1|BQ486140
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|32906533|gb|CF011346.1|CF011346
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|211130928|gb|FL366516.1|FL366516
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|211475203|gb|FL333739.1|FL333739
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTGACA
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTGACA
EST: gi|50325577|gb|CO520703.1|CO520703
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|21330096|gb|BQ485477.1|BQ485477
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG
EST: gi|78109383|gb|DV527799.1|DV527799
EST:     CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG                         GTGGCAAGTCTTCAGACAAGGGTGAACTG
genomic: CGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG

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 2 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 29 (downstream exon)
Score: 2

ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG


Block sizes: 49 (upstream exon), 29 (downstream exon)
Score: 183

ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagc ... cttcattcagGTGGCAAGTCTTCAGACAAGGGTGAACTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAGgtaatgtagctacgctacgacgtgggcgtggcgttcagttcccacagcagtgtgtgctctgtctgaaagctttcttgtgtgcttcattcag

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC