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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGCCGCGGGCCGTACGCCGGCCTCGCCGACGGCCGCGTCGTGCGGTGGATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctcgatatcgctccggcgtccactcgttacatgctataatatagtagtactaagatattttgatctgattttttgcattcttgggagaaacgtcatgcaaaatttgttgtttcttggcaaag

Basic information

species Zea mays
transcript GRMZM2G307906_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|149014537|gb|EE044171.2|EE044171
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148948292|gb|EC893809.2|EC893809
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|149029397|gb|EE286196.2|EE286196
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|111189708|gb|EE287844.1|EE287844
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCCATGGAGTGAACTCAACGACCAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|149069891|gb|EE158287.2|EE158287
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|149084689|gb|EE174175.2|EE174175
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148939886|gb|EC884598.2|EC884598
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148960145|gb|EE153395.2|EE153395
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148933910|gb|EC877891.2|EC877891
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148964761|gb|EC906018.2|EC906018
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAAAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|149106557|gb|EE188449.2|EE188449
EST:     TGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: TGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148932422|gb|EC876118.2|EC876118
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|211080974|gb|FL226428.1|FL226428
EST:     ATGGGCGAGGAGGCCGGGTGGGATACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAG
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAG
EST: gi|149060202|gb|EE157176.2|EE157176
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148953528|gb|EE153037.2|EE153037
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|149073029|gb|EE161296.2|EE161296
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148950757|gb|EC896357.2|EC896357
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148972509|gb|EE023471.2|EE023471
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|211080979|gb|FL226433.1|FL226433
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAA
EST: gi|149107258|gb|EE189140.2|EE189140
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|149061131|gb|EE157391.2|EE157391
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148957624|gb|EC903731.2|EC903731
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|149089005|gb|EE178156.2|EE178156
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148948376|gb|EC893892.2|EC893892
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148960572|gb|EE011188.2|EE011188
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148948226|gb|EC893742.2|EC893742
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|149027056|gb|EE046378.2|EE046378
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148934314|gb|EC878340.2|EC878340
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
EST: gi|148952208|gb|EC898009.2|EC898009
EST:     ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTG                         GTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA
genomic: ATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCA

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: 19 (upstream exon), 31 (downstream exon)
Score: 1

AGGGCCGCGGGCCGTACGCCGGCCTCGCCGACGGCCGCGTCGTGCGGTGGATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCACGAGAAGGAGGAGTTCTGCGGCCGGCCGCTCGGCCTGAGGTTCCACGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2470

AGGGCCGCGGGCCGTACGCCGGCCTCGCCGACGGCCGCGTCGTGCGGTGGATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctc ... cttggcaaagGTCAGAAGAAGTCTGTGCCAATGGAGTGAACTCAACGACGAGGAAGCAGCACGAGAAGGAGGAGTTCTGCGGCCGGCCGCTCGGCCTGAGGTTCCACGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGCCGCGGGCCGTACGCCGGCCTCGCCGACGGCCGCGTCGTGCGGTGGATGGGCGAGGAGGCCGGGTGGGAGACGTTCGCCGTCATGAATCCTGACTGgtaagtgctcgatatcgctccggcgtccactcgttacatgctataatatagtagtactaagatattttgatctgattttttgcattcttgggagaaacgtcatgcaaaatttgttgtttcttggcaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG