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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatacaatatggattgttggtcaagacacaaaaaaatggtacttttggctgaaagcctgaaggttaaactaaaatttcctttttccctgtgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCATGGCTGTAGCTTGCTAGGCCCTGCTTTCCTGTTTGTACAGATACATCAT

Basic information

species Zea mays
transcript GRMZM2G114337_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|211033201|gb|FK982742.1|FK982742
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|211033208|gb|FK982749.1|FK982749
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|211033204|gb|FK982745.1|FK982745
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|211033202|gb|FK982743.1|FK982743
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCACTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|211033206|gb|FK982747.1|FK982747
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|28568846|gb|CB280721.1|CB280721
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|211033207|gb|FK982748.1|FK982748
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|149084285|gb|EE173718.2|EE173718
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|31612154|gb|CD568776.1|CD568776
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|76929761|gb|DV172149.1|DV172149
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|148959781|gb|EE011019.2|EE011019
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|101389979|gb|EB816921.1|EB816921
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|76284048|gb|DV023616.1|DV023616
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGGTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|71772775|gb|DR970700.1|DR970700
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|89248001|gb|DY619787.1|DY619787
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|211033203|gb|FK982744.1|FK982744
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|71433032|gb|DR814082.1|DR814082
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA
EST: gi|74231907|gb|DT639821.1|DT639821
EST:     GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGG                         GTTTTTGGATTTTGATCAGTTATATCAAAGGAGTGCTTATGGATGATTTCA
genomic: GTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCA

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: 44 (upstream exon), 49 (downstream exon)
Score: 136

CTGCCTGTTACCGGCTTCCTGGTGGTCGACCGGTGCGGCGCGGGTCGTCAGTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCATGGCTGTAGCTTGCTAGGCCCTGCTTTCCTGTTTGTACAGATACATCAT


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 70

CTGCCTGTTACCGGCTTCCTGGTGGTCGACCGGTGCGGCGCGGGTCGTCAGTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCATGGCTGTAGCTTGCTAGGCCCTGCTTTCCTGTTTGTACAGATACATCAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 63

CTGCCTGTTACCGGCTTCCTGGTGGTCGACCGGTGCGGCGCGGGTCGTCAGTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCATGGCTGTAGCTTGCTAGGCCCTGCTTTCCTGTTTGTACAGATACATCAT


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 22

CTGCCTGTTACCGGCTTCCTGGTGGTCGACCGGTGCGGCGCGGGTCGTCAGTGAAGCTCCGACTATCCGGATTGACTCGGATCGACCTCTCCTCTCGTGGgtaagcgact ... tgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCATGGCTGTAGCTTGCTAGGCCCTGCTTTCCTGTTTGTACAGATACATCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggctgaaagcctgaaggttaaactaaaatttcctttttccctgtgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCATGGCTGTAGCTTGCTAGGCCCTGCTTTCCTGTTTGTACAGATACATCAT
                      aactaaa  putative branch site (score: 22)
                              tttcctttttccctgt  CT-rich tract
                   ttaaactaaaatttcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatacaatatggattgttggtcaagacacaaaaaaatggtacttttggctgaaagcctgaaggttaaactaaaatttcctttttccctgtgttgtccagGTTTTTGGATTTTGATCAGTTATATCAGAGGAGTGCTTATGGATGATTTCATGGCTGTAGCTTGCTAGGCCCTGCTTTCCTGTTTGTACAGATACATCAT

- - - - - - - -tgttggt
- - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - -tggtact
- - - - - - - - - - - - - - - - - - - - - - - - gctgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa