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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaacacgtgcttgaaaatcaaaacagaacactggtaatcttgtgcttcatggacttcgatgcgcgttaaactctgccaaaattgtcattctgatgcagGCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGGCACTGGATCCAGTTTTGCTTGTTGGAGTGGCATGTAGATATAAGGTTCG

Basic information

species Zea mays
transcript GRMZM2G431314_T01
intron # 5
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|32860432|gb|CF000114.1|CF000114
EST:     CATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
genomic: CATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
EST: gi|211530065|gb|FL044681.1|FL044681
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
EST: gi|89762268|gb|DY689943.1|DY689943
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
EST: gi|37383180|gb|CF628580.1|CF628580
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCTAAAGCTTTGGCCTAAGGATCGGAGCCAGTAGCAGG
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
EST: gi|71445787|gb|DR826837.1|DR826837
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
EST: gi|31352450|gb|CD436807.1|CD436807
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
EST: gi|5847563|gb|AW000642.1|AW000642
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
EST: gi|74243723|gb|DT651637.1|DT651637
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcatggacttcgatgcgcgttaaactctgccaaaattgtcattctgatgcagGCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGGCACTGGATCCAGTTTTGCTTGTTGGAGTGGCATGTAGATATAAGGTTCG
                                            ttctgat  putative branch site (score: 3)
                                         tcattct  CT-rich tract
                                  aaaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaacacgtgcttgaaaatcaaaacagaacactggtaatcttgtgcttcatggacttcgatgcgcgttaaactctgccaaaattgtcattctgatgcagGCAAAGGCGTGAGGCTAAAGCTTTGGCCAAAGGATCGGAGCCAGTAGCAGGCACTGGATCCAGTTTTGCTTGTTGGAGTGGCATGTAGATATAAGGTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
aagaaca
- - - - -tgcttga
- - - - - - - - -aatcaaa
- - - - - - - - - - - - acagaaca
- - - - - - - - - - - - - - - - - - - - - -gtgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcgatgc