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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGGTGGCGGCGCCGGCTTTCTCCATGAACACGGTGGCTTTGTTGTCCTTGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctttgtcccccttcctccttgtttccgggttccgtttcttccctgtttgggcctctctgatgccagaaaccatagtttctgtttctttttctt...

Basic information

species Zea mays
transcript GRMZM2G038487_T03
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|74238024|gb|DT645938.1|DT645938
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAAGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|78104299|gb|DV522717.1|DV522717
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211144702|gb|FL413099.1|FL413099
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|93012412|gb|EB637932.1|EB637932
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211477142|gb|FL427782.1|FL427782
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211151550|gb|FL386542.1|FL386542
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|148963856|gb|EE014962.2|EE014962
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211323397|gb|FL381741.1|FL381741
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GTCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|33467307|gb|CF244356.1|CF244356
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|37421692|gb|CF648547.1|CF648547
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|91055890|gb|EB166308.1|EB166308
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211386924|gb|FL369297.1|FL369297
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|71768332|gb|DR966269.1|DR966269
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211006759|gb|FL429448.1|FL429448
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211454292|gb|FL396775.1|FL396775
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|78113363|gb|DV531755.1|DV531755
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211076904|gb|FL402121.1|FL402121
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211347947|gb|FL254258.1|FL254258
EST:     TTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211116917|gb|FL407739.1|FL407739
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211279400|gb|FL429235.1|FL429235
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211228027|gb|FL407502.1|FL407502
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|211048371|gb|FL399856.1|FL399856
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
EST: gi|148961499|gb|EE012250.2|EE012250
EST:     TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAG                         GGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC
genomic: TGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctt ... ggctgtgcagGGCGTTGGCCGCTATGGCGGAATCAAGGTGTACGCCGTGCTCAGAGACGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGGTGGCGGCGCCGGCTTTCTCCATGAACACGGTGGCTTTGTTGTCCTTGGCGCCGCAGCTGCTCATTAAGCCCTCCCTCACCTGTTTCTCCAGAAAGgtcggttctttgtcccccttcctccttgtttccgggttccgtttcttccctgtttgggcctctctgatgccagaaaccatagtttctgtttctttttctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT