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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgacatccctacccgtgataagcccatcatggttcattttcactatagagtttcactgtatctttcaaacttagtcttatttcttattttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAGGTGACTCCCCACCGCGCCCATGGGTGACAGCCAGTACTCCTTCTCCCTC

Basic information

species Zea mays
transcript GRMZM5G824831_T02
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|71445140|gb|DR826190.1|DR826190
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACG               
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-C-CT-C----TC--CA-A-Ggtctgcacac ...
EST: gi|211156519|gb|FL164233.1|FL164233
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACG               
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-C-CT-C----TC--CA-A-Ggtctgcacac ...
EST: gi|211264908|gb|FL208724.1|FL208724
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-CTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|74241051|gb|DT648965.1|DT648965
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACG               
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-C-CT-C----TC--CA-A-Ggtctgcacac ...
EST: gi|211264911|gb|FL208727.1|FL208727
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-CTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|148956338|gb|EC902144.2|EC902144
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACGCAG            
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-----CC----TCT-C-CA---AGgtctgcacac .
EST: gi|211264912|gb|FL208728.1|FL208728
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-CTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|148931204|gb|EC873960.2|EC873960
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGCAG                       
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCC-A--AGgtctgcacac ... ttgccagc
EST: gi|211264909|gb|FL208725.1|FL208725
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|148952476|gb|EC898302.2|EC898302
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|211264913|gb|FL208729.1|FL208729
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|211264914|gb|FL208730.1|FL208730
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|149076954|gb|EE165611.2|EE165611
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|78112697|gb|DV531091.1|DV531091
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACGCAG            
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-----CC----TCT-C-CA---AGgtctgcacac .
EST: gi|211264910|gb|FL208726.1|FL208726
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|148987620|gb|EE031494.2|EE031494
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACGCAG            
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-----CC----TCT-C-CA---AGgtctgcacac .
EST: gi|91875485|gb|EB405442.1|EB405442
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACG               
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-C-CT-C----TC--CA-A-Ggtctgcacac ...
EST: gi|71447361|gb|DR828411.1|DR828411
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACG               
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-C-CT-C----TC--CA-A-Ggtctgcacac ...
EST: gi|211504926|gb|FL311934.1|FL311934
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|211264915|gb|FL208731.1|FL208731
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagagtttcactgtatctttcaaacttagtcttatttcttattttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAGGTGACTCCCCACCGCGCCCATGGGTGACAGCCAGTACTCCTTCTCCCTC
                               tcttatttcttatttt  CT-rich tract
                               tcttatttcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgacatccctacccgtgataagcccatcatggttcattttcactatagagtttcactgtatctttcaaacttagtcttatttcttattttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAGGTGACTCCCCACCGCGCCCATGGGTGACAGCCAGTACTCCTTCTCCCTC

- - -catccct
- - - - - - - - - - - - cccatca
- - - - - - - - - - - - - - - - - ttcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtatc