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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatctttaacttcgagttgacaaatctaaagggaaaaaaaatgcaatttctcaatgtagttgctctacatcatcccagAACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGGTTCCCCGAAGAGTAATG

Basic information

species Zea mays
transcript GRMZM2G041642_T03
intron # 7
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|78021609|gb|DV489996.1|DV489996
EST:     AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAG                         AACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
genomic: AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAGgttagtatct ... atcatcccagAACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
EST: gi|24769540|gb|CA404669.1|CA404669
EST:     AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAG                         AACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
genomic: AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAGgttagtatct ... atcatcccagAACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
EST: gi|5895643|gb|AW036889.1|AW036889
EST:     AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAG                         AACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
genomic: AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAGgttagtatct ... atcatcccagAACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
EST: gi|5791284|gb|AI978076.1|AI978076
EST:     AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAG                         AACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
genomic: AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAGgttagtatct ... atcatcccagAACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
EST: gi|71759938|gb|DR957875.1|DR957875
EST:     AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAG                         AACATTGCTGTCAACTTCCTTTGACTTTACTGCAAGGGTGACGTACGTTGG
genomic: AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAGgttagtatct ... atcatcccagAACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
EST: gi|211490136|gb|FL479271.1|FL479271
EST:     AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAG                         AACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
genomic: AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAGgttagtatct ... atcatcccagAACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
EST: gi|6194538|gb|AW146642.1|AW146642
EST:     AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAG                         AACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
genomic: AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAGgttagtatct ... atcatcccagAACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG
EST: gi|5608300|gb|AI902072.1|AI902072
EST:     AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAG                         AACATTGCTGTCAACTTCCTTTGNCTCTACTGCAAGGGTGACGTACGTTGG
genomic: AAGGCCCATCTTGGTGTTGTGACTACACTGTCCTTCTCTCAGGATTCAAGgttagtatct ... atcatcccagAACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctaaagggaaaaaaaatgcaatttctcaatgtagttgctctacatcatcccagAACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGGTTCCCCGAAGAGTAATG
 atctaaa  putative branch site (score: 3)
                                              tcatccc  putative PPT
          aaaaaaaatgcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtatctttaacttcgagttgacaaatctaaagggaaaaaaaatgcaatttctcaatgtagttgctctacatcatcccagAACATTGCTGTCAACTTCCTTTGACTCTACTGCAAGGGTGACGTACGTTGGTTCCCCGAAGAGTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA