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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcatctgtctctgtctgtcagaattgtgtatgtttgcgtttccgtgtctgagaatttcaccagaaaattatttcctcttgattctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGTGGCGCTGGACACAGGCAGCGATCTCTTCTGGCTGCCTTGCCAGTGTGAC

Basic information

species Zea mays
transcript GRMZM2G177575_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|211461962|gb|FK971161.1|FK971161
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
EST: gi|211461960|gb|FK971159.1|FK971159
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGG
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGG-
EST: gi|211461956|gb|FK971155.1|FK971155
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGG
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGG-
EST: gi|91875997|gb|EB405954.1|EB405954
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
EST: gi|94480206|gb|EB709164.1|EB709164
EST:     CACTTTCGCCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCCCACCGGGCCAGACGTTCATGG
genomic: CACTTTCGCC-GAGGGAAATGCCACCCTCAAGGTCAGCAACCTC-GGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGG
EST: gi|211464479|gb|FK971166.1|FK971166
EST:     TCACTTTCGCCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TT-GCACTATG
genomic: TCACTTTCGCC-GAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATG
EST: gi|211459438|gb|FK971148.1|FK971148
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGG
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGG
EST: gi|211461954|gb|FK971153.1|FK971153
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGT
EST: gi|88757255|gb|DY541396.1|DY541396
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
EST: gi|148934199|gb|EC878220.2|EC878220
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
EST: gi|211461951|gb|FK971150.1|FK971150
EST:     TCACTTTCGCCGAGGGAAATGCCACCCTCNAGGTCAGCAACCCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGNCACACCGGGCCAGACGTTCATGG
genomic: TCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACC-TCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGG
EST: gi|78086095|gb|DV514488.1|DV514488
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
EST: gi|94479752|gb|EB708710.1|EB708710
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
EST: gi|211464476|gb|FK971163.1|FK971163
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
EST: gi|211461959|gb|FK971158.1|FK971158
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
EST: gi|148971474|gb|EE022168.2|EE022168
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
EST: gi|149005051|gb|EE039576.2|EE039576
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
EST: gi|149079839|gb|EE168839.2|EE168839
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGT
EST: gi|211461963|gb|FK971162.1|FK971162
EST:     CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATT                         TTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGT
genomic: CTCACTTTCGCCGAGGGAAATGCCACCCTCAAGGTCAGCAACCTCGGATTgtaaggcatc ... tctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttccgtgtctgagaatttcaccagaaaattatttcctcttgattctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGTGGCGCTGGACACAGGCAGCGATCTCTTCTGGCTGCCTTGCCAGTGTGAC
                                      tcttgat  putative branch site (score: 4)
                                 tttcctcttgattct  CT-rich tract
                        agaaaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcatctgtctctgtctgtcagaattgtgtatgtttgcgtttccgtgtctgagaatttcaccagaaaattatttcctcttgattctggtgtagTTTGCACTATGCTCTTGTGACCGTTGGCACACCGGGCCAGACGTTCATGGTGGCGCTGGACACAGGCAGCGATCTCTTCTGGCTGCCTTGCCAGTGTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA