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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatacttttcctgttgaatgatttaatcacaccagcatgatttgcttctgctaatatatgtggcttattgcttatttagatttaccttcacctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG

Basic information

species Zea mays
transcript GRMZM2G146472_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|32830032|gb|CD969710.1|CD969710
EST:     GCGGA-CACGCGAG                         GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGTG
genomic: GCGGAGCACGCGAGgtgagattct ... acctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
EST: gi|32829230|gb|CD968908.1|CD968908
EST:     GCGGA-CACGCGAG                         GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGTG
genomic: GCGGAGCACGCGAGgtgagattct ... acctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
EST: gi|22542105|gb|BU092543.1|BU092543
EST:     GGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAG                         GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
genomic: GGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAGgtgagattct ... acctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
EST: gi|76930615|gb|DV172453.1|DV172453
EST:     AGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAG                         GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
genomic: AGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAGgtgagattct ... acctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
EST: gi|211499004|gb|FL379821.1|FL379821
EST:     AGAGGAACCGGGGAGCGGCA-STGCAGC-GCCGAGGGCGGA-CACGCGAG                         GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGTG
genomic: AGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAGgtgagattct ... acctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
EST: gi|32828756|gb|CD968434.1|CD968434
EST:     GCGGA-CACGCGAG                         GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGTG
genomic: GCGGAGCACGCGAGgtgagattct ... acctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
EST: gi|76918295|gb|DV167234.1|DV167234
EST:     AGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAG                         GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
genomic: AGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAGgtgagattct ... acctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
EST: gi|31356464|gb|CD440821.1|CD440821
EST:     TGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAG                         GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
genomic: AGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAGgtgagattct ... acctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
EST: gi|67031337|gb|CO460086.1|CO460086
EST:     AGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAG                         GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
genomic: AGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAGgtgagattct ... acctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
EST: gi|31354397|gb|CD438754.1|CD438754
EST:     AGAGGAACCGGGGAGCGGCCTTTGCAGCGGCCGAGGGCGGAGCACGCGAG                         GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
genomic: AGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAGgtgagattct ... acctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
EST: gi|148939817|gb|EC884519.2|EC884519
EST:     AGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAG                         GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
genomic: AGAGGAACCGGGGAGCGGCAGCTGCAGCGGCCGAGGGCGGAGCACGCGAGgtgagattct ... acctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgctaatatatgtggcttattgcttatttagatttaccttcacctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG
    tgctaat  putative branch site (score: 2)
                                        ccttcacct  putative PPT
                           ttatttagattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatacttttcctgttgaatgatttaatcacaccagcatgatttgcttctgctaatatatgtggcttattgcttatttagatttaccttcacctatttagGTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - cctgttg
- - - - - - - - - - - - - - - caccagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtggct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tattgct