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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaaagatcgcgcgtgtttttttcttcgatctggattaaggaacagattaggcatgcgaaagctgtaacgtattacatatcattgccatccttctactagAAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGTACTGGACTCACCCTAAGGACGATCACTACGACTGGAGAGGGGTGGCGCCTCG

Basic information

species Zea mays
transcript GRMZM2G152477_T03
intron # 2
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|32844410|gb|CD984091.1|CD984091
EST:     GAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGTCAACGCAG                         AAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGT
genomic: GAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGTCAACGCAGgttcaaagat ... cttctactagAAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGT
EST: gi|37426126|gb|CF650813.1|CF650813
EST:     GAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGTCAACGCAG                         AAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGTACT
genomic: GAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGTCAACGCAGgttcaaagat ... cttctactagAAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGTACT
EST: gi|74244004|gb|DT651918.1|DT651918
EST:     GAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGTCAACGCAG                         AAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTTCA-CTCAAGTAC
genomic: GAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGTCAACGCAGgttcaaagat ... cttctactagAAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTT-CAACTCAAGTAC
EST: gi|32845060|gb|CD984741.1|CD984741
EST:     GAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGTCAACGCAG                         AAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGTA
genomic: GAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGTCAACGCAGgttcaaagat ... cttctactagAAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGTA
EST: gi|37393857|gb|CF634195.1|CF634195
EST:     TCGTCAACGCAG                         AAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGTACT
genomic: TCGTCAACGCAGgttcaaagat ... cttctactagAAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGTACT
EST: gi|19821796|gb|BQ047820.1|BQ047820
EST:     GAAGATCGACAGCCGGTTCATCTGCATCAAATCATTCGTCGTCAACGCAG                         AAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGTACT
genomic: GAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGTCAACGCAGgttcaaagat ... cttctactagAAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGTACT
EST: gi|17970297|gb|BM277060.1|BM277060
EST:     GAAGATCGACAGCCGGTTCATCTGCATCAAATCATTCGTCGTCAACGCAG                         AAATCGTGGAGTTCTTCTTCGTTGACACCACC
genomic: GAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGTCAACGCAGgttcaaagat ... cttctactagAAATCGTGGAGTTCTTCTTCGTTGACACCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattaggcatgcgaaagctgtaacgtattacatatcattgccatccttctactagAAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGTACTGGACTCACCCTAAGGACGATCACTACGACTGGAGAGGGGTGGCGCCTCG
                 ctgtaac  putative branch site (score: 3)
                                        ccatccttct  putative PPT
                         tattacatatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcaaagatcgcgcgtgtttttttcttcgatctggattaaggaacagattaggcatgcgaaagctgtaacgtattacatatcattgccatccttctactagAAATCGTGGAGTTCTTCTTCGTTGACACCACCCCGTTTCAACTCAAGTACTGGACTCACCCTAAGGACGATCACTACGACTGGAGAGGGGTGGCGCCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG