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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtagtctctgtgatctcacacgcacaatgtctagctgctagctctggtcacaattcacaacaacacaagtggcctagcctcctagcttactgatgcgatgccttgctgctgctgctgcttttgtcatccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTGCGACAAGGAGGGGCAGTCCGGCACCCAGGCCTTCGTCAAGTCCTACAAG

Basic information

species Zea mays
transcript GRMZM2G106165_T01
intron # 6
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|14245564|gb|BG874146.1|BG874146
EST:     GACCTCATCTGCGCGACCAAAGGCACCATGGACTGNGTTCAGAAGCTCAA                         GTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
genomic: GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAAgtaagtgtag ... catccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
EST: gi|71429064|gb|DR810114.1|DR810114
EST:     GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAA                         GTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
genomic: GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAAgtaagtgtag ... catccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
EST: gi|149108722|gb|EE189800.2|EE189800
EST:     GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAA                         GTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
genomic: GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAAgtaagtgtag ... catccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
EST: gi|4776526|gb|AI665529.1|AI665529
EST:     GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAA                         GTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
genomic: GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAAgtaagtgtag ... catccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
EST: gi|78026508|gb|DV494895.1|DV494895
EST:     GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAA                         GTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
genomic: GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAAgtaagtgtag ... catccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
EST: gi|44901511|gb|CK828056.1|CK828056
EST:     AAGGCACCATGGACTGGGTTCAGAAGCTCAA                         GTGGGACGACCTCAACAGTTTCCTGAGCTCTCCCAGAACGCCCATCTACTG
genomic: AAGGCACCATGGACTGGGTTCAGAAGCTCAAgtaagtgtag ... catccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
EST: gi|211220330|gb|FL435584.1|FL435584
EST:     GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAA                         GTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
genomic: GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAAgtaagtgtag ... catccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
EST: gi|113703586|gb|EE681090.1|EE681090
EST:     GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAA                         GTGGGACGACCTCAACAGTTTCCTGAGCTCTCCCAGAACGCCCATCTACTG
genomic: GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAAgtaagtgtag ... catccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
EST: gi|148953880|gb|EC899258.2|EC899258
EST:     GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAA                         GTGGGACGACCTCAACAGTTTCTTGAGCTCTCCTAGAACGCCCATCTACTG
genomic: GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAAgtaagtgtag ... catccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
EST: gi|148949599|gb|EC895070.2|EC895070
EST:     GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAA                         GTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG
genomic: GACCTCATCTGCGCGACCAAAGGCACCATGGACTGGGTTCAGAAGCTCAAgtaagtgtag ... catccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctagcttactgatgcgatgccttgctgctgctgctgcttttgtcatccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTGCGACAAGGAGGGGCAGTCCGGCACCCAGGCCTTCGTCAAGTCCTACAAG
        tactgat  putative branch site (score: 2)
                                      cttttgtc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtagtctctgtgatctcacacgcacaatgtctagctgctagctctggtcacaattcacaacaacacaagtggcctagcctcctagcttactgatgcgatgccttgctgctgctgctgcttttgtcatccatcagGTGGGACGACCTCAACAGTTTCCTGAGCTCTCCTAGAACGCCCATCTACTGCGACAAGGAGGGGCAGTCCGGCACCCAGGCCTTCGTCAAGTCCTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG