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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggttatttgattgagtttactcaggaatcaatcatatatacctgatcaggtggcaaatgtcataattgttttgctaataacaaatttatgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCCATCCGTTTGCTGGTGACTGAGGATCCATGCAGTGGGCGGTTCGTGTACG

Basic information

species Zea mays
transcript GRMZM2G373175_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G373175_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 12
----gtggttatttgattgagtttactcaggaatcaatcatatatacctgatcaggtggcaaatgtcataattgttttgctaat-aacaaatttatgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCCATCCGTTTGCTGGTGACTGAGGATCCATGCAGTGGGCGGTTCGTGTACG
    |    |  |    |||  ||   | |   | | |  ||| | |  |||   |    |  |||      | |||  | ||| ||    |||   | ||||||||||||||||| |||||||| |||||||| ||||||||||| || ||||| ||  |  |||| || ||||||||||||||||  || || ||||| || |
tacagaacattctcatatgaaattgtacggc--ttagt--tatgtcctcgattgtgcta-atgtgttggtgatatttgaccaattaatcttttttattttaacagCTCCAAAACCCGAGGATGGACATCCAAACCAGTGAAGAGCTTCTGTCAGCGATTAGACTGCTTGTCACTGAGGATCCATGCAACGGTCGTTTCGTATATG
















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|211272990|gb|FL022928.1|FL022928
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAAACCCAAGGATGGA
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCCAAGGATGGA
EST: gi|60398033|gb|DN230849.1|DN230849
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCC
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCC
EST: gi|211272993|gb|FL022931.1|FL022931
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAA-CCCAAGGATGGATATC
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCCAAGGATGGATATC
EST: gi|211272997|gb|FL022935.1|FL022935
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAAACCCAAGGATGGATATCCAAACGAGTGA
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTGA
EST: gi|13316191|gb|BG410638.1|BG410638
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCC
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCC
EST: gi|211272995|gb|FL022933.1|FL022933
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAAACCCAAGGATGGATATCCAAACGAGTG
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTG
EST: gi|32857826|gb|CD997507.1|CD997507
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAAACCCAAGGATAGATATCCAAACGAGGGAAGAGCTGCTATCAGCC
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCC
EST: gi|211272991|gb|FL022929.1|FL022929
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAAACCCAAGGATGG
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCCAAGGATGG
EST: gi|31352989|gb|CD437346.1|CD437346
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCC
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCC
EST: gi|211272994|gb|FL022932.1|FL022932
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCC
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCC
EST: gi|211272992|gb|FL022930.1|FL022930
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAAACCC
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCC
EST: gi|13316192|gb|BG410639.1|BG410639
EST:     CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAG                         CTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCC
genomic: CAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAATCCATTGCAAGgtattgtcga ... tgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcaggtggcaaatgtcataattgttttgctaataacaaatttatgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCCATCCGTTTGCTGGTGACTGAGGATCCATGCAGTGGGCGGTTCGTGTACG
                               taataac  putative branch site (score: 1)
                  ataattgttttgctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggttatttgattgagtttactcaggaatcaatcatatatacctgatcaggtggcaaatgtcataattgttttgctaataacaaatttatgtctaacagCTCCAAAACCCAAGGATGGATATCCAAACGAGTGAAGAGCTGCTATCAGCCATCCGTTTGCTGGTGACTGAGGATCCATGCAGTGGGCGGTTCGTGTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - ttgattg
- - - - - - - - - - - - - - - - - - - -atacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taacaaa