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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctgtttggggtttctcactgagtcaaagtttttggtattttatttttggcctcatccagcttgatagattattgattcatttctgatttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGGCATACAACTCTTTTTTCATGTAAGAGAAGCATTCTGCCATCAAAGAAAC

Basic information

species Zea mays
transcript GRMZM2G178294_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178294_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g11200.1 (Oryza sativa), 3'ss of exon 11
cttctgtttggggtttctcactgagtcaaagtttttggtattttatttttggcctcatcca----gcttgatagattattgattcatttctgatttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGGCATACAACTCTTTTTTCATGTAAGAGAAGCATTCTGCCATCAAAGAAAC
    |  |  |  ||   |     | ||   | | |  |||||  | ||| |  | | |||    | ||| |   ||| |||    | | | | || ||| |||||||||||||| |||||||||||| |  | ||||||||||||   | |||||||   |||| ||||||  | ||||||||||| ||| |||||||||| |
----taatctgaattgtcctgcatggcagcatctgttttatttgttcttttggttgacccactacgattgctgagttagtgacgtgtgtttaaattctctacagTTTTTGGATCTATTTGGGGATGCACAAGCGATCAAGAAGGCTACCAATCGGCATCTTACTCATTTTTCGCGGAAGAGAAGCATGCTGTCATCAAAGAAGC

upper sequence: GRMZM2G178294_T04 (Zea mays), 3'ss of exon 11
lower sequence: Vv07s0005g04290.t01 (Vitis vinifera), 3'ss of exon 7
--cttctgtttggggtttctcactgagtcaa-agtttttggtattttatttttggcctcatccagcttgatagattattgattcatttctgatttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGGCATACAACTCTTTTTTCATGTAAGAGAAGCATTCTGCCATCAAAGAAAC
     |||  |||  | | | |  |  |    |||   || |||||    | ||   |         | | | |    |  ||      |    ||  |||||||| ||||||||||||| |||||| |||| ||||||||||||     ||||||| | |  ||||| | |    |  |||| |        |  || || |
aatggctgaatggtttattttatagcttttttagtaaatgatattt---atgtgaagttgaatgttcttacaaaacccttttttccccatctcctggttgcagTTTCTGGATCTCTTTGGAGATGCACAGTCTATCAAGAAGGCTGATGATCGGCATGCCAAGCTTTTCTTACACCATCGAAGTACATCAGAGTTGAAAAAGC
















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|32930152|gb|CF034964.1|CF034964
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|32933149|gb|CF037961.1|CF037961
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|32935217|gb|CF040029.1|CF040029
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|211488019|gb|FL401529.1|FL401529
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGAATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|60399477|gb|DN232289.1|DN232289
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|211296491|gb|FL380959.1|FL380959
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|211371062|gb|FL377775.1|FL377775
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGAATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|32933726|gb|CF038538.1|CF038538
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|9731923|gb|BE510675.1|BE510675
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|74245848|gb|DT653762.1|DT653762
EST:     ATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: ATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttggcctcatccagcttgatagattattgattcatttctgatttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGGCATACAACTCTTTTTTCATGTAAGAGAAGCATTCTGCCATCAAAGAAAC
                                      ttctgat  putative branch site (score: 3)
                                            tttgtct  CT-rich tract
                         attattgattcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttctgtttggggtttctcactgagtcaaagtttttggtattttatttttggcctcatccagcttgatagattattgattcatttctgatttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGGCATACAACTCTTTTTTCATGTAAGAGAAGCATTCTGCCATCAAAGAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA