Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttctaagttggacaatccattatttattctctcttgtctcaggctatctcttacagcttacccatctccatctctcatttcaaactctactttgtacacactgcaatctatagtgtcactatctgctgggtatagtcttactttcacttttctgacgatatcttttattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG

Basic information

species Zea mays
transcript GRMZM2G096962_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096962_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g57670.1 (Oryza sativa), 3'ss of exon 4
gcaagttctaagttggacaatccattatttattctctcttgtctcaggctatctcttacagcttacccatctccatctctcatttcaaactctactttgtacacactgcaatctatagtgtcactatctgctgggtatagtcttactttcactt--ttctgacgatatcttttattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
                                                                                           | | ||| ||     |  | |  ||||| ||  ||| |   |  | |  | |||||| |||||  |    |   | |||| |||| ||||| ||||| ||||| ||| |||||||||| ||||||||||||||||||||
------------------------------------------------------------------------------------------gcaagttttta-----tcgagtagatagt-tctttatgtatcg--tcttattttacttgcacttaataacaagtttttcttctattctacagCGTCACAGCACAAGATCTTGTTGACATCATAAAGTCACAACTTAATAG
















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|13178137|gb|BG349395.1|BG349395
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGAT
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGAT
EST: gi|13490830|gb|BG517594.1|BG517594
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|211087730|gb|FL054352.1|FL054352
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|14645994|gb|BI180183.1|BI180183
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|211087722|gb|FL054344.1|FL054344
EST:     CTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGAATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: CTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGA-TCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|211518614|gb|FL054337.1|FL054337
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|32830089|gb|CD969767.1|CD969767
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|32860092|gb|CD999773.1|CD999773
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|211087731|gb|FL054353.1|FL054353
EST:     TTTCAAACTCCCCTCGCAAAGGTGGAAAATGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGGATGTTGT
genomic: TTTCAAACTCCC-TCGCAAAGGTGGAAAA-GGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGG-ATGTTGT
EST: gi|33099864|gb|CF059824.1|CF059824
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|32829981|gb|CD969659.1|CD969659
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|32829709|gb|CD969387.1|CD969387
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|211322849|gb|FL127470.1|FL127470
EST:     CTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCNTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAA
genomic: CTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATC-TTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAA
EST: gi|148974517|gb|EE025302.2|EE025302
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|149089632|gb|EE178886.2|EE178886
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAA
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAA
EST: gi|211087721|gb|FL054343.1|FL054343
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|31355725|gb|CD440082.1|CD440082
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|16379884|gb|BI993198.1|BI993198
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|15208882|gb|BI430766.1|BI430766
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|149010029|gb|EE041834.2|EE041834
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|16926981|gb|BM080049.1|BM080049
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|83279377|gb|DV943385.1|DV943385
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|32858543|gb|CD998224.1|CD998224
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|148985808|gb|EE029766.2|EE029766
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|13178451|gb|BG349709.1|BG349709
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTT
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTT
EST: gi|32848919|gb|CD988600.1|CD988600
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|13516046|gb|BG518322.1|BG518322
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|32828996|gb|CD968674.1|CD968674
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|211518613|gb|FL054336.1|FL054336
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACA
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACA
EST: gi|32829797|gb|CD969475.1|CD969475
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|16918822|gb|BM073911.1|BM073911
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|15053619|gb|BI359164.1|BI359164
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|148967374|gb|EE018593.2|EE018593
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|32829763|gb|CD969441.1|CD969441
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|32849657|gb|CD989338.1|CD989338
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|13315933|gb|BG410281.1|BG410281
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
EST: gi|211518615|gb|FL054338.1|FL054338
EST:     GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG                         TGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
genomic: GCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttcta ... tattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgctgggtatagtcttactttcacttttctgacgatatcttttattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG
                             ttctgac  putative branch site (score: 2)
                                        tcttttatt  putative PPT
                                     atatcttttattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagttctaagttggacaatccattatttattctctcttgtctcaggctatctcttacagcttacccatctccatctctcatttcaaactctactttgtacacactgcaatctatagtgtcactatctgctgggtatagtcttactttcacttttctgacgatatcttttattgtacagTGTCACGGCACAGGATGTTGTTGACATAATAAAGTCACAACTTAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG