Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaccaccctttttatgaaattttgtttatgctgaaatgttaaattaacatgacctgctgttatacctctaatttgcatgctaatactacccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAAAGCATGGGATCAAAGT

Basic information

species Zea mays
transcript GRMZM2G100260_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100260_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g14040.1 (Oryza sativa), 3'ss of exon 2
ttaccaccctttttatgaaattttgtttatgctgaaatgttaaat-------taacatgacctgctgttatacctctaatttgcatgctaatactacccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAAAGCATGGGATCAAAGT
        | |||  || ||||||||||||||| | || || | |       | |  |  |||  |||||||     | | | ||| |||| |  ||| ||||  |||||||||||||| |||||||||||||| ||| | ||||| ||||||| ||| |||||||||||||||
-----ttgcgtttcctgcaattttgtttatgctcagatcttcagtaaatgtatgatgtatccttgtgttatattgtcactct-catactaacatgacc-ttacgcagTTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAAGGCATGGGATCAAAGT
















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|211144459|gb|FL048070.1|FL048070
EST:     GTCCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCAACTACAT                         TTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
genomic: GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACATgtataacact ... ccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
EST: gi|211144465|gb|FL048076.1|FL048076
EST:     GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT                         TTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
genomic: GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACATgtataacact ... ccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
EST: gi|211144466|gb|FL048077.1|FL048077
EST:     GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT                         TTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
genomic: GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACATgtataacact ... ccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
EST: gi|211144461|gb|FL048072.1|FL048072
EST:     GTTCTCGTCGGCGTCCACGAGGCGGACACGGATTCCGACGCCGACTACAT                         TTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
genomic: GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACATgtataacact ... ccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
EST: gi|89248178|gb|DY619964.1|DY619964
EST:     GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT                         TTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
genomic: GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACATgtataacact ... ccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
EST: gi|211144462|gb|FL048073.1|FL048073
EST:     GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT                         TTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
genomic: GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACATgtataacact ... ccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
EST: gi|14701176|gb|BI233594.1|BI233594
EST:     GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT                         TTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
genomic: GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACATgtataacact ... ccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
EST: gi|211144469|gb|FL048080.1|FL048080
EST:     GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT                         TTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA
genomic: GTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACATgtataacact ... ccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacatgacctgctgttatacctctaatttgcatgctaatactacccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAAAGCATGGGATCAAAGT
                                         ctaccctt  CT-rich tract
                      tctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaccaccctttttatgaaattttgtttatgctgaaatgttaaattaacatgacctgctgttatacctctaatttgcatgctaatactacccttacatagTTGTCGGAAGGTCCTGAACATGAGGCTGTTTTCAAATGACAAGACTGGAAAAGCATGGGATCAAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT