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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttacatgttccaaaatatgcctaaaaacagtttggaacactgttttgcgcttctcgtccatctgtaactgatcccacaaaaagaacgtgatagattatgctttgttggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGATCTTGAGGCTGCTGGTATTCAG

Basic information

species Zea mays
transcript GRMZM2G165747_T02
intron # 11
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|32922226|gb|CF027038.1|CF027038
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|32862876|gb|CF002558.1|CF002558
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|211327188|gb|FL127497.1|FL127497
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|31361660|gb|CD446017.1|CD446017
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|30087177|gb|CB885385.1|CB885385
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|31362393|gb|CD446750.1|CD446750
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|33091691|gb|CF051685.1|CF051685
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|67026378|gb|CO455127.1|CO455127
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|33100623|gb|CF060583.1|CF060583
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|32849879|gb|CD989560.1|CD989560
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|31361689|gb|CD446046.1|CD446046
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTTGCA-TAAAAAAGGAGGTTGAGG
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTT-GCAATAAAAAAGGAGGTTGAGG
EST: gi|32944358|gb|CF049177.1|CF049177
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|32847292|gb|CD986973.1|CD986973
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|211333680|gb|FL127538.1|FL127538
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|211329356|gb|FL127509.1|FL127509
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|32944605|gb|CF049424.1|CF049424
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|32923062|gb|CF027874.1|CF027874
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
EST: gi|32929227|gb|CF034039.1|CF034039
EST:     GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAG                         GTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA
genomic: GGTCCAGTCACAATCCTCAACTGGTCATTTGTCAGGAACGATCAGCCTAGgtttgttaca ... tggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtaactgatcccacaaaaagaacgtgatagattatgctttgttggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGATCTTGAGGCTGCTGGTATTCAG
     aactgat  putative branch site (score: 3)
                                       ctttgtt  putative PPT
                             atagattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttacatgttccaaaatatgcctaaaaacagtttggaacactgttttgcgcttctcgtccatctgtaactgatcccacaaaaagaacgtgatagattatgctttgttggtgtacagGTTTGAGACATGCTACCAAATAGCTCTTGCAATAAAAAAGGAGGTTGAGGATCTTGAGGCTGCTGGTATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT