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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagattaaactgtagaatgagcacatatttatttgacccatgtttgtttgtacatatttgtgagtacctgtactgctggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGCAG

Basic information

species Zea mays
transcript GRMZM2G025854_T01
intron # 4
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|211022177|gb|FL153050.1|FL153050
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
EST: gi|211456111|gb|FL153032.1|FL153032
EST:     CCTTGTACTTGGGGGTGATGGCCGGTACTTTTACAAGGGAG-CTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGG-AGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
EST: gi|211022165|gb|FL153038.1|FL153038
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
EST: gi|211022178|gb|FL153051.1|FL153051
EST:     CCCTTGTACTTGGGGGTGATGGCCCGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATAAAGATTGCAGCTGGAAATGGGAGTTCAGAGGATCATAGTTGG
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGG-AGTTCAGAAGATCATAGTTGG
EST: gi|211022173|gb|FL153046.1|FL153046
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
EST: gi|211022172|gb|FL153045.1|FL153045
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
EST: gi|211456114|gb|FL153035.1|FL153035
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
EST: gi|211022174|gb|FL153047.1|FL153047
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATG
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATG
EST: gi|211456113|gb|FL153034.1|FL153034
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
EST: gi|211022175|gb|FL153048.1|FL153048
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
EST: gi|211456115|gb|FL153036.1|FL153036
EST:     CCCTTGNACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATA
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAA-GATTGCAGCTGGAAATGGAGTTCAGAAGATCATA
EST: gi|211024619|gb|FL153052.1|FL153052
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
EST: gi|50333167|gb|CO528293.1|CO528293
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
EST: gi|74238594|gb|DT646508.1|DT646508
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
EST: gi|211022168|gb|FL153041.1|FL153041
EST:     CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAG                         ATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC
genomic: CCCTTGTACTTGGGGGTGATGGCCGGTACTTTAACAAGGAGGCTGCTCAGgtacagatta ... ggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacccatgtttgtttgtacatatttgtgagtacctgtactgctggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGCAG
 atttgac  putative branch site (score: 4)
                  tacatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagattaaactgtagaatgagcacatatttatttgacccatgtttgtttgtacatatttgtgagtacctgtactgctggaactatagATCATCATTAAGATTGCAGCTGGAAATGGAGTTCAGAAGATCATAGTTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA