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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgccttatgaatccaaagtttcattttcattttgtttatattgtgcattgcctatatctcttatgtaagtatgaaacatattttttccccaaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTGTTCACAAAATCAGGAATGTTATTCTTGGAAGTCAGTTTGATAGCCTTTC

Basic information

species Zea mays
transcript GRMZM2G123732_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123732_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 1
ctgccttatgaatccaaa---gtttcattttcattttgt-ttatattgtgcattgcctatatctcttatgtaagtatga-aacatattttttccccaaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTGTTCACAAAATCAGGAATGTTATTCTTGGAAGTCAGTTTGATAGCCTTTC
    |     | |    |    ||| | ||  ||  | |  || | |    ||||  ||| ||||||||    |||| | | | | ||| || |     |||||||| ||||||||||||||||| ||||| || || ||||||||  |||| ||||| || |||||||| ||||||||||||||||| ||| | ||||| ||||
----caagcaagttttgacctattttaattctatcatatgctacactacatattgt-tatttctcttattcttgtataacagcctttttatttctttgttggcagGCGTGGCAATGTATGCCTGATAGGGCGTTCTCATGGAATGTGCTGTCTCTGTTTACCAAATCAGGGATGTTATTCTTGGAAGTTAGTCTCATAGCATTTC
















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|211226896|gb|FL228432.1|FL228432
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|211226890|gb|FL228426.1|FL228426
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|76291714|gb|DV031282.1|DV031282
EST:     CGCTCCTCTGGGTCGTCGCTGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|211226895|gb|FL228431.1|FL228431
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|50329533|gb|CO524659.1|CO524659
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|211224834|gb|FL228419.1|FL228419
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|71323879|gb|DR798616.1|DR798616
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|149005849|gb|EE040139.2|EE040139
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|211226889|gb|FL228425.1|FL228425
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|211226887|gb|FL228423.1|FL228423
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTC
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTC
EST: gi|211226885|gb|FL228421.1|FL228421
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACA
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACA
EST: gi|211224832|gb|FL228417.1|FL228417
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|91867966|gb|EB399869.1|EB399869
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|67034439|gb|CO462989.1|CO462989
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|211224833|gb|FL228418.1|FL228418
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
EST: gi|74244184|gb|DT652098.1|DT652098
EST:     CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAG                         GCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG
genomic: CGCTCCTCTGGGTCGTCGCCGTACTCAACCTCCTCTGGTGCTTCCTGCAGgttcggattg ... caaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattgcctatatctcttatgtaagtatgaaacatattttttccccaaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTGTTCACAAAATCAGGAATGTTATTCTTGGAAGTCAGTTTGATAGCCTTTC
                                catattttttcccc  CT-rich tract
                     taagtatgaaacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgccttatgaatccaaagtttcattttcattttgtttatattgtgcattgcctatatctcttatgtaagtatgaaacatattttttccccaaatggcagGCATGGCAATGTATGCCTGACAGGGCATTTTCTTGGAATGTATTGTCACTGTTCACAAAATCAGGAATGTTATTCTTGGAAGTCAGTTTGATAGCCTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
-tgcctta
- - - - tgaatcc
- - - - - - - - - -tttcatt
- - - - - - - - - - - - - - - - - - - - - -gtgcatt