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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCTCGCTCGCGGGTCACTCCCTCCACTCGGTCCCGCCCTCTATCGCAGGCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcacccaccctttgctttatgattatccgttttgaatgtgctgcactgctgctacctttccgttgccggagtatcgaatgccgacgcttagacgatcagtagcgcttatgtatattttttggttggtatggtatcgattatttaacctgctgctaacag

Basic information

species Zea mays
transcript GRMZM2G060842_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060842_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g20640.1 (Oryza sativa), 5'ss of exon 1
---------CTCCTCGCTCGCGGGT-CACTCCCTCCACTCGGTCCCGCCCTCTATCGCAGGCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcacccaccctttgctttatgattatccgttttgaatgtgctgcactgctgctacctttccgttgccggagtatcgaatgccgacgcttagacgatcagtagcgcttatgtatattttttggttggtatggtatcgattatttaacctgctgctaacag
         |||  ||| |||||   | | |||||  ||||| ||||||| |   |||    ||| |   ||  |||| |||||||||||||||||||||||||      ||| |  ||  |  | | |   |   |   |    | | | |     | |   | |  ||  |||   || | ||  |  |   ||| ||  |       || |||   |||| || ||  |    |                                      
TGCCGCGGCCTCGACGC-CGCGGCCGCGCGCCCTCTTCTCGGCCCCGCCCGCGCCCGCGCCTCCCCG---CGCGCCTCCGCTCTCCGCTACTCCTCCCTCCAAG-
















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|211288681|gb|FL312632.1|FL312632
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|211050404|gb|FL363822.1|FL363822
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|76280845|gb|DV020413.1|DV020413
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|37417224|gb|CF646264.1|CF646264
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|50327397|gb|CO522523.1|CO522523
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|211271929|gb|FL194754.1|FL194754
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|91875732|gb|EB405689.1|EB405689
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|211290817|gb|FL312641.1|FL312641
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|211305896|gb|FL324269.1|FL324269
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|76912690|gb|DV164849.1|DV164849
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|101386086|gb|EB815086.1|EB815086
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|50323043|gb|CO518169.1|CO518169
EST:     TACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: TACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|211386003|gb|FL329687.1|FL329687
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|50326968|gb|CO522094.1|CO522094
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
EST: gi|211265830|gb|FL364906.1|FL364906
EST:     GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAG                         CTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC
genomic: GCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcac ... ctgctaacagCTGGGGACAGTATTGGGGAGGAGGCCCTGCGCATGTTCCTTGAGGACAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCTCGCTCGCGGGTCACTCCCTCCACTCGGTCCCGCCCTCTATCGCAGGCCCCTGGAGCGAACCTCGGCTCTCCGCTACTCCTCCCTCCAAGCTCAAGgtattttcacccaccctttgctttatgattatccgttttgaatgtgctgcactgctgctacctttccgttgccggagtatcgaatgccgacgcttagacgatcagtagcgcttatgtatattttttggttggtatggtatcgattatttaacctgctgctaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA