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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatcccttattgccttgttgaaactatgaaggtggagttctatacttctatgaacttgtggatcgctttgtccttaaaaaaaacttatgatgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGAAAGCAGATTCATTCCATCATGAATATAGCTCTATGGCCTGCACAATTGA

Basic information

species Zea mays
transcript GRMZM2G375504_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375504_T03 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 14
gatcccttattgccttgttgaaactatgaa-ggtgga--gttctatacttctatgaacttgtggatcgctttgtccttaaa---aaaaacttatgatgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGAAAGCAGATTCATTCCATCATGAATATAGCTCTATGGCCTGCACAATTGA
      | |  |   |  |     | || |   ||||  ||| | ||||| |||  ||  |   ||   ||| ||| |       | |   |    | |||  ||||||||  ||||||||| || ||| |||| ||  |||  ||| |  |||| ||||| | |||||| |||||||| ||||| ||||||||||||||  ||||
------tcacagatgtagtatgtttctggatactggattgttttttacttgtatatacagggccatgattttctccctgcttcttagataatgctgtatatttcagGAGTTAATATTTATGGTGGACCTATTGCGCACAAAGCTCTGGGATTTCCAAAAGCTGTTTCATTTCATCATGAGTATAGTTCTATGGCCTGCACTGTTGA
















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|19436126|gb|BM952536.1|BM952536
EST:     TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAG                         GAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
genomic: TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAGgtttgagttt ... tgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
EST: gi|60348148|gb|DN215121.1|DN215121
EST:     TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAG                         GAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
genomic: TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAGgtttgagttt ... tgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
EST: gi|32934077|gb|CF038889.1|CF038889
EST:     TATAAAGGCTCCGGGTCTTGATGATATACTCCTATCACTCAAAACAGAAG                         GAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGT
genomic: TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAGgtttgagttt ... tgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGT
EST: gi|87154005|gb|DY398794.1|DY398794
EST:     TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAG                         GAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
genomic: TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAGgtttgagttt ... tgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
EST: gi|32933434|gb|CF038246.1|CF038246
EST:     TATAAAGGCTCCGGGTCTTGATGATATACTCCTATCACTCAAAACAGAAG                         GAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTA
genomic: TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAGgtttgagttt ... tgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTA
EST: gi|26456773|gb|CA828356.1|CA828356
EST:     TACTCCTATCACTCAAAACAGAAG                         GAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
genomic: TACTCCTATCACTCAAAACAGAAGgtttgagttt ... tgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
EST: gi|32934404|gb|CF039216.1|CF039216
EST:     TATAAAGGCTCCGGGTCTTGATGATATACTCCTATCACTCAAAACAGAAG                         GAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGT
genomic: TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAGgtttgagttt ... tgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGT
EST: gi|22491554|gb|BU051477.1|BU051477
EST:     TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAG                         GAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
genomic: TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAGgtttgagttt ... tgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
EST: gi|78024065|gb|DV492452.1|DV492452
EST:     TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAG                         GAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
genomic: TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAGgtttgagttt ... tgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
EST: gi|6021994|gb|AW066922.1|AW066922
EST:     TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAG                         GAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA
genomic: TATAAAGGCTCCAGGTCTTGATGATATACTCCTATCACTCAAAACAGAAGgtttgagttt ... tgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctatgaacttgtggatcgctttgtccttaaaaaaaacttatgatgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGAAAGCAGATTCATTCCATCATGAATATAGCTCTATGGCCTGCACAATTGA
                            ttaaaaaaaacttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatcccttattgccttgttgaaactatgaaggtggagttctatacttctatgaacttgtggatcgctttgtccttaaaaaaaacttatgatgtatcacagGAGTTGCTATTTATGGAGGGCCTGTTGCACATGAAGTACTGTGTATTCCGAAAGCAGATTCATTCCATCATGAATATAGCTCTATGGCCTGCACAATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT