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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGATTCTTTCCCGTATCAAGGTCCACTTGAATGCACTGAAAAGGTACACCTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagatcccaagacccaaagctatatactgaaaaccatttatccttgtcatttgaccactgagcgtttgcattttgtttgtgtttcttatcatccttttcag

Basic information

species Zea mays
transcript GRMZM2G123537_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123537_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g57390.1 (Oryza sativa), 5'ss of exon 10
TTGATTCTTTCCCGTATCAAGGTCCACTTGAATGCACTGAAAAGGTACACCTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagatcccaagacccaaagctatatactgaaaaccattta-tccttgtcatttgaccactgagcgtttgcattttgtttgt-----gtttcttatcatccttttcag
||||| ||||| |||||||| || || ||||||||||| || || |||||||||||||| ||||||||  |||| ||||||||||||||||| ||||||||| |||   || ||   |       |  ||| |  |   |||  | ||  | | |  ||    |||    ||      | ||||||     | ||||    ||   ||||||
TTGATCCTTTCACGTATCAAAGTACATTTGAATGCACTAAAGAGATACACCTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatt--tcgcagtccatgttcatgcatagtacagttcatccactctcttttacatgtttcctggttattactgactcgtttgtttgttgcttctgtaaatatatttcag
















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|47961753|gb|CN844462.1|CN844462
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|211232325|gb|FK959922.1|FK959922
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|32867178|gb|CF006860.1|CF006860
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|89760633|gb|DY688965.1|DY688965
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AAGGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|24763548|gb|CA398720.1|CA398720
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60394394|gb|DN227264.1|DN227264
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60355644|gb|DN222617.1|DN222617
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|113702621|gb|EE680125.1|EE680125
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60355743|gb|DN222716.1|DN222716
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60398356|gb|DN231172.1|DN231172
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60399207|gb|DN232021.1|DN232021
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60357180|gb|DN224153.1|DN224153
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGATTCTTTCCCGTATCAAGGTCCACTTGAATGCACTGAAAAGGTACACCTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagatcccaagacccaaagctatatactgaaaaccatttatccttgtcatttgaccactgagcgtttgcattttgtttgtgtttcttatcatccttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC