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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGGGCTGGCGAAGCTGAGTTCTTTTGGCTTGGATAGGATGTCAGATGCTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAGgtaacctttaatttttctccctgagctgtaaaaaagggaaaacccattactgacacttaacttttcaag

Basic information

species Zea mays
transcript GRMZM2G136296_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136296_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 5'ss of exon 12
AGCTGGGCTGGCGAAGCTGAGTTCTTTTGGCTTGGATAGGATGTCAGATGCTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAGgtaacctttaatttttctccctgagctgtaaaaaagggaaaacccattactgacacttaacttttcaag
 ||||| ||||| ||||| ||||| |||||||||||||||||  | |||||  |||| ||||  || |||||||||| ||| ||||| || ||  | |||||||||    | || | | | ||| ||  | ||  | ||||||    |     |  ||   ||||||||
GGCTGGTCTGGCCAAGCTTAGTTCATTTGGCTTGGATAGGATTCCGGATGCAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaacc----acttctattcttgaactacacaag-gagaaaacatgctgacatccttttctttttcaag
















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|211483956|gb|FL010659.1|FL010659
EST:     CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCACACCT
genomic: CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAGgtaaccttta ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCGCACCT
EST: gi|29946640|gb|CB816251.1|CB816251
EST:     CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCGCACCT
genomic: CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAGgtaaccttta ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCGCACCT
EST: gi|67011396|gb|CO440145.1|CO440145
EST:     CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCACACCT
genomic: CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAGgtaaccttta ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCGCACCT
EST: gi|211388224|gb|FL201917.1|FL201917
EST:     CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCACACCT
genomic: CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAGgtaaccttta ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCGCACCT
EST: gi|211388219|gb|FL201912.1|FL201912
EST:     CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCACACCT
genomic: CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAGgtaaccttta ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCGCACCT
EST: gi|67040223|gb|CO466478.1|CO466478
EST:     CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCACACCT
genomic: CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAGgtaaccttta ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCGCACCT
EST: gi|211483958|gb|FL010661.1|FL010661
EST:     CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCACACCT
genomic: CTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAGgtaaccttta ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAGAATGCTTCAAATGGATCCGCACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGGGCTGGCGAAGCTGAGTTCTTTTGGCTTGGATAGGATGTCAGATGCTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAGgtaacctttaatttttctccctgagctgtaaaaaagggaaaacccattactgacacttaacttttcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA