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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGGTCATGATCAGCTTTATAACCTGCAAATGCTAGAAGCTGCATTCCACAAGCTTCCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCGgtatgactttttgaagaacatggtgcctgctacaaagtttctactttgtagcccattgttcttattttcttacccgccttcattttcag

Basic information

species Zea mays
transcript GRMZM2G340749_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G340749_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g44900.2 (Oryza sativa), 5'ss of exon 12
TTCTGGTCATGATCAGCTTTATAACCTGCAAATGCTAGAAGCTGCATTCCACAAGCTTCCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCGgtatgactttttgaagaacatggtgcctgctacaaagtttctactttgtagcccattgttcttattttcttacccgccttcattttcag
| || ||||||||| ||||||||| ||||||||||| |||||||| ||||| | ||||||||||||||||||||| ||||| |  |||| ||| || |||||| ||   ||| |  |   |      || ||  ||     || | ||  ||  |||||||| | ||  ||  |  |  | ||||||||
TACTAGTCATGATCTGCTTTATAATCTGCAAATGCTTGAAGCTGCTTTCCATAGGCTTCCACAACCAAAGGACTCGGAGCGAGTCAAAAATTATATTCCGgtaagatcattttagtagagt------tgttatgaacaaaatattctg--gcgtattgttctaacttctttgtcttctgttattttcag

upper sequence: GRMZM2G340749_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g44944.1 (Oryza sativa), 5'ss of exon 1
TTCTGGTCATGATCAGCTTTATAACCTGCAAATGCTAGAAGCTGCATTCCACAAGCTTCCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCGgtatgactttttgaagaacatggtgcctgctacaaagtttctactttgtagcccattgttcttattttcttacccgccttcattttcag---
                               ||||| |||||||| | ||| | ||||||||||||||||||||| ||||| |  |||| ||| || || ||| ||   |||    |   |      || ||  ||     || | ||  ||  |||||||| | ||  ||  |     | || |||||   
-------------------------------ATGCTCGAAGCTGCTTACCATAGGCTTCCACAACCAAAGGACTCAGAGCGAGTCAAAAATTATATTCCAgtaagatcatttcggtagagt------tgttatgaacaaaatattctg--gcgtattgttctaacttctttgtcatgtgttatgttcagaag
















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|50331351|gb|CO526477.1|CO526477
EST:     ACAAGCTTCCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCG                         CGGCACCCTGCAGTTACCCCTGCTAGCTATCCCCAAGTTCAGCCATCAATT
genomic: ACAAGCTTCCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCGgtatgacttt ... tcattttcagCGGCACCCTGCAGTTACCCCTGCTAGCTATCCCCAAGTTCAGCCATCAATT
EST: gi|67024274|gb|CO453023.1|CO453023
EST:     ACAAGCTTCCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCG                         CGGCACCCTGCAGTTACCCCTGCTAGCTATCCCCAAGTTCAGCCATCAATT
genomic: ACAAGCTTCCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCGgtatgacttt ... tcattttcagCGGCACCCTGCAGTTACCCCTGCTAGCTATCCCCAAGTTCAGCCATCAATT
EST: gi|31359147|gb|CD443504.1|CD443504
EST:     ACAAGCTTCCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCG                         CGGCACCCTGCAGTTACCCCTGCTAGCTATCCCCAAGGTCAGCCATCAATT
genomic: ACAAGCTTCCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCGgtatgacttt ... tcattttcagCGGCACCCTGCAGTTACCCCTGCTAGCTATCCCCAAGTTCAGCCATCAATT
EST: gi|166497331|gb|EG148181.1|EG148181
EST:     CCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCG                         CGGCACCCTGCAGTTACCCCCTGCTAGCTATCCCCAAGTTCAGCCATCAAT
genomic: CCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCGgtatgacttt ... tcattttcagCGGCACCCTGCAGTTACCCC-TGCTAGCTATCCCCAAGTTCAGCCATCAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTGGTCATGATCAGCTTTATAACCTGCAAATGCTAGAAGCTGCATTCCACAAGCTTCCACAACCAAAGGACTCTGAGCGTGCTAAAACTTACATCCCGgtatgactttttgaagaacatggtgcctgctacaaagtttctactttgtagcccattgttcttattttcttacccgccttcattttcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT