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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATTGCATGTAAACAAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagcttacttcgaatatcgtttctggttctacatatcatcagacagctctttaaaagataacattcttaacctcttcgcag

Basic information

species Zea mays
transcript GRMZM2G070218_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070218_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g51410.3 (Oryza sativa), 5'ss of exon 8
AGATTGCATGTAAACAAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgta------aaagcttacttcgaatatcgtttctggttctacatatcatcagacagctctttaa------aagataacattcttaac----ctcttcgcag-------
||||||||| |||||| |||||||||||||| || ||||| ||||| ||||| ||||| |||||||||      | |   || |  |||       || ||  | | ||   |||  |    | | |||       | | ||  | | ||||     |||| |||        
AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTGACATTGCTATTGAGgtatgcatgataagctattctgaacccacaatcaggagcaatatga-atcttatttttttctaacgtactgaaacaatttccctaacaacattcttggcattttacag
















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|60358208|gb|DN225181.1|DN225181
EST:     AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|50324617|gb|CO519743.1|CO519743
EST:     AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|60338581|gb|DN205554.1|DN205554
EST:     AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|211208198|gb|FL442564.1|FL442564
EST:     AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|211208197|gb|FL442563.1|FL442563
EST:     AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|148966442|gb|EE017448.2|EE017448
EST:     AAGGTCATGATGATGTCTTTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|86468677|gb|DY235047.1|DY235047
EST:     AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|149095243|gb|EE180868.2|EE180868
EST:     AAGGTCATGATGATGTCTTTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCCCACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|60337499|gb|DN204472.1|DN204472
EST:     AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|78073864|gb|DV502298.1|DV502298
EST:     AAGGTCATGATGATGTCTTTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|211026346|gb|FL457625.1|FL457625
EST:     AAGGTCATGATGATGTCTYTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|60354260|gb|DN221233.1|DN221233
EST:     AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|60337794|gb|DN204767.1|DN204767
EST:     AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|93281433|gb|EB673697.1|EB673697
EST:     AAGGTCATGATGATGTTTTTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCTTCGAGCCCACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
EST: gi|86466258|gb|DY232630.1|DY232630
EST:     AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG                         TCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA
genomic: AAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagctt ... ctcttcgcagTCACTTCATAAGATCGAGAGCTTCGTCATCGAGCACACTGCTGATAGTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATTGCATGTAAACAAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAGgtaaaagcttacttcgaatatcgtttctggttctacatatcatcagacagctctttaaaagataacattcttaacctcttcgcag

- - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - AGCTGA