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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAGAAAGTTAATGGGGCTGAGAGTACAACCACTTCACCCTTTCTCTCAGTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattatttacaactttcaaaggattcttacatgtgttgattgtatcctatgcctacagcctttccgttatcaacatggtggatgtttttcag

Basic information

species Zea mays
transcript GRMZM2G101502_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101502_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g43100.1 (Oryza sativa), 5'ss of exon 3
ATAAGAAAGTTAATGGGGCTGAGAGTACAACCACTTCACCCTTTCTCTCAGTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattatttacaactttcaaaggattcttacatgtgttgattgtatcctatgcctacagcctttccgttatcaacatggtggatgtttttcag
| |||||   || ||| | ||| ||| ||||   |||||| |||||||||||||||||||| |||||| ||||||| || ||| ||||||| ||| ||||| ||         | |||||   | || ||||||| || |||||    | ||  ||    | | |   ||  | ||||||   |  |||||||
AAAAGAATACTAGTGGAGTTGAAAGTGCAACTGTTTCACCTTTTCTCTCAGTTGATCCAGCACTGCCTGCAAAGCAAGGACTTCCAGTAGAACAACTAAGgcat-------gtcgttcaacacagtcctacatgtcttcattgtgctttgtgtgtattatcatgctactaatagcatggttattaattttcag

upper sequence: GRMZM2G101502_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g06620.1 (Oryza sativa), 5'ss of exon 4
ATAAGAAAGTTAATGGGGCTGAGAGTACAACCACTTCACCCTTTCTCTCAGTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattatttacaactttcaaaggattcttaca-tgtgttgattgtatcctatgcctacagcctttccgttatcaacatggtggatgtttttcag
| ||||| | |  ||   |||| || ||||||| |||||| ||||||||||||||||||||  | ||| ||||||| || ||||| ||| | ||| ||||||||           ||  | | | || |||| | ||||  ||||||   ||   ||    ||| |   ||  |   ||||  || ||||||||
AAAAGAATGCTGGTGTTTCTGAAAGCACAACCATTTCACCATTTCTCTCAGTTGATCCAGCATTACCTGCAAAGCAAGGACTTTCGGTACACCAACTAAGgtat--------gtctttgaggcagtcgtacactttgtttgttgtatttcatatgtattttcttgctagtactagtgtggtcaatatttttcag
















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|76914577|gb|DV165582.1|DV165582
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|78106816|gb|DV525234.1|DV525234
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|71436021|gb|DR817071.1|DR817071
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|94472329|gb|EB701287.1|EB701287
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|78092612|gb|DV520986.1|DV520986
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|93012503|gb|EB638023.1|EB638023
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|86855912|gb|DY306923.1|DY306923
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|76909001|gb|DV163174.1|DV163174
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|76914576|gb|DV165581.1|DV165581
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|78078333|gb|DV506748.1|DV506748
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|78115922|gb|DV534310.1|DV534310
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGGTATGCCAGCTC
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGC-AGCTC
EST: gi|93016960|gb|EB642480.1|EB642480
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|78078332|gb|DV506747.1|DV506747
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|74246445|gb|DT654359.1|DT654359
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|89757602|gb|DY687134.1|DY687134
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCCGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|76293315|gb|DV032883.1|DV032883
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|74236077|gb|DT643991.1|DT643991
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|74236078|gb|DT643992.1|DT643992
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|60398795|gb|DN231611.1|DN231611
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|61118901|gb|DN559862.1|DN559862
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|109179127|gb|EC379824.1|EC379824
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|149014196|gb|EE043749.2|EE043749
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|67019156|gb|CO447905.1|CO447905
EST:     GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: GTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
EST: gi|76293314|gb|DV032882.1|DV032882
EST:     CTTTCAGTAGATCAATTAAG                         GGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT
genomic: CTTTCAGTAGATCAATTAAGgtattattta ... tgtttttcagGGGCCTTCTTCTCAATGAGCAAGAGAGCATGTACCAACGTTATGCAGCTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAGAAAGTTAATGGGGCTGAGAGTACAACCACTTCACCCTTTCTCTCAGTTGATCCAGCGCTGCCTTCAAAGCATGGGCTTTCAGTAGATCAATTAAGgtattatttacaactttcaaaggattcttacatgtgttgattgtatcctatgcctacagcctttccgttatcaacatggtggatgtttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA