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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGTCCTCAACCCCCTAGCGAGGGAGTTCAAGTCGATCGGGACCTTGAGGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctacagtaccggaacaggaaaccattcgatacagactacagattactgtataccagttaggcgattaccaataccatcacatcacatggaacctaatcttatgttgcag

Basic information

species Zea mays
transcript GRMZM2G038487_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038487_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 3
AGAGGTCCTCAACCCCCTAGCGAGGGAGTTCAAGTCGATCGGGACCTTGAGGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctacagtaccggaacaggaaaccattcgatacagactacagattactgtataccagttaggcgattaccaataccatcacatcacatggaacctaatcttatgttgcag
|||||| || || ||  |||| |||||||||||||| || || |||||||||||||||||||| ||  ||||| | ||  ||||||||||||||||||||||||  |||  |   |  ||||||  | | |  |   | ||| ||   || | |||   | |  |  | ||  ||   | |   ||                            
AGAGGTTCTTAATCCTTTAGCAAGGGAGTTCAAGTCAATTGGAACCTTGAGGAAAGAGCTTGCAGAATTACAGGAAGAATTGGCAAAAGCTCACAATCAGgtattgtactttcaggagacaggagccaaatgaa---aaacttcaa--tattatatgg-attctgatgttttacatgtctaatccag---------------------------

upper sequence: GRMZM2G038487_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 5'ss of exon 3
AGAGGTCCTCAACCCCCTAGCGAGGGAGTTCAAGTCGATCGGGACCTTGAGGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatg----ctacagtaccggaacaggaaaccattcgatacagactacagattactgtataccagttaggcgattaccaataccatcacatcacatggaacctaatcttatgttgcag
|||||| |||||  |  |||| |  ||||||||||| |  || |||||||||||||||||||| ||| | ||| | ||  |||| |||||||||||||||||||      | ||| |    ||  |  |||| ||| ||     ||   ||||    | |   | ||    |||  |||                                       
AGAGGTTCTCAAATCTTTAGCAATAGAGTTCAAGTCAAATGGAACCTTGAGGAAAGAGCTTGCAGAGTTGCAGGAAGAATTGGCCAAAGCTCACAATCAGgtattgcacttgcaggagtcaaat-gataacccttcaatctcatctg--gattctgatgttttatttgtctgat--ccag--------------------------------------
















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|74238024|gb|DT645938.1|DT645938
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|78104299|gb|DV522717.1|DV522717
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|211144702|gb|FL413099.1|FL413099
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|93012412|gb|EB637932.1|EB637932
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|148963856|gb|EE014962.2|EE014962
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|211323397|gb|FL381741.1|FL381741
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAAGCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|33467307|gb|CF244356.1|CF244356
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|91055890|gb|EB166308.1|EB166308
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|211386924|gb|FL369297.1|FL369297
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|71768332|gb|DR966269.1|DR966269
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|78113363|gb|DV531755.1|DV531755
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|211076904|gb|FL402121.1|FL402121
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCG
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCG
EST: gi|211347947|gb|FL254258.1|FL254258
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|211116917|gb|FL407739.1|FL407739
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACCATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTACCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|211279400|gb|FL429235.1|FL429235
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACCAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|211228027|gb|FL407502.1|FL407502
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
EST: gi|211048371|gb|FL399856.1|FL399856
EST:     GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAG                         GTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT
genomic: GGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctaca ... tatgttgcagGTTCATCTCTCGGAAACCAGAGTCTCATCTGCGCTCGACAAGCTAGCGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGGTCCTCAACCCCCTAGCGAGGGAGTTCAAGTCGATCGGGACCTTGAGGAAAGAGCTTGCCGAGCTACAGCAGGAGCTGGCAAAAGCTCACAATCAGgtatgctacagtaccggaacaggaaaccattcgatacagactacagattactgtataccagttaggcgattaccaataccatcacatcacatggaacctaatcttatgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA