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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCTGCACTACCTCCGCAGCCGCGCCACCGCCGGGCAGTGCCCCGTCCCCATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttcttcctcgatcatatcgatggatcgattgagttggtcgttcggtcaattgctactggttaattaattgcag

Basic information

species Oryza sativa
transcript LOC_Os07g48450.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48450.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G042494_T01 (Zea mays), 5'ss of exon 2
ATCCTGCACTACCTCCGCAGCCGCGCCACCGCCGGGCAGTGCCCCGTCCCCATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttcttcctcgatcatatcgatggatcgattgagttggtcgttcggtcaattgctactggttaattaattgcag--------------------------------------------------------------------------
||| |  |||||||||||| ||||||| ||  |  || |||||| ||| |||||||||||||||| |||||||||||||| ||||| ||||||||||||||| ||    |  |  ||  |    |        || | || | |     |       ||  |        | |  ||||                                                                           
ATCGTCAACTACCTCCGCAACCGCGCCGCCAACACGCCGTGCCCGGTCGCCATCATCGCCGACGTTGACATCTACAAGTTGGATCCTTGGGACCTGCCATgttagtac-ccgcgccgcgcgcgcctgcactcagactcagctcgcatcacatatcgctgtgatcc-ccgctcacatgcacatgacgcgtgatcgaccgagatccccgctcacaatttctagctagctagctgattgatgtgtatattattgcag

upper sequence: LOC_Os07g48450.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G011598_T01 (Zea mays), 5'ss of exon 1
ATCCTGCACTACCTCCGCAGCCGCGCCACCGCCGGGCAGTGCCCCGTCCCCATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttcttcctcgatcatatcgatggatcgattgagttg-gtcgttcggtcaattgcta--ctggttaattaattgcag--------------------------------------------------
||||| ||||||||||||| ||||||| ||  || || |||||| ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||   |  | | ||  | |      |      |  | | |  ||| ||| ||    |  |  ||   |  || |   | |                                                  
ATCCTCCACTACCTCCGCAACCGCGCCGCCAACGCGCCGTGCCCGGTCGCCATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgttagtagtactacccg-ccgtgcgcgcgcgcgcctgcactcgcatcgatcgatctgcagggaaactctcttttttaacaccgatagattttgccctaattattaattgatgtgtactgtattatcattgcag
















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|88343042|gb|CI641568.1|CI641568
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88340880|gb|CI637040.1|CI637040
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCCGCGAGAA
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCC-GCGAGAC
EST: gi|88306193|gb|CI636575.1|CI636575
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88734147|gb|CI757655.1|CI757655
EST:     -ATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTNTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88349457|gb|CI653736.1|CI653736
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88592662|gb|CI710781.1|CI710781
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGAACTGCCAT                         CGAAGGCGGTGTANGGGGAGAGTGAGTGGTATTTCTTCAGCCCCGCGAGAC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCC-GCGAGAC
EST: gi|88726289|gb|CI749944.1|CI749944
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88336492|gb|CI656763.1|CI656763
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGGGGTGTACGGGGAGAGTGAGTGGTATTTCTCCAGCCCCGCGAG
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCC-GCGAG
EST: gi|88340558|gb|CI659764.1|CI659764
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCCGCGAGAC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCC-GCGAGAC
EST: gi|86901187|gb|CI306376.1|CI306376
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88340456|gb|CI659662.1|CI659662
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|58593345|gb|CF991653.1|CF991653
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGCGAGTGGTATTTCTTCAGCCCGCGAGAAC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88336172|gb|CI647366.1|CI647366
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88583081|gb|CI700538.1|CI700538
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88336530|gb|CI656801.1|CI656801
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88734408|gb|CI757916.1|CI757916
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCA
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCA
EST: gi|88296187|gb|CI667577.1|CI667577
EST:     CATCATCGCCGANGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|58592461|gb|CF990769.1|CF990769
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGCGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCTGCACTACCTCCGCAGCCGCGCCACCGCCGGGCAGTGCCCCGTCCCCATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttcttcctcgatcatatcgatggatcgattgagttggtcgttcggtcaattgctactggttaattaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CGCCGACG