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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTCCTCTCATGGCCGCCGCCGCAGCTGACGACGCAGCCGAGGTGGAGCGGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaatccctcccgtagtttgttaaggctggtctgcgttcaggctagggttttgggtgacgtggagttttcggtttcggaattgcag

Basic information

species Zea mays
transcript GRMZM2G059039_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059039_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g20930.1 (Oryza sativa), 5'ss of exon 1
CTCTCCTCTCATGGCCGCCGCCGCAGCTGACGACGCAGCCGAGGTGGAGCGGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtg--cctcgaatccctc--ccgtagtttgttaag---gctggtctgcgttcag--gctagggttttgggtgacgtggagttttcggttt--cggaattgcag---------------
||| ||   |      |||||| | |  | |||||| || ||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||| |||||  ||||   |||| |  |||  |  || |      || | |  | |  | |  ||    |  | ||||   |  | | ||||| |||    |    || |               
CTCCCCCGCCGCCATGGCCGCCTCCGACGCCGACGCCGCGGAGGTCGAGCGGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAGgtgcgcctccgctcccccctccgccgcctgctccattcgccgctacgggccccgccgccgccgcctagggttttgacggggtttcgttttgctcggggggcggccttccgcatcgcag
















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|211179438|gb|FL364366.1|FL364366
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211344380|gb|FL313708.1|FL313708
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|148969036|gb|EE019749.2|EE019749
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211444762|gb|FL341640.1|FL341640
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|71766575|gb|DR964512.1|DR964512
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211281795|gb|FL349528.1|FL349528
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211012398|gb|FL319259.1|FL319259
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211407222|gb|FL345640.1|FL345640
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211433492|gb|FL365020.1|FL365020
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|148943964|gb|EC889044.2|EC889044
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211185388|gb|FL309812.1|FL309812
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211314239|gb|FL336753.1|FL336753
EST:     GGCTTTACGAGCTCGGGGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|76014976|gb|DT942146.1|DT942146
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211158733|gb|FL327703.1|FL327703
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211170432|gb|FL336616.1|FL336616
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211306674|gb|FL363564.1|FL363564
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211375331|gb|FL327051.1|FL327051
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211041006|gb|FL343143.1|FL343143
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211050490|gb|FL366022.1|FL366022
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211103808|gb|FL341011.1|FL341011
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211055963|gb|FL348933.1|FL348933
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|89761569|gb|DY689527.1|DY689527
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|149105666|gb|EE291222.2|EE291222
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|50326790|gb|CO521916.1|CO521916
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211416754|gb|FL321419.1|FL321419
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
EST: gi|211145125|gb|FL324993.1|FL324993
EST:     GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAG                         CATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC
genomic: GGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaa ... ggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCC

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTCCTCTCATGGCCGCCGCCGCAGCTGACGACGCAGCCGAGGTGGAGCGGCTTTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAATGACAAGTCCGAGgtgcctcgaatccctcccgtagtttgttaaggctggtctgcgttcaggctagggttttgggtgacgtggagttttcggtttcggaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC