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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAGGCTTAGATGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggattgatacagattaagcttctatcttctctaaaaaaaccgcagtacaccatcttatatacatacatatttgccattgcag

Basic information

species Zea mays
transcript GRMZM2G052875_T02
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052875_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 14
GTTAGGCTTAGATGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggattgatacagattaagcttctatcttctctaaaaaaaccgcagtacaccatcttatatacatacatatttgccattgcag
||||||||| |||| ||||||| |||||| |||||||  || ||||||||||| |||||||||||||| ||||  |  | ||  | |||| | ||| ||   ||||  | || ||| |  | | |  ||||| | || ||    |  |||
GTTAGGCTTCGATGCGGGCTGAACAATGAACTTAATGGTGTCGATGAGCCTAGTAGATGCGAgtatgttgatttctctacatacaccttccaccttttcctgaaaatgcacattactc--tttaacttacatgcctacttcatgtgacag
















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|60350253|gb|DN217226.1|DN217226
EST:     TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGA                         GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
genomic: TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
EST: gi|211376353|gb|FL146646.1|FL146646
EST:     TGTGGGCTGAGCAATGAGCTTAATGATGTCGATGAGCCTAGCAGATGCGA                         GTATGTGGCTGTATTGTCGACGCCCGCACTCTGCGTTGAGGAGAAGCTGAA
genomic: TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
EST: gi|18964528|gb|BM661058.1|BM661058
EST:     TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGA                         GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
genomic: TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
EST: gi|18964529|gb|BM661059.1|BM661059
EST:     TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGA                         GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
genomic: TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
EST: gi|33092076|gb|CF052070.1|CF052070
EST:     TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGA                         GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
genomic: TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
EST: gi|211376351|gb|FL146644.1|FL146644
EST:     TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGA                         GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
genomic: TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
EST: gi|87151897|gb|DY396686.1|DY396686
EST:     TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGA                         GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
genomic: TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
EST: gi|211084967|gb|FL399106.1|FL399106
EST:     TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGA                         GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
genomic: TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
EST: gi|110950038|gb|EE170195.1|EE170195
EST:     GCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGA                         GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
genomic: GCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
EST: gi|211376352|gb|FL146645.1|FL146645
EST:     TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGA                         GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
genomic: TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
EST: gi|67026048|gb|CO454797.1|CO454797
EST:     TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGA                         GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
genomic: TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
EST: gi|30306637|gb|CD001310.1|CD001310
EST:     TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGA                         GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA
genomic: TGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 84

GTTAGGCTTAGATGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

GTTAGGCTTAGATGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GTTAGGCTTAGATGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GTTAGGCTTAGATGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggat ... gccattgcagGTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAGGCTTAGATGTGGGCTGAGCAATGAGCTTAATGACGTTGATGAGCCTAGCAGATGCGAgtatgtggattgatacagattaagcttctatcttctctaaaaaaaccgcagtacaccatcttatatacatacatatttgccattgcag

- - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG