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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGAAGAAGCTCGAGAGGAAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAGgtatgtactattcttccatgacacttctgatttggaatagctgggctgattgacacgagtgagcgctctctgcag

Basic information

species Zea mays
transcript GRMZM2G132060_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132060_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA13G25110.1 (Glycine max), 5'ss of exon 17
GTATGAAGAAGCTCGAGAGGAAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAGgtatgtactattcttccatgacactt--ctgatttggaatagctgggctgattgacacgagtgagcgctctctgcag---------------------------------
||||||||||||  | |||||||||||| | || || ||    ||||| ||||||||||||||||||||||| |||   |||      | | |  |  |  | |       | ||   |  ||   |  | | |   |  |||  |                                  
GTATGAAGAAGCAAGGGAGGAAGAGAAGTTACGAAATCAGCGTGAGGATTTCAGTGACATGGTGGCAGAGgtgtgttacatttaattttcatatcttacaaactcacgcatgttgttgttgttattattaataacttcagtctttatttgtatatttaatcacgtaaccaactggtgcag

upper sequence: GRMZM2G132060_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA13G25110.2 (Glycine max), 5'ss of exon 17
GTATGAAGAAGCTCGAGAGGAAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAGgtatgtactattcttccatgacactt--ctgatttggaatagctgggctgattgacacgagtgagcgctctctgcag-----------------------------------------------------
||||||||||||  | |||||||||||| | || || ||    ||||| ||||||||||||||||||||||| |||   |||      | | |  |  |  | |       | ||   |  ||   |  | | |   |  |||  |                                                      
GTATGAAGAAGCAAGGGAGGAAGAGAAgttacgaaatcagcgtgaggatttcagtgacatggtggcagaggtgtgttacatttaattttcatatcttacaaactcacgcatgttgttgttgttattattaataacttcagtctttatttgtatatttaatcacgtaaccaactggtgcagaatgagaagaggaagaagag
















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|9952816|gb|BE639399.1|BE639399
EST:     AAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAG                         AATGCTCACAAGAGGAAGAGGAAGCAAGAGAAGGAAGGCAAGTCGA
genomic: AAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAGgtatgtacta ... ctctctgcagAATGCTCACAAGAGGAAGAGGAAGCAAGAGAAGGAAGGCAAGTCGA
EST: gi|211159310|gb|FL243896.1|FL243896
EST:     AAGRGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAG                         AATGCTCACAAGAGGAAGAGGAAGCAAGARAAGGAAGGCAAGTCGAAGAA
genomic: AAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAGgtatgtacta ... ctctctgcagAATGCTCACAAGAGGAAGAGGAAGCAAGAGAAGGAAGGCAAGTCGAAGAA
EST: gi|211159307|gb|FL243893.1|FL243893
EST:     AAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAG                         AATGCTCACAAGAGGAAGAGGAAGCAATGAGAAGG
genomic: AAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAGgtatgtacta ... ctctctgcagAATGCTCACAAGAGGAAGAGGAAGCAA-GAGAAGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 308

GTATGAAGAAGCTCGAGAGGAAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAGgtatgtacta ... ctctctgcagAATGCTCACAAGAGGAAGAGGAAGCAAGAGAAGGAAGGCAAGTCGAAGAAGAAGGAATTCAAGTTTTAAGGGCAGGCGGGCGATGTAGGTCATGAGGCAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 178

GTATGAAGAAGCTCGAGAGGAAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAGgtatgtacta ... ctctctgcagAATGCTCACAAGAGGAAGAGGAAGCAAGAGAAGGAAGGCAAGTCGAAGAAGAAGGAATTCAAGTTTTAAGGGCAGGCGGGCGATGTAGGTCATGAGGCAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 148

GTATGAAGAAGCTCGAGAGGAAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAGgtatgtacta ... ctctctgcagAATGCTCACAAGAGGAAGAGGAAGCAAGAGAAGGAAGGCAAGTCGAAGAAGAAGGAATTCAAGTTTTAAGGGCAGGCGGGCGATGTAGGTCATGAGGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

GTATGAAGAAGCTCGAGAGGAAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAGgtatgtacta ... ctctctgcagAATGCTCACAAGAGGAAGAGGAAGCAAGAGAAGGAAGGCAAGTCGAAGAAGAAGGAATTCAAGTTTTAAGGGCAGGCGGGCGATGTAGGTCATGAGGCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGAAGAAGCTCGAGAGGAAGAGAAGCTTCGGAACCAAAAGGAGGACTTCAGTGACATGGTGGCAGAGgtatgtactattcttccatgacacttctgatttggaatagctgggctgattgacacgagtgagcgctctctgcag

- - - - - - - - - - AAGAGA
- - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG