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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG

Basic information

species Oryza sativa
transcript LOC_Os01g68320.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68320.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G362850_T01 (Zea mays), 3'ss of exon 6
gcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG
| |  | ||  |||||||       ||   | ||  | | |    |  ||  ||    | |      ||   |||  || || | |   |||||||| |||||||||||||||||||| ||||||||||| ||||| |||||||| ||| |||| || ||||| ||||| || || || ||||||
gtacagtttcgtttagaaatgcagaattcttactaatatct--attgtcttgcctagctctaatgcttgtccaacacttctgctatccttagATCCGCCCAGACAGGCAAACCTTGTACTGGAGTGCCACATGGCCTAGAGAAGTTGAAGCCTTAGCAAGACAGTTTCTACAAAATCCTTACAAG

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G059020_T01 (Zea mays), 3'ss of exon 7
gcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG
| |    |   |||||||       ||   | ||  | | |    |  || |||    | |      ||   |||  || || | |   |||||||| ||||| |||||||||||||| ||||||||||| ||||| |||||||| ||| |||| || ||||||||||| || || || ||||||
gtacatttccgtttagaaatgcagaattcttactaatatct--attgtctttcctagctctaatgcttgtccaacacttctgctatccttagATCCGCCCAGATAGGCAAACCTTGTACTGGAGTGCCACATGGCCTAGAGAAGTTGAAGCCTTAGCAAGACAATTTCTACAAAATCCTTACAAG
















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|87023569|gb|CI286320.1|CI286320
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAA
EST: gi|29664446|gb|CB660721.1|CB660721
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29633338|gb|CB638347.1|CB638347
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|33797128|gb|CF324429.1|CF324429
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|88417599|gb|CI581622.1|CI581622
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29629642|gb|CB634651.1|CB634651
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGATAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|218485924|gb|FG959170.1|FG959170
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29661777|gb|CB658052.1|CB658052
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAA
EST: gi|29678103|gb|CB674378.1|CB674378
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29633337|gb|CB638346.1|CB638346
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCATACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29669296|gb|CB665571.1|CB665571
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG
                              tgctaaa  putative branch site (score: 2)
                                       tttttgtt  putative PPT
                                       tttttgttgttaata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG