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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcctatccccagttgtgatcactactgggaggtataataccctctcgcatataactagaagattataataatctgttaatctgctcaatcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTTAGGGATAACAAGCAGCTGGAATCAAGATGGGCAATTATGCAAGAAACTC

Basic information

species Oryza sativa
transcript LOC_Os02g23890.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g23890.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AC217358.3_FGT011 (Zea mays), 3'ss of exon 1
tgtcctatccccagttgtgat--cactactggga--ggta-taataccctctcgcatataactagaagattataataatctgttaatctgctcaatcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTTAGGGATAACAAGCAGCTGGAATCAAGATGGGCAATTATGCAAGAAACTC
    |   |   |||| |  |  |||  || |    |||  ||     || ||    ||    | ||   | | |   ||||     ||| || ||  | | ||||||||| ||||||| || || |||||||| ||| | |||||||||||||| ||||||||||| || ||||||||||||||||| || ||||||||||| |
--agcaggcaaaagttattgtgccacggcttgagatggtgctagggtgctttctgccattgtcataattctctgacg-tctgacctgctgttctat--tgtttagGAGAAGTCAGCTCCGAAGAAAGATGTTTATCAATTGTTTGCTGAGAAGGTCAGGGATAACAAACAACTGGAATCAAGATGGGCGATCATGCAAGAAACCC
















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|88294564|gb|CI602284.1|CI602284
EST:     AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAG                         GAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
genomic: AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAGgtaagttcga ... tcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
EST: gi|29658010|gb|CB654285.1|CB654285
EST:     AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAG                         GAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
genomic: AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAGgtaagttcga ... tcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
EST: gi|88826675|gb|CI777240.1|CI777240
EST:     AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAG                         GAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
genomic: AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAGgtaagttcga ... tcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
EST: gi|88385636|gb|CI566498.1|CI566498
EST:     AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAG                         GAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
genomic: AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAGgtaagttcga ... tcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
EST: gi|29678599|gb|CB674874.1|CB674874
EST:     AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCTCAG                         GAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
genomic: AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAGgtaagttcga ... tcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
EST: gi|88390512|gb|CI607548.1|CI607548
EST:     AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAG                         GAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
genomic: AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAGgtaagttcga ... tcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
EST: gi|88403266|gb|CI571007.1|CI571007
EST:     AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAG                         GAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
genomic: AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAGgtaagttcga ... tcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
EST: gi|87015520|gb|CI303126.1|CI303126
EST:     AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAG                         GAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
genomic: AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAGgtaagttcga ... tcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
EST: gi|88765740|gb|CI774834.1|CI774834
EST:     AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAG                         GAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
genomic: AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAGgtaagttcga ... tcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
EST: gi|88573256|gb|CI664827.1|CI664827
EST:     AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAG                         GAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
genomic: AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAGgtaagttcga ... tcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
EST: gi|66912874|gb|CX099722.1|CX099722
EST:     AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAG                         GAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT
genomic: AAAAGGGGAAGAAGGCCCCCGTATCCCGCTCATCCCGCGCCGGGTCCCAGgtaagttcga ... tcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgcatataactagaagattataataatctgttaatctgctcaatcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTTAGGGATAACAAGCAGCTGGAATCAAGATGGGCAATTATGCAAGAAACTC
                              tgttaat  putative branch site (score: 3)
     atataactagaagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcctatccccagttgtgatcactactgggaggtataataccctctcgcatataactagaagattataataatctgttaatctgctcaatcatatgtagGAGAAGCCAGCTCCAAACAAGGATGTTTACCAACTATTTGCTGAGAAGGTTAGGGATAACAAGCAGCTGGAATCAAGATGGGCAATTATGCAAGAAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA