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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagcctttactgtctgctaatgcttcatatgaacaccttgataatgtgaatggtggcctgcatgagtttcaatggctaacttttgtgcggcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAAGAGTTCTACCAGCAGCCAGGGTGGAAACAAGAACTACAGAAAAGGAAGC

Basic information

species Oryza sativa
transcript LOC_Os03g24220.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G359566_T01 (Zea mays), 3'ss of exon 8
acagcctttactgtctgctaa-tgcttcatatgaacaccttgataatgtgaatggtggcctgcatgagtttc-aatggctaacttttgtgcggcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAAGAGTTCTACCAGCAGCCAGGGTGGAAACAAGAACTACAGAAAAGGAAGC
  |   | |     ||| |   ||| || | |   ||  ||||     | |   ||    |  ||| ||||| || |||| |  |   ||  |||||||||||||||||||  |||||  || ||| |||| || ||||| || || || || ||||||||| |||||||| ||||||| |||||  | ||||| | |||  
ctattttatcacaactgatggctgcctcttctctgca--ttgagtgcattacatgttatgtttatgggtttccaaaggcttaagtccatgttgcttctgcagACATATTTGGTGGACAATGAGTTCGAGACCGTGTTTGGCATGACCAAAGAGGAGTTCTACGAGCAGCCAAGGTGGAAGCAAGAGTTGCAGAAGAAGAAAG

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 24
acagcctttactgtctgctaatgcttcatatgaacacct-tgataatgtgaatggtggcctgcatg------agtttcaatggctaacttttgtgcggcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAAGAGTTCTACCAGCAGCCAGGGTGGAAACAAGAACTACAGAAAAGGAAGC
      |  | |  |||  |  |||   ||||    ||| |  |  ||  | | |||  |  ||||       ||| ||| |||||| ||   |   |||||||||||||||||||  |||||| |||||| |||| |||||||| || || ||||| ||||||||| |||||||| ||||||| |||||  | ||||||| |||  
---cgttggattacctgtcacagct---tatggctgcctcttcttctgcaattagtgcacctcatgtttatgggttccaaaggctaa-ttccatcttgcttctgcagACATATTTGGTGGACAGTGAATTCGAGACCGTATTTGGCATGACTAAGGAGGAGTTCTACGAGCAGCCAAGGTGGAAGCAAGAGTTGCAGAAAAAGAAAG
















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|86479401|gb|CI122034.1|CI122034
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|29669713|gb|CB665988.1|CB665988
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|16754192|gb|BM038571.1|BM038571
EST:     TCTACCAACCCTGTTCGTGGGATAGATTCCCAACCCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86479378|gb|CI122011.1|CI122011
EST:     TATCGAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|87022895|gb|CI269831.1|CI269831
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|89193062|gb|CI050360.1|CI050360
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|33794451|gb|CF323110.1|CF323110
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCC
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCC
EST: gi|86597638|gb|CI274629.1|CI274629
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86437319|gb|CI119041.1|CI119041
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|218505177|gb|FG951529.1|FG951529
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86502671|gb|CI145304.1|CI145304
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|38479352|gb|CF963481.1|CF963481
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|163923599|gb|EG713316.1|EG713316
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86480869|gb|CI123502.1|CI123502
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTTGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|58667525|gb|CK056211.1|CK056211
EST:     AGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATGACGAAGGAA
genomic: AGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|9864985|gb|AU100735.1|AU100735
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTAC-AACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86252596|gb|CI003932.1|CI003932
EST:     TTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|38480301|gb|CF964390.1|CF964390
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86480878|gb|CI123511.1|CI123511
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|88260846|gb|CI361434.1|CI361434
EST:     CAACCCTGTTCCTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: CAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|29674448|gb|CB670723.1|CB670723
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaatggtggcctgcatgagtttcaatggctaacttttgtgcggcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAAGAGTTCTACCAGCAGCCAGGGTGGAAACAAGAACTACAGAAAAGGAAGC
                             ggctaac  putative branch site (score: 2)
                                              cttctgc  putative PPT
                                taactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagcctttactgtctgctaatgcttcatatgaacaccttgataatgtgaatggtggcctgcatgagtttcaatggctaacttttgtgcggcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAAGAGTTCTACCAGCAGCCAGGGTGGAAACAAGAACTACAGAAAAGGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA