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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagatgtgtttacataatttagtgctcctatcttttgaacagattcattgagtgaaaccaagtattaataatgtttactgttaacaatcggcgatctatttctatttcattaaagatactgatttgccattggacttattatgagatcaaagattgctaatctgcatgtgttattcctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATGGGCACATTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAA

Basic information

species Oryza sativa
transcript LOC_Os04g23890.3
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 15
gtatagatgtgtttacataatttagtgctcctatcttttgaacagattcattgagtgaaaccaagtattaataatgtttactgttaacaatcggcgatctatttctatttcattaaagatactgatttgccat--tggacttattatgagatcaaagattgctaatctgcatgtgttattcctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATGGGCACATTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAA
                                                                                          |  || || | || ||||| | |  |||  |    |||    |  |  | ||  | ||    || | || | |  |    ||    | || |   |||||| || ||||||||||| || |||||||||||||||||||||||||  ||||| ||||| || |||||||||||||| || || ||||||||  | |||||
------------------------------------------------------------------------------------------tgtgccatgtgttcctattccttagaagtaatgtgtttaatgtgtttaaatttctctggtgacataaatggttggtgattatacagtgtttccattgtagGAATAATATACCGTGACCTAAAGCCAGAAAACATTTTGCTCCAAGAGGATGGCCACATCGTTCTGACTGATTTTGACCTCTCTTTTTTGACTTCCTCAAA
















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|702138|gb|D48429.1|D48429
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|33799059|gb|CF325389.1|CF325389
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|38470322|gb|CF954453.1|CF954453
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|88306572|gb|CI671324.1|CI671324
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|88578420|gb|CI687351.1|CI687351
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|88580457|gb|CI697388.1|CI697388
EST:     GTTTCATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|29684157|gb|CB680432.1|CB680432
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|33381050|gb|CF196393.1|CF196393
EST:     CTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: CTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggacttattatgagatcaaagattgctaatctgcatgtgttattcctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATGGGCACATTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAA
                        tgctaat  putative branch site (score: 2)
                                        ttattcct  putative PPT
     ttattatga  TA-rich tract