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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgataacttgtatggtacctttttatatgagtcgcggttgatgatgctggcctaatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAAGAAGAATAATGTGGCTCTTGACATCGTTGACTTTGGTGAAACCGATGAT

Basic information

species Oryza sativa
transcript LOC_Os03g13970.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147671_T01 (Zea mays), 3'ss of exon 4
----------gtatgataacttgtatggtacct-----ttttatatgagtcgcggttgatgatgctggcctaatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAAGAAGAATAATGTGGCTCTTGACATCGTTGACTTTGGTGAAACCGATGAT
          ||  | |||||||||||  |  |     || | | ||| |   |||| ||||  || | |   | | |||| |||||||| |||||||||||| ||||||| ||||||||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||| | ||||||
gtaggcctgggtgggttaacttgtatgacaattattaattctctttgaatttaggttaatgaatctcgtcatgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCTGATGAT

upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G165926_T02 (Zea mays), 3'ss of exon 4
----------gtatgataacttgtatggtacct-----ttttatatgagtcgcggttgatgatgctggcctaatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAAGAAGAATAATGTGGCTCTTGACATCGTTGACTTTGGTGAAACCGATGAT
          ||   ||||||| |||||          || | | ||| |    ||| ||||  || | |   | | |||| |||||||| |||||||||||||||||||| || || ||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||| ||||||||
gtatgcagtggtggcataacttttatggcgatcattaattctgtttgaatttaagttaatgagtcttgtcatgtgtatcagTCCTGTGAAGTACGACAAGAAAGTTTTGGAGACCATTGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCCGATGAT
















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|163919850|gb|EG710352.1|EG710352
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|33657883|gb|CF280497.1|CF280497
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|33654150|gb|CF276764.1|CF276764
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATAC-ACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|58663975|gb|CK052661.1|CK052661
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAACAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|88358175|gb|CI605100.1|CI605100
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|33681541|gb|CF309780.1|CF309780
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|88434013|gb|CI586891.1|CI586891
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CC-TGTGAAATACGAGAAGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAA
EST: gi|33654616|gb|CF277230.1|CF277230
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|2309803|gb|C25958.1|C25958
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGNCAAGAAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAA
EST: gi|33681744|gb|CF309983.1|CF309983
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGANAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|88425160|gb|CI564677.1|CI564677
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCT
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCT
EST: gi|163926719|gb|EG713735.1|EG713735
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|218488524|gb|FG963297.1|FG963297
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatggtacctttttatatgagtcgcggttgatgatgctggcctaatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAAGAAGAATAATGTGGCTCTTGACATCGTTGACTTTGGTGAAACCGATGAT
                                         gcctaat  putative branch site (score: 3)
                                               tctttc  CT-rich tract
           tttttatatga  TA-rich tract