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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctacaaccttgatttatgtatacattttagagatgtttcagccttttagtcagttcataataaccaaaatcttgttcttcttgtgcatgtatttcagAGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT

Basic information

species Oryza sativa
transcript LOC_Os04g53240.4
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53240.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G419694_T05 (Zea mays), 3'ss of exon 2
----cttctacaaccttgatttatgtatacattttagagatgtttcagccttttagtcagttcataataaccaaaatcttgttcttcttgtgcatgtatttcagAGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT
     | ||||||| ||  |  |||  | |  |   |  ||   | ||  ||||| |||| | | | ||||  ||  |||  | |       | | | || |||||| ||||||  |||||||||||||||||||||| ||||||  |||||||||||| 
tcagttgctacaacttttttccatggtttccct---gccatacattagttttttattcaggttaca-taactgaacccttaatatgtcacaccttttgttacagAGAAGAGGCAATCTGAGGCTAACCGTATCAGAGAGAAGTACCCTGACAGAATTCCA

upper sequence: LOC_Os04g53240.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G076826_T02 (Zea mays), 3'ss of exon 3
cttctacaaccttgatttatgtatacattttagagatgtttcagcct-tttagtcagttcataataaccaaaatcttgttcttcttg-tgcatgtattt-cagAGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT
 | ||||  ||||| |  ||  ||     |   | |   || ||| | |||| |||| | | | ||||  ||  |||  |||   || ||| | |  || |||||| ||||||| |||||||||| || |||||||| ||||||  |||||||||||| 
-tgctacggccttgttccat-catttccctgcaatacaatttagcttctttattcaggttaca-taactgaacccttaatctgtgtgatgccttttcttacagAGAAGAGGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA
















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|33688345|gb|CF316584.1|CF316584
EST:     CAAGAGCTCGTTCAAGCTGGACCACACGCTCG                         AGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAA
genomic: CAAGAGCTCGTTCAAGCTGGACCACACGCTCGgtcggtttgt ... tgtatttcagAGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAA
EST: gi|86418393|gb|CI032602.1|CI032602
EST:     GAAGGAGCGCCATGGCCAAGAGCTCGTTCAAGCTGGACCACACGCTCG                         AGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAA
genomic: GAAGGAGCGCCATGGCCAAGAGCTCGTTCAAGCTGGACCACACGCTCGgtcggtttgt ... tgtatttcagAGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttagtcagttcataataaccaaaatcttgttcttcttgtgcatgtatttcagAGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT
               taataac  putative branch site (score: 1)
              ataataaccaaaat  TA-rich tract