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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatataaatatgatactttatatttatctctcctttatcctctttatatccaatttcacccaaaagtactgaagccatgttaggttcatgtattaatcatttataatacagctactccagcctgtccagaacatatgctaacagcgacattcacaaatcatttttcagCTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTCATCATAGAGGCTTGGTTACAGGTTAGTTTTCATTGCCAAGTTTAGTTCT

Basic information

species Oryza sativa
transcript LOC_Os04g41470.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41470.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 11
gtatataa---atatgatactttatatttatctctcctttatcctctt---tatatccaatttcacccaaaa-----------gtactgaagccatgttaggttcatgtattaatcat-ttataatacagcta---ctccagcctgtccagaacatatgctaacagcgacattcacaaatcatttttcagCTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTCATCATAGAGGCTTGGTTACAGGTTAGTTTTCATTGCCAAGTTTAGTTCT
|||||| |   ||   ||  ||||| ||  |  ||  |||   |  |    |  | |  ||   |||  | |           | ||  || | || |    ||     |||||  |  |||||||  |||||   ||  | ||| |||||||| ||| || | |  ||| ||  | | |  ||||||||||||||| ||||||||| |||||||| ||||| ||||||||||| |||||||| |||||||| |||||||||                            
gtatatgacacatcccattgtttatcttctttccttatttgctcattcacatgaacctgataaaaccatatacattttttcttgaacaaaaacaatatactattggaacattaaaaaccttataatgtagctatctctttaacctatccagaacttatactcatactgac-ttgtccatttctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAG----------------------------

upper sequence: LOC_Os04g41470.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G876621_T01 (Zea mays), 3'ss of exon 11
gtatataaatatgatactttatatttatctctcctttatcctctttatatccaatttcacccaaaagtactgaagccatgttaggttcatgtattaatcatttataatacagcta-ctccagcctgtccagaacatatgctaacagcgacattcacaaatcatttttcagCTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTCATCATAGAGGCTTGGTTACAGGTTAGTTTTCATTGCCAAGTTTAGTTCT
                                                                     ||      |||||    |  |  |  || |  ||||| |  ||||  ||  | ||| |||||||| | | ||||||  ||| |   ||  ||  | |||||||||||| ||||||||| |||||||| ||||| ||||||||||| ||||||||  ||||||| |||||||||                            
--------------------------------------------------------------------gcttgcttaatgttttccttttcaagcaacc--ttatagtttagctctctgtaacctatccagaacttgtactaacattgacttctccatttctctcttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG----------------------------
















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|29681156|gb|CB677431.1|CB677431
EST:     TCGAGGCAAAAGGCATTAGGAGATCTGCTGAGTTTGCAAAACGACAAG                         CTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTC
genomic: TCGAGGCAAAAGGCATTAGGAGATCTGCTGAGTTTGCAAAACGACAAGgtatataaat ... catttttcagCTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTC
EST: gi|33797267|gb|CF324496.1|CF324496
EST:     TGCAAAACGACAAG                         CTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTC
genomic: TGCAAAACGACAAGgtatataaat ... catttttcagCTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actccagcctgtccagaacatatgctaacagcgacattcacaaatcatttttcagCTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTCATCATAGAGGCTTGGTTACAGGTTAGTTTTCATTGCCAAGTTTAGTTCT
                      tgctaac  putative branch site (score: 1)
                                            tcatttttc  putative PPT
                                         aaatcattttt  TA-rich tract