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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatcaaaccaagaacctccttttgttcatggacctttaactataagcatgttttttatggcccctaactttgctaatcatttatcatatttgtaacagGTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAATCTGGCCTCTAAAATTCGTAGCAACTTGACTAATTCGATGAAAGCTTTGG

Basic information

species Oryza sativa
transcript LOC_Os01g23610.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 2
-------aatatcaaaccaagaacctccttttgttcatggacctttaactata-agcatgttttttatggcccctaactttgctaatcatttatcatatttgtaacagGTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAATCTGGCCTCTAAAATTCGTAGCAACTTGACTAATTCGATGAAAGCTTTGG
         | | ||||||  | |     | |||  |    | |||  || |  | || ||| || ||  ||| | ||    |||||||||| | ||  |||||| |||| ||| || | |||||||| ||||||| |||||| || |||||||||||||| || |||||||| || ||||||||||||||||| ||||||||| |||
taccttttctcttaaaccattagctatgatgtgtatac---cttttccctttgtatcaagttattcat--cccttgacc---ctaatcatttgtgatggttgtaatagGTCTCATCACCAGGATATGACAGGCAGGTTGTTGCTGACCATGCAAATAATCTTGCATCTAAAATCCGCAGCAACTTGACTAATTCAATGAAAGCTCTGG

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------aatatcaaaccaagaacctccttt----tgttcatggacctttaactataagcatg--ttttttatggcccctaactttgctaa-----tcatttatcatatttgtaacagGTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAATCTGGCCTCTAAAATTCGTAGCAACTTGACTAATTCGATGAAAGCTTTGG
                             | |  ||| |   |    |  | |    || |  | ||   |  |       || |  ||  | ||  ||  | ||| |  ||      |   || || | |  | ||||||||||| | |||||||||||| | |||| ||| ||||||||||| |||||||||||  | ||||| || | |||  |||| ||||| ||||| ||  | |
gtaaatatcaactcatgttctctgtttaaagttgcaagctttgtctttggtgtgaaatggttgtagaagatcgagctagttcaggaattactcattacctttcactatcttatggtttttggttttcctttgggaaacagGTTTCAGCTGCTGGATATGATCGTCAGGGTGTGGCAGATCATGCTAATAATCTGGCTACCAAAATACGAAACAATCTGACCAATTCAATGAAGGCAATTG

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 3'ss of exon 1
aatatcaaaccaagaacctccttttgttcatggacctttaact-ataagcatgttttttatggcccctaactttgctaatcattt-atcatatttgtaacagGTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAATCTGGCCTCTAAAATTCGTAGCAACTTGACTAATTCGATGAAAGCTTTGG
  |     ||   |  | |   ||  | |||     |  || |  || ||||    || |  | |   |  | || | ||  ||| |  ||  |  | | ||||| |  ||||||| ||||||||||| |  || || ||||||||||||||||| ||||| |||||  | || |||||||| |||||  |||| | | | |
gttcatgcactctgctcttgggttgttacattttgttcgaatttgtatgcatcaacttca--gtcatgagatatgatgatgttttgaagattctgatgatagGTTGCTGCAGCTGGGTATGATAGGCAAGGAGTAGCTGATCATGCAAATAATCTTGCCTCAAAAATCAGAAGTAACTTGACCAATTCATTGAAGGGTCTTG

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 2
aatatcaaaccaagaacctcctt--ttgttcatggacctttaactataagcatgttttttatggcccctaactttgctaatcattt-atcatatttgtaacagGTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAATCTGGCCTCTAAAATTCGTAGCAACTTGACTAATTCGATGAAAGCTTTGG
    |  |  ||     ||  ||  |||||        ||  | | |       |    |   | |   |  | ||   ||  ||| |  ||  |  | | ||||| |  ||||||| ||||||||||| |  || || ||||||||||||||||| ||||| |||||  | || |||||||| |||||  |||| | | | |
---gttcatgcactctgctgtttggttgttacccattgttggaatttgtatgcatcaacttcagtcatgagatatgacgatgttttgaagattctgatgatagGTTGCTGCAGCTGGGTATGATAGGCAAGGAGTAGCTGATCATGCAAATAATCTTGCCTCAAAAATCAGAAGTAACTTGACCAATTCATTGAAGGGTCTTG

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 2
aatatcaaaccaagaacctccttttgttcatggacctttaactataagcatgttttttatggccc---ctaactttgctaatcatttatcatatttgtaac--agGTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAATCTGGCCTCTAAAATTCGTAGCAACTTGACTAATTCGATGAAAGCTTTGG
    |  |||      |  ||||||  ||| | |  |    || |  ||||| | |  ||   ||   |  | ||  || ||  ||        ||| |||  |||||||| | || || ||||| || || |  || || || ||||| ||||| || || |||||||||||||  || ||||||||||| |||||||| ||||
tgcttataacttgatgcaacctttt--tca-gaatttcccccttt--gcatgctatcaatattccaaccctatttgactcattgttctgatctcttgaaactcagGTTTCAGCTGCAGGGTATGACAGACAAGGAGTGGCTGACCATGCCAATAACCTTGCTTCTAAAATTCGTAATAATTTGACTAATTCAATGAAAGCATTGG

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|58675783|gb|CK064470.1|CK064470
EST:     GGATGAGGGAACTTCAAGATGAACACCACATGAAATCGTTGGGTCTACAG                         GTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAAT
genomic: GGATGAGGGAACTTCAAGATGAACACCACATGAAATCGTTGGGTCTACAGgtgatatatt ... tttgtaacagGTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAAT
EST: gi|58670429|gb|CK059115.1|CK059115
EST:     GGATGAGGGAACTTCAAGATGAACACCACATGAAATCGTTGGGTCTACAG                         GTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAAT
genomic: GGATGAGGGAACTTCAAGATGAACACCACATGAAATCGTTGGGTCTACAGgtgatatatt ... tttgtaacagGTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcatgttttttatggcccctaactttgctaatcatttatcatatttgtaacagGTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAATCTGGCCTCTAAAATTCGTAGCAACTTGACTAATTCGATGAAAGCTTTGG
                           tgctaat  putative branch site (score: 2)
                              taatcatttatcatat  TA-rich tract