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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