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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcataccctagttttttctgatttaatacagatttattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC

Basic information

species Oryza sativa
transcript LOC_Os06g45120.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 17
gtgagtcataccctagttttttctgatttaatacagatttattggttgtctctattttaatgat-taaccattttctttagtctgatcatctctatataa-tgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC
                     |  |      |  | |||  ||   |   |  |  || || || | |   | |||||  || || |    ||| | |   ||  | |||||||| || || || || ||||||||||||||||||||||||||||||||||| |||||| | |  || |||||||||                     
--------------------gtaagggcccttgta-attggttaacttctttaacatttattatattattgtgttcttatgt-tggtaccttctgtgtggctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAG---------------------

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 17
gtgagtcataccctagtttttt--ctgatttaatacagatttattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataa-tgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC
|| ||  |     || ||  ||  ||  |||||||   |||   |  |||| | |||||               |||||  ||  |  | | | | | |   ||  | ||||||||||| ||||| || ||||||||||||||||||||||||||||||||||| |||||| | |  || |||||||||                     
gtaagggaccttgtaattggttaacttctttaatatgtattatattattgtttttatttg--------------ttcttatgttggtacctttttgtgtggctgtgatagATATGACAAATTCTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAG---------------------

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 16
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
gtgagtcataccctagttttttctgatttaatacagatttattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC
|| ||  ||    | | |   |  | |||  |  ||   || |   | | ||| | | || |  | |      |||| |  ||     |   |  ||  |   ||||||||||||| |||||||| ||||||||||| || ||||||||||| |||||||| |||||| | |   |||| || |||                     
gtaag--atttgttggctcccttcgttttggtttag---tactctctctttctctctcaacgggttatt-cactcttgaacct---tttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG---------------------

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 17
gtgagtcataccctagttttttctgatttaatacagatt--tattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC
      ||   | ||||   |   |   | | |  | ||  | || |||   || | |  |||  || |  || |||  |  | |  | || | |   |      |||||||||||||||| ||||| || |||||||| |||||||||||| | ||||||||||||||| |||  || || ||||||                     
------cac-tcttagtcactgtaggactgacatgggttattttttgttacttccaatcaaatt-ttcattatcttccatgat-tattgattttttggttggttgacagATATGACAAGTTTTGTCCCTTTTACAAGTCAGTTTGGATGATGAGGAACATTATTCATTTCTATAATTTGGCCAATCAG---------------------

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 17
--------------------gtgagtcataccctagttttttctgatttaatacagatttattggtt------gtctctattttaatgat----taaccattttctttagtctgatcatctctatataatgaa------acagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC
                     ||| ||| |   | ||  ||| | ||||  |    | ||| |  ||      ||  |  |||| ||| |    ||   ||| | |||   || |  || | ||| | |||        |||||||||| |||||||| || ||||||||||| ||||||||||||||||| ||||| |||||| |||  || || ||||||                     
gtaagtcccagattaagtttttgattcaaattttcgtcctttttaatttt-tgtttacttactatttccttatgttcccctttttatgctggtctagaaattctttttccacttaatatatgtatctcatgtggctgtgacagATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAG---------------------

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 16
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17
gtgagtcataccctagttttttc-----------tgatttaatacagatttattggttgtctctat-----tttaatgattaaccattttctttagtctgat-catctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC
|||||   |     | |||| |            |  ||   || |  ||| |   |  ||| | |     ||  | ||||     |||      ||||||| |    || |   | |  |||| |||||||| ||||| ||||||||||||||||| ||||||||||| || ||| | || ||||| ||  | |||||||||                     
gtgagctttgttgaaattttgttgtgtaggatgtttgttgggtagatgtttttcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctcatacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG---------------------

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16
gtgagtcataccctagttttttctgatttaatacagatttattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC
                                                         ||    ||      || || | || |     |  | || |  |    |||||| || ||||| ||||| ||||||||||| |||||||||||||| |||||  ||||||||       |  | | ||||                     
--------------------------------------------------------gtacgtgttccgggcttgctcttgtttatcgctaacaatctgct---ccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG---------------------

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 17
gtgagtcataccctagttttttctgatttaatacagatttattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC
                                                         ||    ||      || || | || |     |  | || |  |    |||||| || ||||| ||||| ||||||||||| |||||||||||||| |||||  | ||||||       |  | | ||||                     
--------------------------------------------------------gtacgtgttccgggcttgctcttgtttatcgctaacaatctgct---ccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAG---------------------

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|33804193|gb|CF327971.1|CF327971
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGTGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|116875037|gb|EC365545.1|EC365545
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATCTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|88735905|gb|CI757480.1|CI757480
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTC
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTC
EST: gi|116875538|gb|EC366046.1|EC366046
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATCTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttaatgattaaccattttctttagtctgatcatctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC
                                      tctatataatgaaa  TA-rich tract