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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgataaatttttcaaatccaaatgatattatttttgcatagaatttcccaacaagttctcaatttcggattgcagGAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCTTTATAGCTTTTGGTGATATTCTTGAGTTACATAAAAAATTCCTTGAACT

Basic information

species Oryza sativa
transcript LOC_Os01g73530.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G074241_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------gttgataaatttttcaaatccaaatgatattatttttg-catagaatttcccaacaagttctcaatttcgga-ttgcagGAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCTTTATAGCTTTTGGTGATATTCTTGAGTTACATAAAAAATTCCTTGAACT
                                              |||  |    || ||  ||     | | ||  ||||| |||||| |||    |     ||    ||||||| || ||||||||||||||||||| ||  | ||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||| || || |||||||||||
gttggcattaatcttgaaagttccattattaaaaaaaaacaaaatcttggcagcgcttccatttctgtgcggtgttccttttggcatagagttt----atgctctcatgttttcggaattacagGAGAGTTGGCACATGCTCTGAGGTTCTTGGCATCTGTGGTGTCACAAAGCTTCATAGCGTTTGGTGATATTCTTGAGTTACACAAGAAGTTCCTTGAACT

upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA08G14480.1 (Glycine max), 3'ss of exon 16
gtt-gataaatttttcaaatc--caaatgatattatttttgcatagaatttcccaacaagttctcaatttcggattg-cagGAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCTTTATAGCTTTTGGTGATATTCTTGAGTTACATAAAAAATTCCTTGAACT
||  ||||  |   |  ||||    | |    |||| |||   | |    || |  |       || |     | |   ||| ||| | |||||||||||  | || ||||||||||| || || ||||||||| ||||||| |||||||||||||| ||  ||||||| ||  | || ||
gtaagatatttccattgaatcatttactctctttatatttctcttgttgctctcctctctcagacagtactatactaatagGTGAGCTAGCACATGCACTGAGGTTTTTGGCATCTGTTGTTTCTCAAAGCTTTTTAGCTTTCGGTGATATTCTTGAATTGAATAAAAAGTTTGTAGAGCT

upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA05G31270.1 (Glycine max), 3'ss of exon 18
gtt-gataaatttttcaaatc--caaatgatattatttttgcatagaatttcccaacaagttctcaatttcggattg-cagGAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCTTTATAGCTTTTGGTGATATTCTTGAGTTACATAAAAAATTCCTTGAACT
||  ||||  |   |  ||||    | |     ||||| |        | |||   |       ||||     | |   ||| ||| |||||||||||||  | || ||||||||||| || || ||||||||| ||||||| |||||||||||||| || |||| ||| ||  | |||||
gtaagatatttgcattgaatcatttactctctatatttctcttgttgctctcctctctcacagacaatactatactaatagGTGAGCTGGCACATGCACTGAGGTTTTTGGCATCTGTTGTTTCTCAAAGCTTTTTAGCTTTCGGTGATATTCTTGAATTGCATAGAAAGTTTGTAGAACT

upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA11G38160.1 (Glycine max), 3'ss of exon 20
-----gttgataaatttttcaaatccaaatgatattatttttgcatagaatttcccaacaagttctcaatttcgga-ttgcagGAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCTTTATAGCTTTTGGTGATATTCTTGAGTTACATAAAAAATTCCTTGAACT
      ||| |  | | |||  |   |     | |        | |        |  |||     |  | | |    || |||| ||| ||||||||||| |  | ||||| |||||||| || || ||||||||| |||||||||| |||||||| || || || | ||| ||  | |||||
gtagaattgttggactgttctcagttactctctttatcaccctcttgccccccactgacatacgttgtactactatcttacagGTGAGCTGGCACATGCATTGAGGTTCTTAGCATCTGTTGTTTCTCAAAGCTTTTTAGCTTTTGGAGATATTCTAGAATTGCACAGAAAGTTTGTAGAACT

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|33796779|gb|CF324255.1|CF324255
EST:     GTTATATGCTTTGGAACACAAGGGGGACCGAGCTTTGACTTCAACTCAAG                         GAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCT
genomic: GTTATATGCTTTGGAACACAAGGGGGACCGAGCTTTGACTTCAACTCAAGgttgataaat ... cggattgcagGAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCT
EST: gi|8955961|gb|BE229765.1|BE229765
EST:     GTTATATGCTTTGGAACACAAGGGGGACCGAGCTTTGACTTCAACTCAAG                         GAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCT
genomic: GTTATATGCTTTGGAACACAAGGGGGACCGAGCTTTGACTTCAACTCAAGgttgataaat ... cggattgcagGAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCT
EST: gi|58679369|gb|CK068056.1|CK068056
EST:     GTTATATGCTTTGGAACACAAGGGGGACCGAGCTTTGACTTCAACTCAAG                         GAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCT
genomic: GTTATATGCTTTGGAACACAAGGGGGACCGAGCTTTGACTTCAACTCAAGgttgataaat ... cggattgcagGAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCT
EST: gi|58601488|gb|CK012016.1|CK012016
EST:     ACCGAGCTTTGACTTCAACTCAAG                         GAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCT
genomic: ACCGAGCTTTGACTTCAACTCAAGgttgataaat ... cggattgcagGAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgatattatttttgcatagaatttcccaacaagttctcaatttcggattgcagGAGAGTTGGCACATGCACTTCGATTCTTGGCATCTGTGGTGTCACAAAGCTTTATAGCTTTTGGTGATATTCTTGAGTTACATAAAAAATTCCTTGAACT
     tattatttttgcatag  TA-rich tract