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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttccttttctcgcacttcattttgttgtgtattcaatattcttcctactgttattctgtctccatactacatgtggtctgatgcacaatttttcttgcagTTCTTGGGTTACCCTACGACCACCCATTAGACATGTGGTCAGTTGGCTGCTGTCTATATGAACTTTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAA

Basic information

species Oryza sativa
transcript LOC_Os12g44330.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G151236_T03 (Zea mays), 3'ss of exon 8
--------------------------gtgagttccttttctcgcacttcattt---tgttgtgtattca-atattcttcctactgttattctgtctccatac-tacatgtggtctgatgcacaatttttcttgcagTTCTTGGGTTACCCTACGACCACCCATTAGACATGTGGTCAGTTGGCTGCTGTCTATATGAACTTTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAA
                           |   ||   |||||  |     | |    |||||| | |  | ||||   |     | |   | | | |  |||  || || ||     |   |||  |||||||||||||||||||||| |||| || || || ||||||||||||||||||||||||||||||||||| ||||| ||||| |||||| ||||||| |||||||||||
gtgagttctttcatcctgcaatgtttttagattttctttcttacttagtactcatatgttgtctgtatatatatatatatatatatatatatatatatatatatatatatgtgacaactaacatgttttcttgcagTTCTTGGGTTAGCCTATGATCATCCTTTAGACATGTGGTCAGTTGGCTGCTGTCTATATGAGCTTTATACCGGTAAAGTCTTATTTCCTGGTCCATCAAA

upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G147811_T01 (Zea mays), 3'ss of exon 9
gtgagttccttttctcgcacttcattttgttgtgtattcaatatt--cttcctactgttattctgtctccatactacatgtggtctgatgcacaat-----ttttcttgcagTTCTTGGGTTACCCTACGACCACCCATTAGACATGTGGTCAGTTGGCTGCTGTCTATATGAACTTTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAA
|||||||| ||       || |    |  || |  ||||  |     |||  | ||  |||  |||||  || |  | |     |  ||  |  |      |||||||||||||||||||||| |||| || ||||| |||||||||||||||||||| |||||||||||||| ||||| ||||| |||||| ||||||| |||||||||||
gtgagttctttcatctttacctgggatgtttttagattcctttcctactttatgctcatatgttgtctgtatgcatcttacctacctatatatgaaacatgttttcttgcagTTCTTGGGTTAGCCTATGATCACCCTTTAGACATGTGGTCAGTTGGTTGCTGTCTATATGAGCTTTATACCGGGAAAGTCTTATTTCCTGGTCCATCAAA

upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G13350.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagttccttttctcgcacttcattttgttgtgtattcaatattcttcctactgttattctgtctccatactacatgtggtctgatgcacaatttttcttgcagTTCTTGGGTTACCCTACGACCACCCATTAGACATGTGGTCAGTTGGCTGCTGTCTATATGAACTTTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAA
|| ||||||  |  | ||  ||   ||  |  | || |    ||  ||| |     |||  | | |    |||| |  ||  ||    | |  ||||  ||| |||||||||  | ||||||||||| || ||||| || ||||||||||| |||||||| ||||| ||||  | ||| ||| |  | || || ||  |  ||||
gtaagttccactgtt-gctgttgtcttaatcatctacttgg-atatttcatggctgtatgttctattataactaaagctgtact----ctcttttttcattgtagTTCTTGGACTTCCCTACGACCATCCGTTAGATATATGGTCAGTTGGTTGCTGTCTGTATGAGCTTTTTAGCGGGAAAATTATGTTCCCTGGCTCCACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgttattctgtctccatactacatgtggtctgatgcacaatttttcttgcagTTCTTGGGTTACCCTACGACCACCCATTAGACATGTGGTCAGTTGGCTGCTGTCTATATGAACTTTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAA
                              gtctgat  putative branch site (score: 4)
                                           tttttcttgc  putative PPT
                                         aatttttctt  TA-rich tract