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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtggatctcccatttccccccctctccccgcgagctcgccccgggcgggggatcctagtcttgacccgtgtgcgtgtgtgattcattccgccgcagGAAGAGCGTGCTTGGATCGCGCGGGGGAGGCAACGCTGGCGGCGCGCAGGTGATGGCGGATCCGCCTGGCGGTGGGGGATCTAGCGCTTGCGTCTGTGAG

Basic information

species Oryza sativa
transcript LOC_Os10g27230.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g27230.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G043509_T02 (Zea mays), 3'ss of exon 1
gtgagtggatctcccatttccccccctctccccgcgagctcgccccgggcgg-gggatcctagtcttgacccgtgtgcgtgtgtgattcattccgccgcagGAA-GAGCGTGCTTGGATCGCGCGGGGGAGGCAACGCTGGCGGCGCGCAG---------GTGATGGCGGATCCGCCTGGCGGTGGGGGATCTAGCGCTTGCGTCTGTGAG
| |||      | ||    ||    ||| ||       | || || | |||| ||||||||     || | | |||  |   | | ||| |   |  |||||   ||||| |  ||  | |  || ||||||||||||||||||| |||||         |||||||||||| ||||| ||||||| |||||||| |||||          
gcgaggcctcgttccccgcccgtatctccccatttccacccggccggcgcggcgggatcctgactctggcgc-tgtctgctggggtttcgtgtaggagcagGCGCGAGCGCGGGTGTTTGGATCGTGGGAGGCAACGCTGGCGGCTCGCAGCGGCAGCAGGTGATGGCGGATTCGCCTAGCGGTGGAGGATCTAGGGCTTG----------

upper sequence: LOC_Os10g27230.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G043509_T03 (Zea mays), 3'ss of exon 1
gtgagtggatctcccatttccccccctctccccgcgagctcgccccgggcgg-gggatcctagtcttgacccgtgtgcgtgtgtgattcattccgccgcagGAA-GAGCGTGCTTGGATCGCGCGGGGGAGGCAACGCTGGCGGCGCGCAG---------GTGATGGCGGATCCGCCTGGCGGTGGGGGATCTAGCGCTTGCGTCTGTGAG
| |||      | ||    ||    ||| ||       | || || | |||| ||||||||     || | | |||  |   | | ||| |   |  |||||   ||||| |  ||  | |  || ||||||||||||||||||| |||||         |||||||||||| ||||| ||||||| ||||||||                
gcgaggcctcgttccccgcccgtatctccccatttccacccggccggcgcggcgggatcctgactctggcgc-tgtctgctggggtttcgtgtagGAGCAGGCGCGAGCGCGGGTGTTTGGATCGTGGGAGGCAACGCTGGCGGCTCGCAGCGGCAGCAGGTGATGGCGGATTCGCCTAGCGGTGGAGGATCTAG----------------

upper sequence: LOC_Os10g27230.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G118467_T03 (Zea mays), 3'ss of exon 1
gtgagtggatctcccatttccccccctctccccgcgagctcgccccgggcgg-gggatcctagtcttgacccgtgtgcgtgtgtgattcattccgccgcagGAA-GAGCGTGCTTGGATCGCGCGGGGGAGGCAACGCTGGCGGCGCGC---------AGGTGATGGCGGATCCGCCTGGCGGTGGGGGATCTAGCGCTTGCGTCTGTGAG
| ||| |  || | |  | |||       ||      || || || | |||| ||||||||  |  ||   | |||  |   | | ||| |   |  | |||   ||||| |  ||  | |  |||||||||||||||||||||| |||         |||||||||||||||||||| ||||||||||||||||                
gcgag-gcctcgctccgtgcccggatctcccatttccgcccggccggcgcggcgggatcctgatactggtgc-tgtctgctggggtttcgtgtagGAGAAGGCGCGAGCGCGGGTGTTTGGATCGGGGGAGGCAACGCTGGCGGCTCGCGGCGGCAGCAGGTGATGGCGGATCCGCCTAGCGGTGGGGGATCTAG----------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgggcgggggatcctagtcttgacccgtgtgcgtgtgtgattcattccgccgcagGAAGAGCGTGCTTGGATCGCGCGGGGGAGGCAACGCTGGCGGCGCGCAGGTGATGGCGGATCCGCCTGGCGGTGGGGGATCTAGCGCTTGCGTCTGTGAG
                 tcttgac  putative branch site (score: 3)
                                        ttcattcc  putative PPT
                                       attcatt  TA-rich tract