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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttagcgaatcttatcttacattcactgctgagactacaaaagttttaatacttagtagttactcaaatgtttctagttctctactcagattgcaatgcaggttatagttaacttccgtttcatggtcacaccagGATATTTCTCATCCTCCAGCTCATAAGCATGTCACACTTCATCTCGTGGTGCAATAAGCGTTGGATGCCAGATTCTCAATCAAATCAATG

Basic information

species Oryza sativa
transcript LOC_Os04g42720.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g42720.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G018756_T01 (Zea mays), 3'ss of exon 5
gtaattttagcgaatcttatcttacattcactgctgagactacaaaagttttaatacttagtagttactcaaatgtttctagttctctactcagattgcaat---gcaggttatagttaacttccgtttcatggtcacaccagGATATTTCTCATCCTCCAGCTCATAAGCATGTCACACTTCATCTCGTGGTGCAATAAGCGTTGGATGCCAGATTCTCAATCAAATCAATG
|||| || |  |||  |   ||||||||    ||| | | |    | |||| ||  | || |    |      |   | || || |  |    | |   | |     ||   | |  | ||||| |||||||  || | |||||||||||||| ||||||||||||||||||||   |||||||| || ||||||||||| || |||||||||||| ||  ||||||||||||
gtaagttaaatgaaagt--ccttacatt----gctcaaatttgggatgtttcaagccctaatgaacaacattttacgttta-ttttagatggtggtcttatttttatagtaaacatgttacttctgtttcattatccctccagGATATTTCTCCTCCTCCAGCTCATAAGCATGCTCCACTTCATATCATGGTGCAATAAACGATGGATGCCAGATCCTGGATCAAATCAATG

upper sequence: LOC_Os04g42720.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G018756_T02 (Zea mays), 3'ss of exon 5
gtaattttagcgaatcttatcttacattcactgctgagactacaaaagttttaatacttagtagttactcaaatgtttctagttctctactcagattgcaat---gcaggttatagttaacttccgtttcatggtcacaccagGATATTTCTCATCCTCCAGCTCATAAGCATGTCACACTTCATCTCGTGGTGCAATAAGCGTTGGATGCCAGATTCTCAATCAAATCAATG----------
|||| || |  |||  |   ||||||||    ||| | | |    | |||| ||  | || |    |      |   | || || |  |    | |   | |     ||   | |  | ||||| |||||||  || | |||||||||||||| ||||||||||||||||||||   |||||||| || ||||||||||| || |||||||||||| ||  ||||||||||||          
gtaagttaaatgaaagt--ccttacatt----gctcaaatttgggatgtttcaagccctaatgaacaacattttacgttta-ttttagatggtggtcttatttttatagtaaacatgttacttctgtttcattatccctccagGATATTTCTCCTCCTCCAGCTCATAAGCATGCTCCACTTCATATCATGGTGCAATAAACGATGGATGCCAGATCCTGGATCAAATCAATGGTAAGGATTG


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctactcagattgcaatgcaggttatagttaacttccgtttcatggtcacaccagGATATTTCTCATCCTCCAGCTCATAAGCATGTCACACTTCATCTCGTGGTGCAATAAGCGTTGGATGCCAGATTCTCAATCAAATCAATG
                          agttaac  putative branch site (score: 3)
                      ttatagttaa  TA-rich tract