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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttttctttattttttttttgtgcgaggaaccttttagtttagttgctgaagggaatattgtgtgaacaaataacattagaggtaaaaatgcttgcagGTGATGGTGATCGAAACATGATTCTTGGAAGAAGGTTCTTTGTTACACCATCAGACTCTGTTGCAATAATTGCAGCGAATGCACAGGCAGCAATTCCTTA

Basic information

species Oryza sativa
transcript LOC_Os10g11140.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 13
tctttttctttattttttttttgtgcgaggaaccttttagtttagttgctgaagggaatatt--gtgtgaacaaataaca--ttagaggtaaaaatgcttgcagGTGATGGTGATCGAAACATGATTCTTGGAAGAAGGTTCTTTGTTACACCATCAGACTCTGTTGCAATAATTGCAGCGAATGCACAGGCAGCAATTCCTTA
   | |  ||  ||| ||   | |   ||  |  |||   |||| |   | |||  |||  |  || | |   |||||||  | | | | |  |||  || |||||||||||||||| |||||||||||||| | |||||||||| |||| ||||||||||||||||||||||||||||| ||||||||| |||||||||||||
--ctatatttggtttgttgcattttatagtgatattt--atttattgtttcaagcaaatgcttggtctaactgaataacaactgataagcatgaattgtttcagGTGATGGTGATCGGAACATGATTCTTGGGAAAAGGTTCTTTATTACCCCATCAGACTCTGTTGCAATAATTGCAGCCAATGCACAGACAGCAATTCCTTA

upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 13
tctttttctttattttttttttgtgcgaggaaccttttagtttagttgctgaagggaatattgtgtgaacaaataacattagaggtaaaaatgcttg--cagGTGATGGTGATCGAAACATGATTCTTGGAAGAAGGTTCTTTGTTACACCATCAGACTCTGTTGCAATAATTGCAGCGAATGCACAGGCAGCAATTCCTTA
  | || |   |  | |  ||  ||   |  |   |     |   ||| |     |  | |||| |     |  |   | |    |   |||  |||  |||| ||||||||| |||| |||||| | |||||||| |||||||| || || ||||||||||| ||| | |||||||| ||||||   | ||| ||||| ||
-ttattgcagaagatgtggttgatgtatgccagtgtaacaatgttttgttagtctgtgt-ttgtttatttgatgatgttcatgtatttcaatctttgttcagGGGATGGTGATAGAAATATGATTTTAGGAAGAAGTTTCTTTGTAACTCCTTCAGACTCTGTAGCAGTTATTGCAGCCAATGCAAGAGAAGCGATTCCATA
















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|58691145|gb|CK079832.1|CK079832
EST:     GTTTACCATGTTTGGAAGCGGAGCACCTGACTTTGGTGCAGCAAGTGATG                         GTGATGGTGATCGAAACATGATTCTTGGAAGAAGGTTCTTTGTTACACCAT
genomic: GTTTACCATGTTTGGAAGCGGAGCACCTGACTTTGGTGCAGCAAGTGATGgtatgcctat ... atgcttgcagGTGATGGTGATCGAAACATGATTCTTGGAAGAAGGTTCTTTGTTACACCAT
EST: gi|58676489|gb|CK065176.1|CK065176
EST:     GTTTACCATGTTTGGAAGCGGAGCACCTGACTTTGGTGCAGCAAGTGATG                         GTGATGGTGATCGAAACATGATTCTTGGAAGAAGGTTCTTTGTTACACCAT
genomic: GTTTACCATGTTTGGAAGCGGAGCACCTGACTTTGGTGCAGCAAGTGATGgtatgcctat ... atgcttgcagGTGATGGTGATCGAAACATGATTCTTGGAAGAAGGTTCTTTGTTACACCAT
EST: gi|33796171|gb|CF323951.1|CF323951
EST:     GTTTACCATGTTTGGAAGCGGAGCACCTGACTTTGGTGCAGCAAGTGATG                         GTGATGGTGATCGAAACATGATTCTTGGAAGAAGGTTCTTTGTTACACCAT
genomic: GTTTACCATGTTTGGAAGCGGAGCACCTGACTTTGGTGCAGCAAGTGATGgtatgcctat ... atgcttgcagGTGATGGTGATCGAAACATGATTCTTGGAAGAAGGTTCTTTGTTACACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgaagggaatattgtgtgaacaaataacattagaggtaaaaatgcttgcagGTGATGGTGATCGAAACATGATTCTTGGAAGAAGGTTCTTTGTTACACCATCAGACTCTGTTGCAATAATTGCAGCGAATGCACAGGCAGCAATTCCTTA
                         aaataac  putative branch site (score: 2)
                      aacaaataacatta  TA-rich tract