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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaccaaccgccctgctgttactactctctctctcctccagttttcctccattttcgccctaatctgacctgcatctgggcctcccgcatgtccagAGGAGCCGCTGCTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGCCGCCGGCGTGGATGATGCGGCAGGCCGGGCGGTACATGGCGGAGTACCA

Basic information

species Oryza sativa
transcript LOC_Os01g43390.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43390.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G377609_T03 (Zea mays), 3'ss of exon 1
gtaaaaccaaccgccctgctgttactactctctctctcctccagttttcctccattttcgccctaatctgacctgcatctgggcctcccgcatgtccagAGGAGCCGCTGCTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGCCGCCGGCGTGGATGATGCGGCAGGCCGGGCGGTACATGGCGGAGTACCA
                    || |   |     |  |||||    |  || ||||||   ||||||||||| || ||          |||| |||||||||||||||||||||||||| |||||| ||||||||||||| || || || || || |||||||||||||| ||||| |||||||||||||||||||||||
--------------------gtaaacccaactcccttcctct--ctccccaccatttcgcccctaatctgaactacac--------gccgcgtgtccagAGGAGCCGCTGCTGGTGCGCGCGGCGCGGGGCGAGGACGGCCTCCCACGCCCACCCGCGTGGATGATGCGACAGGCAGGGCGGTACATGGCGGAGTACCA

upper sequence: LOC_Os01g43390.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G024738_T03 (Zea mays), 3'ss of exon 1
gtaaaaccaaccgccctgctgttactactctctctctcctccagttttcctccattttcgccctaatctgacctgcatctgggcctcccgcatgtccagAGGAGCCGCTGCTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGCCGCCGGCGTGGATGATGCGGCAGGCCGGGCGGTACATGGCGGAGTACCA
                 |      | | || || ||   ||    |  || ||||||     ||||||||| || ||           ||| || ||||||||||||||||||||||| |||||| ||||||||||||| || || || ||||| |||||||||||||||||||| |||||||||||||||||||||||
-----------------gtaaacccaattccctttcctttc----tcaccaccatttcgcttctaatctgaactacac--------gacgcgtgcccagAGGAGCCGCTGCTGGTGCGCGCGGCGCGGGGCGAGGACGGCCTCCCACGCCCGCCCGCGTGGATGATGCGGCAGGCAGGGCGGTACATGGCGGAGTACCA
















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|117250413|gb|CT844019.1|CT844019
EST:     CAGCCGCCTTCCCGCCATCTCCGCGTCCCTCGCAACCGCCTCCTCCACTG                         AGGAGCCGCTGCTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGC
genomic: CAGCGGCCTTCCCGCCATCTCCGCGTCCCTCGCAACCGCCTCCTCCACTGgtaaaaccaa ... gcatgtccagAGGAGCCGCTGCTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGC
EST: gi|88387768|gb|CI587856.1|CI587856
EST:     CAGCGGCCTTCCCGCCATCTCCGTGTCCCTCGCAACCGCCTCCTCCATTG                         AGGAGCCGCTGTTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGA
genomic: CAGCGGCCTTCCCGCCATCTCCGCGTCCCTCGCAACCGCCTCCTCCACTGgtaaaaccaa ... gcatgtccagAGGAGCCGCTGCTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGC
EST: gi|88722641|gb|CI746151.1|CI746151
EST:     CAGCGGCCTTCCCGCCATCTCCGCGTCCCTCGCAACCGCCTCCTCCACTG                         AGGAGCCGCTGCTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGC
genomic: CAGCGGCCTTCCCGCCATCTCCGCGTCCCTCGCAACCGCCTCCTCCACTGgtaaaaccaa ... gcatgtccagAGGAGCCGCTGCTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGC
EST: gi|86595710|gb|CI288403.1|CI288403
EST:     CAGCGGCCTTCCCGCCATCTCCGCGTCCCTCGCAACCGCCTCCTCCACTG                         AGGAGCCGCTGCTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGC
genomic: CAGCGGCCTTCCCGCCATCTCCGCGTCCCTCGCAACCGCCTCCTCCACTGgtaaaaccaa ... gcatgtccagAGGAGCCGCTGCTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcctccattttcgccctaatctgacctgcatctgggcctcccgcatgtccagAGGAGCCGCTGCTGGTGCGGGCGGCGAGGGGCGAGGACGGGCTGCCGCGGCCGCCGGCGTGGATGATGCGGCAGGCCGGGCGGTACATGGCGGAGTACCA
                     atctgac  putative branch site (score: 3)
                                       cctcccgc  putative PPT
         atttt  TA-rich tract