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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaattcaatctctatatatatatatctacaatattaaaggatagtacatattgttgttgttcatattttgtcagcaaaagttgaaatggtttgatcgttcatattctgttggcaaagttaatttgaaatgtattgggttgttgtgtgtagGTGACATGGGTGGAGCATGTGGAGGTGGACGACAGCTCGGTGCACAACATCTACAAGCCATTGGTGAACTCCGGCCTCGCATTCGGCGCGAAACGGTGGG

Basic information

species Oryza sativa
transcript LOC_Os08g08820.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G118063_T02 (Zea mays), 3'ss of exon 7
gtaattaattcaatctctatatatatatatctacaatattaaaggatagtacatattgttgttgttcatattttgtcagcaaaagttgaaatggtttgatcgttc--atattctgt--tggcaaagttaatttgaaatgtattgggttgttgtgt-gtagGTGACATGGGTGGAGCATGTGGAGGTGGACGACAGCTCGGTGCACAACATCTACAAGCCATTGGTGAACTCCGGCCTCGCATTCGGCGCGAAACGGTGGG
                                            | ||||  |  |        | ||| | |    ||||||| || |  |     |   ||    | |||  ||  || |||  |  || | | ||      |  |||||  | | ||||||| ||||| |||||||| |||||||||||||| || ||||||||  |||||| ||| |||||||| || ||||| | ||| || |||| | ||||||
--------------------------------------------gctagt-taactcaacaacatgcatgtctc-caagcaaaactttatgtttccggcatgtcaggaaattaagtcatgtcaatatatatataacatcaggctgtgtgttgcattgcagGTGACCTGGGTTGAGCATGTTGAGGTGGACGACAGATCAGTGCACAATCTCTACAGGCCTTTGGTGAATTCAGGCCTGGGATTTGGTGCGACAAGGTGGG

upper sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G130442_T02 (Zea mays), 3'ss of exon 6
gtaattaattcaatctctatatatatatatctacaatattaaaggatagtacatattgttgttgttcatattttgtcagcaaaagttgaaatggtttgatcgttcatattctgttggcaaagttaat---ttgaaatgtattgggttgttgtgtgtagGTGACATGGGTGGAGCATGTGGAGGTGGACGACAGCTCGGTGCACAACATCTACAAGCCATTGGTGAACTCCGGCCTCGCATTCGGCGCGAAACGGTGGG
                                                                              | || |  ||||    |||  |  ||  |   | |   |   | |   |   | ||||   ||     | |   ||| ||||||| |||||||||||||| ||||| |||||||| || ||||||||| |||||| ||| ||||| || || |||||||| || ||||||||  ||||||
------------------------------------------------------------------------------gtaataagtgaa-cattttccttcttgttggccggccagtttactgcgtgcatggaaactcatgttcatatctcgtgcagGTGACCTGGGTGGAGCATGTTGAGGTCGACGACAGATCAGTGCACAACCTCTACAGGCCTTTGGTCAATTCAGGCCTCGCGTTTGGCGCGAAGAGGTGGG
















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|58601718|gb|CK012246.1|CK012246
EST:     GCAGGCCGTCTGGCTGCCTCATCCAAGAAATGCCCAATGGCTACTCCAAG                         GTGACATGGGTGGAGCATGTGGAGGTGGACGACAGCTCGGTGCACAACATC
genomic: GCAGGCCGTCTGGCTGCCTCATCCAAGAAATGCCCAATGGCTACTCCAAGgtaattaatt ... ttgtgtgtagGTGACATGGGTGGAGCATGTGGAGGTGGACGACAGCTCGGTGCACAACATC
EST: gi|87006799|gb|CI285833.1|CI285833
EST:     GCAGGCCGTCTGGCTGCCTCATCCAAGAAATGCCCAATGGCTACTCCAAG                         GTGACATGGGTGGAGCATGTGGAGGTGGACGACAGCTCGGTGCACAACATC
genomic: GCAGGCCGTCTGGCTGCCTCATCCAAGAAATGCCCAATGGCTACTCCAAGgtaattaatt ... ttgtgtgtagGTGACATGGGTGGAGCATGTGGAGGTGGACGACAGCTCGGTGCACAACATC
EST: gi|58662401|gb|CK051081.1|CK051081
EST:     GCAGGCCGTCTGGCTGCCTCATCCAAGAAATGCCCAATGGCTACTCCAAG                         GTGACATGGGTGGAGCATGTGGAGGTGGACGACAGCTCGGTGCACAACATC
genomic: GCAGGCCGTCTGGCTGCCTCATCCAAGAAATGCCCAATGGCTACTCCAAGgtaattaatt ... ttgtgtgtagGTGACATGGGTGGAGCATGTGGAGGTGGACGACAGCTCGGTGCACAACATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttcatattctgttggcaaagttaatttgaaatgtattgggttgttgtgtgtagGTGACATGGGTGGAGCATGTGGAGGTGGACGACAGCTCGGTGCACAACATCTACAAGCCATTGGTGAACTCCGGCCTCGCATTCGGCGCGAAACGGTGGG
                    agttaat  putative branch site (score: 4)
                  aaagttaatttgaaat  TA-rich tract