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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgaccaacggttttgctgtgtctcgtacactctcgttctgttcctccatgagaaatgtggcgttctgctcacacgcgctttgctacgccttgtgctagTCTCGGCGCTCATCGCGTTCAAGCGCGCAATCATCGAGGACCCCCGGTCGGCGCTCGCGGACTGGAGCGATGCGGACGGGAACGCCTGCGACTGGCACGG

Basic information

species Oryza sativa
transcript LOC_Os04g58700.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58700.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G119759_T03 (Zea mays), 3'ss of exon 1
tgtgaccaacggttttgctgtg-tctcgta-cactctcgttctgttcctccatgagaaatgtggcgttctgctcacacgcgctttgctacgc---cttgtgctagTCTCGGCGCTCATCGCGTTCAAGCGCGCAATCATCGAGGACCCCCGGTCGGCGCTCGCGGACTGGAGCGATGCGGACGGGAACGCCTGCGACTGGCACGG
     | ||   |     | || |||||     |||  || ||||    | |  |       | | || | |||   |   |  ||   ||     |||||| ||| ||||||||||| || ||||||||||| |||||||||||||| |  || | |||| |||||||||  || |||||||| |||||||||||||||| |||
-----cgaattctccccgtctggtctcgcggtgctcatgtcctgtgaaacaagtaaccgccagcccttttcctctgtctaacactgacgcgtggatttgtgccagTGTCGGCGCTCATGGCATTCAAGCGCGCCATCATCGAGGACCCTCACTCCGTGCTCTCGGACTGGACTGACGCGGACGGCAACGCCTGCGACTGGCGCGG
















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|58676811|gb|CK065498.1|CK065498
EST:     GGTGGTGGTGGTGGTGTTGCAGTGCTCGGCGAATGCGTTGGGCAGTGACG                         TCTCGGCGCTCATCGCGTTCAAGCGCGCAATCATCGAGGACCCCCGGTCGG
genomic: GGTGGTGGTGGTGGTGTTGCAGTGCTCGGCGAATGCGTTGGGCAGTGACGgtgagtgttg ... cttgtgctagTCTCGGCGCTCATCGCGTTCAAGCGCGCAATCATCGAGGACCCCCGGTCGG
EST: gi|86884287|gb|CI311697.1|CI311697
EST:     GGTGGTGGTGGTGGTGTTGCAGTGCTCGGCGAATGCGTTGGGCAGTGACG                         TCTCGGCGCTCATCGCGTTCAAGCGCGCAATCATCGAGGACCCCCGGTCGG
genomic: GGTGGTGGTGGTGGTGTTGCAGTGCTCGGCGAATGCGTTGGGCAGTGACGgtgagtgttg ... cttgtgctagTCTCGGCGCTCATCGCGTTCAAGCGCGCAATCATCGAGGACCCCCGGTCGG
EST: gi|58664033|gb|CK052719.1|CK052719
EST:     GGTGGTGGTGGTGGTGTTGCAGTGCTCGGCGAATGCGTTGGGCAGTGACG                         TCTCGGCGCTCATCGCGTTCAAGCGCGCAATCATCGAGGACCCCCGGTCGG
genomic: GGTGGTGGTGGTGGTGTTGCAGTGCTCGGCGAATGCGTTGGGCAGTGACGgtgagtgttg ... cttgtgctagTCTCGGCGCTCATCGCGTTCAAGCGCGCAATCATCGAGGACCCCCGGTCGG
EST: gi|88579514|gb|CI688511.1|CI688511
EST:     GGTGGTGGTGGTGGTGTTGCAGTGCTCGGCGAATGCGTTGGGCAGTGACG                         TCTCGGCGCTCATCGCGTTCAAGCGCGCA
genomic: GGTGGTGGTGGTGGTGTTGCAGTGCTCGGCGAATGCGTTGGGCAGTGACGgtgagtgttg ... cttgtgctagTCTCGGCGCTCATCGCGTTCAAGCGCGCA
EST: gi|88328695|gb|CI678496.1|CI678496
EST:     GGTGGTGGTGGTGGTGTTGCAGTGCTCGGCGAATGCGTTGGGCAGTGACG                         TCTCGGCGCTCATCGCGTTCAAGCGCGCAATCATCGAGGACCCCCGGTCGG
genomic: GGTGGTGGTGGTGGTGTTGCAGTGCTCGGCGAATGCGTTGGGCAGTGACGgtgagtgttg ... cttgtgctagTCTCGGCGCTCATCGCGTTCAAGCGCGCAATCATCGAGGACCCCCGGTCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccatgagaaatgtggcgttctgctcacacgcgctttgctacgccttgtgctagTCTCGGCGCTCATCGCGTTCAAGCGCGCAATCATCGAGGACCCCCGGTCGGCGCTCGCGGACTGGAGCGATGCGGACGGGAACGCCTGCGACTGGCACGG
                      tgctcac  putative branch site (score: 2)