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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagcagagcagagctgtccggtggcagcctgtccgtccctttcgagacagcctcgcgcttctcttccgctgcgagtgaactggaccgaatggggcagactggttccttaactgaaatagactaactcgatcagtcgtcccagaatctaacctcgttcgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG

Basic information

species Oryza sativa
transcript LOC_Os02g47470.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G126505_T02 (Zea mays), 3'ss of exon 3
--------gtgagcagcagagcagagctgtccggtggcagcct-gtccgtccctttcgagacagcctcgcgcttct--cttccgctgcga--gtgaactg-gaccgaatggggcagactggttccttaactgaaatagactaactcgatcagtcgtcccagaatctaacctcgttcgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG
          | |   | |  |   ||||||||   ||  ||  |  |  || ||||  |   |  | | ||| |   |  | |   |    |||  ||| |   |||  || | |   |    |||        ||  | || |  ||       | ||        ||| |   |   |   |||   |||||||||||||||||||||||||||||| ||| | || |||||||| ||||||||||||| |||||||||||||||||||||||| ||||||||||| |||||
gtgagacgtcgcgtcacggcccctcgctgtccgcccgcgcccccgcgccaccgtttcacgttggattggagctccctgcccctgtccctgtcgtgcgctgcggatgaactggacggggggacggcttcctaatcctaaccgaaatgaatagactaactcatcgctgtgccttgcctg--tgctggctggctgcagGGTACCTGATCCCCAAGGGCTGGAAGGTGTTGCCCCTGTTCCGGAACATCCACCACAGCCCCGACCACTTCCCCTGCCCGGACAAGTTCGACCCCTCCCG

upper sequence: LOC_Os02g47470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G179147_T02 (Zea mays), 3'ss of exon 3
gtgagcagcagagcagagctgtccggtggcagcctgtccgtccctttcgagacagcctcgcgcttctcttccgctgcgagtgaactggaccgaatggggcagactggttccttaactgaaatagactaactcgatcagtcgtcccagaatctaacctcgttcgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG
                                                         || |  |  |   | ||||||  ||||||||||      || | |   |  | | |||| |||||  |   ||                 |  || || || | ||   || ||||   |||||||||||||||||||||||||||||| ||| | || |||||||| ||||||||||||| |||||||||||||||||||||||| ||||||||||| |||||
--------------------------------------------------------gtccctgtcgtgcgctgctgcggatgaactggac------ggacgggacgcgttcctaaccgaaatgaatagac-----------------agactgac-tcatccg-ctgtgtgctggctgcagGGTACCTGATCCCCAAGGGCTGGAAGGTGATGCCCCTGTTCCGGAACATCCACCACAGCCCCGACCACTTCCCCTGCCCGGAGAAGTTCGACCCCTCCCG

upper sequence: LOC_Os02g47470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ30794 (Selaginella moellendorffii), 3'ss of exon 6
gtgagcagcagagcagagctgtccggtggcagcctgtccgtccctttcgagacagcctcgcgcttctcttccgctgcgagtgaactggaccgaatggggcagactggttccttaa-ctgaaatagactaactcgatcagtcgtcccagaatctaacctcgtt--cgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG
                                                                                             | |  | || |  |  |||    ||| || |       | |  ||   |     ||| ||||||   ||  |       |||| || ||||| ||| |||| |||||||||||||||||| | ||||||||| | |||||||| |||| ||||||    ||||     ||| | |||||| |||| ||| |
----------------------------------------------------------------------------------------gtaagaagttgtagcccagcccctccctctgtaacatcacggttgg--caaaagaaaaggaagctaaccgttttacccggaacttgctttg-gcagGATACGTGATTCCCAAGGGCTGGAAAGTGATGCCTCTGTTCAGAAACATCCATCACAGCCCCGAGTTTTTCCTGGAGCCGCAGAAGTTCAACCCCTCCAG

upper sequence: LOC_Os02g47470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ22851 (Selaginella moellendorffii), 3'ss of exon 6
gtgagcagcagagcagagctgtccggtggcagcctgtccgtccctttcgagacagcctcgcgcttctcttccgctgcgagtgaactggaccgaatggggcagactggttccttaa-ctgaaatagactaactcgatcagtcgtcccagaatctaacctcgtt--cgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG
                                                                                             | |  | || |  |  |||    ||| || |       | |  ||   |     ||| ||||||   ||  |       |||| || ||||| ||| |||| |||||||||||||||||| | ||||||||| | |||||||| |||| ||||||    ||||     ||| | ||||||||||| ||| |
----------------------------------------------------------------------------------------gtaagaagttgtagcccagcccctccctctgtaacatcacggttgg--caaaagaaaaggaagctaaccgttttacccggaacttgctttg-gcagGATACGTGATTCCCAAGGGCTGGAAAGTGATGCCTCTGTTCAGAAACATCCATCACAGCCCCGAGTTTTTCCTGGAGCCGCAGAAGTTCGACCCCTCCAG

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|66914874|gb|CX101722.1|CX101722
EST:     CATCCTCTCCTTCACCTTCAGGGAGGCCGTGGAGGACGTGGAATACCAAG                         GGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCC
genomic: CATCCTCTCCTTCACCTTCAGGGAGGCCGTGGAGGACGTGGAATACCAAGgtgagcagca ... ctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCC
EST: gi|58599154|gb|CK009682.1|CK009682
EST:     CATCCTCTCCTTCACCTTCAGGGAGGCCGTGGAGGACGTGGAATACCAAG                         GGTACCTGATCCCCAAGGGCTGGAAAGTGCTACC
genomic: CATCCTCTCCTTCACCTTCAGGGAGGCCGTGGAGGACGTGGAATACCAAGgtgagcagca ... ctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactcgatcagtcgtcccagaatctaacctcgttcgatcgtctgctctgtgcagGGTACCTGATCCCCAAGGGCTGGAAAGTGCTACCTCTGTTCCGCAACATCCACCACAACCCCGACCACTTCCCCTGCCCGGAAAAGTTCGACCCGTCCCG
                                         tctgctct  CT-rich tract
                     aatctaa  TA-rich tract