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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagctttatttttggaaaaaaaataactgtgccatgtattttggattaatctggatgttttgactgacagCACAGAAGCTCTTGAGTTTGGTCAGAAAAAGTTGACGCCATTTGGGAAAGTGCCCAAGTACGTTGAGAAACTAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g56820.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G085602_T03 (Zea mays), 3'ss of exon 3
gtaagtagctttatttttggaaaaaaaat---aactgtgccatgtattttggattaatctggatgttttgactgacagCACAGAAGCTCTTGAGTTTGGTCAGAAAAAGTTGACGCCATTTGGGAAAGTGCCCAAGTACGTTGAGAAACTAGAG
|| |||   |  ||||||  |  |  | |   |||| |          ||  ||||| |||| | |||||| ||||||||||||||||||||| ||||| |||||||| |||||  |||||  ||| ||  |||||||  ||||||||||||||
gtgagtttgtgaattttttaactaggattgaaaactatttttacatccttttattaacctggctattttgattgacagCACAGAAGCTCTTGACTTTGGCCAGAAAAAATTGACATCATTTCAGAAGGTTACCAAGTATATTGAGAAACTAGAG

upper sequence: LOC_Os01g56820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g13280.t01 (Vitis vinifera), 3'ss of exon 3
----gtaag-tagctttatttttggaaaaaaaataactgtgccatgtattttggattaatctggatgttttgactgacagCACAGAAGCTCTTGAGTTTGGTCAGAAAAAGTTGACGCCATTTGGGAAAGTGCCCAAGTACGTTGAGAAACTAGAG
    ||||  || |  |  |||    |||   |||| |    ||   ||  |   ||| | |  |  |||||  |||||||||||||||||| || |||| ||||| ||||||||| || ||||| |||||||  || || |||||||| || || 
gtgtgtaaaataacaattctttctccaaattcataagttccacaaccatggtatcttagtttt-acattttgg-tgacagCACAGAAGCTCTGGAATTTGCTCAGACAAAGTTGACCCCTTTTGGAAAAGTGCAAAATTATGTTGAGAAGCTTGAA
















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|40486859|gb|BX898175.1|BX898175
EST:     TTTGATCTTTTAAGTCTTCACTTCATTGAGTTAGTTCGTTCTAGAAAATG                         CACAGAAGCTCTTGAGTTTGGTCAGAAAAAGTTGACGCCATTTGGGAAAGT
genomic: TTTGATCTTTTAAGTCTTCACTTCATTGAGTTAGTTCGTTCTAGAAAATGgtaagtagct ... tgactgacagCACAGAAGCTCTTGAGTTTGGTCAGAAAAAGTTGACGCCATTTGGGAAAGT
EST: gi|117234957|gb|CT847981.1|CT847981
EST:     TTTGATCTTTTAAGTCTTCACTTCATTGAGTTAGTTCGTTCTAGAAAATG                         CACAGAAGCTCTTGAGTTTGGTCAGAAAAAGTTGACGCCATTTGGGAAAGT
genomic: TTTGATCTTTTAAGTCTTCACTTCATTGAGTTAGTTCGTTCTAGAAAATGgtaagtagct ... tgactgacagCACAGAAGCTCTTGAGTTTGGTCAGAAAAAGTTGACGCCATTTGGGAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaataactgtgccatgtattttggattaatctggatgttttgactgacagCACAGAAGCTCTTGAGTTTGGTCAGAAAAAGTTGACGCCATTTGGGAAAGTGCCCAAGTACGTTGAGAAACTAGAG
                     tattttggattaat  TA-rich tract