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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgttccttatattttttaaccttttttatgccaagtgaatcatctttgctgtatgatcgtaaagctttgcttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAGAAAACACCAAAACCATCTGTCCTGGTTGTGTATTATGCCAAGTTGACTG

Basic information

species Oryza sativa
transcript LOC_Os01g03070.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03070.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G070487_T04 (Zea mays), 3'ss of exon 2
gtccgttccttatattttttaaccttttttatgccaagtgaatcatctttgctgtatgatcgtaaagctttgcttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAGAAAACACCAAAACCATCTGTCCTGGTTGTGTATTATGCCAAGTTGACTG
||  ||||| ||  ||   ||   |  |  ||   |||||   ||  ||   || ||        | | |  | |||||||||| |||||  | || |||||||| ||||||||  |||||||||||||||||||||  |||||||| ||| || |||| ||||||||||| ||| |||| |
gtttgttccataacttgcgtattttaatccatat-aagtg--ccacattccttgaattgctactgaacataccatcttgcagGAAGCCTTCCGATCCGTGGAAGATATCCATGGTCTGATGAGCATGGTGAAGAAAATGCCAAAACCTTCTATCTTGGTGGTGTATTATGCAAAGCTGACCG

upper sequence: LOC_Os01g03070.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G093050_T03 (Zea mays), 3'ss of exon 4
-----gtccgttccttatattttttaaccttttttatgccaagtgaatcatctttgctgtatgatcgtaaagctttgcttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAGAAAACACCAAAACCATCTGTCCTGGTTGTGTATTATGCCAAGTTGACTG
      ||| || ||||| | ||||||    || | | || | |  |  |    ||||  ||      ||   |       |||||||| |||||  | || |||||||| |||||||| ||||||| ||||||||||||||  |||||||||||| || |||| || |||||||| ||||||||||
gtttgttccattacttatgtattttaattaattctttaccca-tatacaaa---tgctacattccttgaattgtccctggattgcagGAAGCCTTCCGATCGGTGGAAGATATCCATGGTTTGATGACCATGGTGAAGAAAATGCCAAAACCATCTATCTTGGTGGTCTATTATGCAAAGTTGACTG

upper sequence: LOC_Os01g03070.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0060g01630.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gtccgttcct-tatattttttaacctttttta-tgccaagtgaatcatctttgctgtatgatcgtaaagct-ttgcttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAGAAAACACCAAAACCATCTGTCCTGGTTGTGTATTATGCCAAGTTGACTG
                 | || ||  | ||  |   ||  | | || || |  ||| |  || |||| |     |  ||  |     | |||  ||   ||||| || ||| | ||||| ||||| || ||||| |||||| ||||||| |||||||| || ||| ||||| |  |||| || |||||||||||||| || |
catagataaatgcacaaggccattgatgtaactgcatttgcatcttgtagtctcaaat--attatctgtttctcaccatttttttcttcttgtatcccacagGAAGCGTTTCGCTCTGTTGAAGATATTCATGGATTGATGTGCATGGTTAAGAAAACCCCCAAAGCATCTTTGATGGTCGTTTATTATGCCAAGTTAACAG

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|58655699|gb|CK044379.1|CK044379
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|33678088|gb|CF306327.1|CF306327
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTATCTGGCAG                         GAGGCCTTTAGGTCTGCGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|2427680|gb|C72143.1|C72143
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGNAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|58657791|gb|CK046471.1|CK046471
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|33677589|gb|CF305828.1|CF305828
EST:     GAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: GAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|33678827|gb|CF307066.1|CF307066
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|58661569|gb|CK050249.1|CK050249
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgccaagtgaatcatctttgctgtatgatcgtaaagctttgcttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAGAAAACACCAAAACCATCTGTCCTGGTTGTGTATTATGCCAAGTTGACTG
                                        ctttgcttctt  CT-rich tract