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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaagtgttgactacgctttgctttacttccagcactgttagacgctttgttcatcccaatgtttgttttacacctgtctgtccatttgttgttctctagTTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTGCTAGCACCAAAGTTTATGAGTACATACTTTTCCGGGGAAGTGATATCAA

Basic information

species Oryza sativa
transcript LOC_Os01g02090.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02090.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AC190588.3_FGT003 (Zea mays), 3'ss of exon 1
-tcaagtgttgactacgctttgctttacttccagcactgttagacgctttgttcatcccaatgtttgttttacacctgtctgtccatttgttgttctctagTTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTGCTAGCACCAAAGTTTATGAGTACATACTTTTCCGGGGAAGTGATATCAA
 | | || |  |   |        |  | |   |||||||     |||| | |        || |  | | |       ||||| |||  ||||| | |||| || || ||||||||| ||||| | |||||||| |||||||| ||||||||||||  ||||||||| ||||| || || |||||||||| |||||||||
gtgaggtctccaacccatccccactctccttaggcactgtctattgcttcgcttcagatgctgctgttgtgatctacacctgtcaattccttgttttgtagTGCGGTCCTTTGGAACCCAAGGGTGGAAGAAAGACGGAGTGCAGATTCCTGCTAGCGACAAAGTTTACGAGTATATCCTCTTCCGGGGAACTGATATCAA

upper sequence: LOC_Os01g02090.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G051622_T02 (Zea mays), 3'ss of exon 1
tcaagtgttga-ctacgctttgctttacttccagcactgttagacgctttgttcatcccaatgtttgttttacacctgtctgtccatttgttgttctctagTTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTGCTAGCACCAAAGTTTATGAGTACATACTTTTCCGGGGAAGTGATATCAA
|||  | |  | ||  |   |||    | |   |   |       |||||  |           |  | | |        |||| |||  ||||| | |||| || || ||||| |||||||| || |||||||||||| |||| ||||||||||||  |||||| || ||||| || || || ||||||| |||||||||
tcagttttcaaactgagacgtgcac-gccttaggtcttagctattgctttacttcagatgccactgttatgatgtacacttgtcaattcattgttttgtagTGCGGTCCTTTGGGACCGAAGGTCGGAAGAAAGATGGAATGCAGATTCCTGCTAGCGACAAAGTATACGAGTATATCCTCTTTCGGGGAACTGATATCAA

upper sequence: LOC_Os01g02090.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G132796_T01 (Zea mays), 3'ss of exon 1
-tcaagtgttgactacgctttgctttacttccagcactgttagacgctttgttcatcccaatgtttgttttacacctgtctgtccatttgttgttctctagTTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTGCTAGCACCAAAGTTTATGAGTACATACTTTTCCGGGGAAGTGATATCAA
 ||   |    |||  |   || |   | |   |||||||     |||| | |        || |  | | |       ||||| |||  ||||| | |||| || || |||||||||||||| || |||||||| |||||||| ||||||||||||  ||||||||| ||||| || || |||||||||| |||||||||
ttctgtttcgaactgagacgtg-tgcgccttaggcactgtctattgcttcgcttcagatgctgctgttgtgatctacacctgtcaattccttgttttgtagTGCGGTCCTTTGGAACCGAAGGTCGGAAGAAAGACGGAGTGCAGATTCCTGCTAGCGACAAAGTTTACGAGTATATCCTCTTCCGGGGAACTGATATCAA

upper sequence: LOC_Os01g02090.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G120584_T01 (Zea mays), 3'ss of exon 1
-tcaagtgttgactacgctttgctttacttccagcactgttagacgctttgttcatcccaatgtttgttttacacctgtctgtccatttgttgttctctagTTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTGCTAGCACCAAAGTTTATGAGTACATACTTTTCCGGGGAAGTGATATCAA
 | | || |  |   |        |  | |   ||||| |     |||| | |        || |  | | |       ||||| |||  ||||| | |||| || || ||||||||||||||||| |||||||| |||||||| ||||||||||||  ||||||||| ||||| || || ||| |||||| |||||||||
gtgaggtctccagcccatccccactctccttaggcactatctattgcttcgcttcagatgctgctgttgtgatctacacctgtcaattccttgttttgtagTGCGGTCCTTTGGAACCGAAGGGCGGAAGAAAGACGGAGTGCAGATTCCTGCTAGCGACAAAGTTTACGAGTATATCCTCTTCTGGGGAACTGATATCAA

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|29638811|gb|CB643820.1|CB643820
EST:     GGCTTGCGCAATG                         TTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTG
genomic: GGCTTGCGCAATGgtattaattc ... tgttctctagTTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTG
EST: gi|29638770|gb|CB643779.1|CB643779
EST:     GGCTTGCGCAATG                         C
genomic: GGCTTGCGCAATGgtattaattc ... tgttctctag-
EST: gi|29638770|gb|CB643779.1|CB643779
EST:     GGCTTGCGCAATG                         C
genomic: GGCTTGCGCAATGgtattaattc ... tgttctctag-
EST: gi|29636683|gb|CB641692.1|CB641692
EST:     GGCTTGCGCAATG                         TTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTG
genomic: GGCTTGCGCAATGgtattaattc ... tgttctctagTTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTG
EST: gi|58671766|gb|CK060452.1|CK060452
EST:     CATCCTCTACAACATCAACACCGAGGAGTCCAGCATCGGCTTGCGCAATG                         TTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTG
genomic: CATCCTCTACAACATCAACACCGAGGAGTCCAGCATCGGCTTGCGCAATGgtattaattc ... tgttctctagTTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgttcatcccaatgtttgttttacacctgtctgtccatttgttgttctctagTTCGATCATTTGGAACCGAAGGGCGCAAGAAAGATGGAGTGCAAATTCCTGCTAGCACCAAAGTTTATGAGTACATACTTTTCCGGGGAAGTGATATCAA
                                            ttgttctct  CT-rich tract
                 tttgtttta  TA-rich tract