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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaatacatgactaattcctgtgtacattgtttttcttcacagttctctctaaccagaccattcaacttacatttcttgttcaagcgtcaactcgatcactactctaaccttgtcccatactgttgtctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACAGTATCTTGAGGCATACCCTGCACACCAACTCGGGCTTAGCATATTCGCA

Basic information

species Oryza sativa
transcript LOC_Os01g56580.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 16
gtacgaatacatgactaattcctgtgtacattgtttttcttcacagttctctctaaccagaccattcaacttacatttcttgttcaagcgtcaactcga-tcactactctaaccttgtccca-tactgttgtctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACAGTATCTTGAGGCATACCC---TGCACACCAACTCGGGCTTAGCATATTCGCA
                                                           || |||  |  ||  ||  ||||  |  |||     || | ||||   | |||| | | |  | || | | |   ||||| ||||||||||||||||||| |||||||||||||| |||||||||||||||||||| || |||||| | | |   ||||  || | | |||   ||||| |||   
-------------------------------------------------------gtatgatcatata-tttgtatc-cttgacc--gcgctgtttcaaatcacccatttaacgtcgacaaaataatctggatcttttgcagGAGAAATGGGCCAAGAACCTTTACATTGCTTCAATATGCTATGGCCGGACAGTGTCATGAGGCTTGCTCGGCTGCATCCCTAGTTGGGAAGAGCATGTTC---

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 16
gtacgaatacatgactaattcctgtgtacattgtttttcttcacagttctc-tctaaccagaccattcaacttacatttcttgttcaagcgtcaactcgatcactactctaaccttgtcccatactgttgtctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACAGTATCTTGAGGCATACCCTGCACACCAACTCGGGCTTAGCATATTCGCA
                                          | | | ||  | |  |       | | |||  |  ||  || ||      ||      || || |       ||     || || |  |   |||| |||| ||||||||||||||||| |||||||| || ||||| ||||| || || || |  |      |    || |||    ||    | |   | ||     
------------------------------------aaaaataaaatcctgatttttctgaggtgtgctact-gctgttgatgctct----ccagagttttccctccctaggtattaatatattctttgatgcctttgcagGAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACTGTTTGCTAGCTTCTGTAGTGAACATTTGCTGTATCATGAAAAATGAAGC

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 16
gtacgaatacatgactaattcctgtgtacattgtttttcttcacagttctctctaaccagaccattcaacttacatttcttgttcaagcgtcaactcgatcactactctaaccttgtcccatactgttgtctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACAGTATCTTGA-GGCATACCCTGCACACCAACTCGGGCTTAGCATATTCGCA
                              |  | ||     |||  |    |      |     | ||  ||||    | |        || | | | ||  |   || || | | ||   | |    |  | ||  ||||||||||||| || ||||| |||||||| || ||||||||||| |||||||| |  ||| |  | |    | | ||    ||   | |  |  | || | 
---------------------------gtgtgttcttaggaaacaaatgaagcatgttggctacatgaaactacaaaattcggattcttctccatttgttctatgtactgacttggacctgcatt----ttctatttcagGAGAAATGGGCGAAAAATCTGTACATTGCATCAATATGCTATGGTCGGACAGTTTGCTGATGAAACATGGAGTATACTGTTTCAA-CCTCTCTCACTCTCT

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|29676349|gb|CB672624.1|CB672624
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|218502457|gb|FG966789.1|FG966789
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|88691408|gb|CI733486.1|CI733486
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|88228655|gb|CI228135.1|CI228135
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|218479830|gb|FG949479.1|FG949479
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|66925445|gb|CX112293.1|CX112293
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|86477548|gb|CI120181.1|CI120181
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|29676347|gb|CB672622.1|CB672622
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|87022158|gb|CI259230.1|CI259230
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|86415053|gb|CI069456.1|CI069456
EST:     CAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTTCATTGCTTCGATATGCTATGGCCGGACA
genomic: CAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|29685518|gb|CB681793.1|CB681793
EST:     CTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: CTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|32948151|gb|BP184723.1|BP184723
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|29623308|gb|CB628319.1|CB628319
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|4714663|gb|AU055780.1|AU055780
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGAC
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAA-Ggtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGAC
EST: gi|163918227|gb|EG714811.1|EG714811
EST:     CTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTGGATATGCTATGGCCGGACA
genomic: CTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|88691475|gb|CI733553.1|CI733553
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|87022798|gb|CI269734.1|CI269734
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|29629025|gb|CB634036.1|CB634036
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|88691488|gb|CI733566.1|CI733566
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|58678949|gb|CK067636.1|CK067636
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcgtcaactcgatcactactctaaccttgtcccatactgttgtctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACAGTATCTTGAGGCATACCCTGCACACCAACTCGGGCTTAGCATATTCGCA
                    ctctaac  putative branch site (score: 2)
                                         ttgtcttttt  putative PPT
                                              tttttgta  TA-rich tract