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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagtcaattcaatcggcattgatcttcactggaatctggatgctgctgactccatctgcatcaaagaaacttatacgggatcactttttctacatgcagGTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGTGCATTGGATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTG

Basic information

species Oryza sativa
transcript LOC_Os04g59494.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.4 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 19
aaagtcaattcaatcggcattgatcttcactggaatctgg--atgctgctgactccatctgcatcaaagaaacttatacgggatcactttttctacatgcagGTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGTGCATTGGATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTG
|| | ||  | ||    ||   |   | ||    |   ||  |     |  |  | |     | ||       || |  | |||| | ||  | |  ||||| |||||||| |||||||||||||  | |||||||  ||||||||||| ||| | ||||| ||  |||| |||||||||||||| ||||||||||||||||
aaggccacctgaaaaaacaacaaatatgacaactacaaggtcaaatcacatatacgactcata-cattttctgttctttgtgatctccttc-caatgtgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTG
















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|29623086|gb|CB628097.1|CB628097
EST:     CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAG                         GTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGT
genomic: CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAGgtctgtgaaa ... ctacatgcagGTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGT
EST: gi|58611878|gb|CK039590.1|CK039590
EST:     CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAG                         GTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGT
genomic: CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAGgtctgtgaaa ... ctacatgcagGTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGT
EST: gi|58660018|gb|CK048698.1|CK048698
EST:     CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAG                         GTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGT
genomic: CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAGgtctgtgaaa ... ctacatgcagGTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGT
EST: gi|58667508|gb|CK056194.1|CK056194
EST:     CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAG                         GTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGT
genomic: CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAGgtctgtgaaa ... ctacatgcagGTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGT
EST: gi|58666235|gb|CK054921.1|CK054921
EST:     CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAG                         GTTGATCCTGCTGCAGCTGGTGCATTATATGA
genomic: CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAGgtctgtgaaa ... ctacatgcagGTTGATCCTGCTGCAGCTGGTGCATTATATGA
EST: gi|58662883|gb|CK051569.1|CK051569
EST:     CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAG                         GTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGT
genomic: CAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAGgtctgtgaaa ... ctacatgcagGTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgactccatctgcatcaaagaaacttatacgggatcactttttctacatgcagGTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGTGCATTGGATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTG
 tgctgac  putative branch site (score: 2)
                                    tcactttttct  putative PPT
                      aaacttata  TA-rich tract