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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatgatttgcatagagaagggtggttaatggtatacttcaatactgcagcgatactgtgatagtgatccacctctaacattgtttctactttattcagGTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAAGAAATACTGAGAACATTTCACAACCAAACAGACAATGTTATGTGCTCGT

Basic information

species Oryza sativa
transcript LOC_Os03g52630.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G110735_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------aaaatgatttgcatagagaagggtggttaatggtatac---ttcaatactgcagcgatactgtgatagtgatccacctctaacattgtttctactttattc-agGTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAAGAAATACTGAGAACATTTCACAACCAAACAGACAATGTTATGTGCTCGT
                                                                                             |    |   | | || |   |    || ||  ||    |  |||| ||||||     | |||   |    || | ||||||  ||  |||||| || | |||||||||| ||||||||||| || ||||||||||| || || |||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| |
gttagcacatttcatactccaatccaatgttgagtctgataaaagtattcagcgtggtcttaatgtaaaggaaaagaaaacatgatccttcgtacatgtcagaaacaggaaaatcagaaaaggcttatcagtgtaataatgcagcttccttatgaatattgatcatcactaacacagtccctacttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAATGTTATGTGCTCAT

upper sequence: LOC_Os03g52630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 3
----aaaatgatttgcatagagaagggtggttaatggtatacttcaatactgcagcgatactgtgatagtgatccacctctaacattgtttctactttattc-agGTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAAGAAATACTGAGAACATTTCACAACCAAACAGACAATGTTATGTGCTCGT
      || ||    || | | |||| |  | | ||  ||| | ||    |  |  ||     |||   |    | ||  ||| |   |||||||| ||| | |||||||||| ||||||||||| || ||||||||||| || || |||||||||||||||||||| ||||| ||||||||||| ||||| || ||||||||||
actgtcaaggaaaatcaga-aaaaggcttatcagtgtgataatgcagctttctaatga----atgaatatcgatcgccattaagacactttctactctatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAACGTCATGTGCTCGT
















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|58670607|gb|CK059293.1|CK059293
EST:     GTCCGAATTATGGAGTTTTTACCTGGGATGACAAGCTTCCAGGAGCTCAG                         GTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAA
genomic: GTCCGAATTATGGAGTTTTTACCTGGGATGACAAGCTTCCAGGAGCTCAGgttagcatac ... ctttattcagGTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAA
EST: gi|29639818|gb|CB644827.1|CB644827
EST:     GTCCGAATTATGGAGTTTTTACCTGGGATGACAAGCTTCCAGGAGCTCAG                         GTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAA
genomic: GTCCGAATTATGGAGTTTTTACCTGGGATGACAAGCTTCCAGGAGCTCAGgttagcatac ... ctttattcagGTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAA
EST: gi|396941140|gb|HO188349.1|HO188349
EST:     GTCCGAATTATGGAGTTTTTACCTGGGATGACAAGCTTCCAGGAGCTCAG                         GTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAA
genomic: GTCCGAATTATGGAGTTTTTACCTGGGATGACAAGCTTCCAGGAGCTCAGgttagcatac ... ctttattcagGTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAA
EST: gi|7593822|gb|AU066038.2|AU066038
EST:     GTCCGAATTATGGAGTTTTTACCTGGGATGACAAGCTTCCAGGAGCTCAG                         GTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAA
genomic: GTCCGAATTATGGAGTTTTTACCTGGGATGACAAGCTTCCAGGAGCTCAGgttagcatac ... ctttattcagGTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcagcgatactgtgatagtgatccacctctaacattgtttctactttattcagGTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAAGAAATACTGAGAACATTTCACAACCAAACAGACAATGTTATGTGCTCGT
                            ctctaac  putative branch site (score: 2)
                                       tttctactttattc  putative PPT
                                           tactttatt  TA-rich tract