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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatcccgtgttattctttttaattctgaagcatgtcaagagccaaatgtctatactcctagattaatcactgtgccttattcccctccttccttgaagGTTAATAAATGCTTTCGAGGACCATATTAGAGCTGCAGTTGAGAAGGCAATACCAGAAAATATTATTGACGGCACATCCAAACTTGACTCGTTGCTTCAA

Basic information

species Oryza sativa
transcript LOC_Os06g20430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g20430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G352607_T02 (Zea mays), 3'ss of exon 2
-----atgatcccgtgttattctttttaatt---ctgaagcatgtcaagagccaaatgtctatactcctagattaatcactgtgccttattcccctccttccttgaagGTTAATAAATGCTTTCGAGGACCATATTAGAGCTGCAGTTGAGAAGGCAATACCAGAAAATATTATTGACGGCACATCCAAACTTGACTCGTTGCTTCAA
     |   | || ||  ||| | | |||||   ||    ||  ||||||  ||||  |  |||||      | |  |||| ||   ||||  | | |||   |||||||| ||||||||||| || || ||||||| ||||||||||||||||||| |||| |||||||| ||||| ||| |    ||||| ||||| || || |||
ttactagagttccctgg-attttatataattgtacttggacacatcaagaagcaaaatttcatact------taatccactatgttgtattgtc-tacttgtctgaagGTTTATAAATGCTTTTGAAGATCATATTAAAGCTGCAGTTGAGAAGGCAGTACCTGAAAATATCATTGAAGGCGCTGGGAAACTGGACTCCTTTCTGCAA
















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|58598981|gb|CK009509.1|CK009509
EST:     AAGGACCTAGTGATATCCCTGGATGGTGGAGCATCTTGGTTTTATCAGGG                         GTTAATAAATGCTTTCGAGGACCATATTAGAGCTGCAGTTGAGAAGGCAAT
genomic: AAGGACCTAGTGATATCCCTGGATGGTGGAGCATCTTGGTTTTATCAGGGgtatgtatct ... ttccttgaagGTTAATAAATGCTTTCGAGGACCATATTAGAGCTGCAGTTGAGAAGGCAAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgtctatactcctagattaatcactgtgccttattcccctccttccttgaagGTTAATAAATGCTTTCGAGGACCATATTAGAGCTGCAGTTGAGAAGGCAATACCAGAAAATATTATTGACGGCACATCCAAACTTGACTCGTTGCTTCAA
                 gattaat  putative branch site (score: 3)
                       tcactgtgccttattc  CT-rich tract
               tagattaat  TA-rich tract