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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccttgttaagtaaatatcatcagctaaagtagtttatatcatgtttggttatttgagtaacgtattaattcttctatgcaccaaataacttggctgcagGAAATTTATTCCATTAAATTGCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGC

Basic information

species Oryza sativa
transcript LOC_Os03g02756.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G44150.2 (Glycine max), 3'ss of exon 35
cccttgttaagtaaatatcatcagctaaagtagtttatatca-tgtttggttatttgagtaacgtattaattcttctatgcaccaaataacttggct--gcagGAAATTTATTCCATTAAATTGCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGC
   |  ||   ||  |  | |    | |  |    ||  ||  | ||   |||  |   |    ||||  |   || ||     |  |   ||       ||||| || || ||  | || |||||||| |||   ||  ||||||| |||||||| || || ||||||||||| ||  |||| || |||||||||||||| |
---taattgcttaggttgctttcttttacttttcctacctctctattgaattagatagctttgatatttgtcactccatttgtaagttttttttatctcacagGAGATATACTCGGTGAAGTTGCCTGGAAATCCCAAATTGGGTGAAGGGAAGCCCGAGAATCAAAATCATGCAATTGTATTTACGCGTGGAAATGCAGTCC

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 37
cccttgttaagtaaatatcatcagctaaagtagtttatatcatgtttggttatttgagtaacgtattaattcttctatgcaccaaataacttggctg---cagGAAATTTATTCCATTAAATTGCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGC
   ||| ||  |   | | ||    | |  | |   |||     || ||||  ||   |    | ||  | | ||  |  |   ||    || | ||   ||||| || || ||  | ||||| ||||| |||   ||  |||| || |||||||| || || ||||||||||| || ||||| || |||||||||||||| |
-ttttgctagcttt-tgttattgaattagattgcc-ataattgcttaggttgctttcttttacttttgctacctccctttattgaagttttttgttgtcgcagGAGATATACTCAGTAAAATTACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCC

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S13_132V6.1 (Physcomitrella patens), 3'ss of exon 34
cccttgttaagtaaatatcatcagctaa-agtagtttat-atcatgtttggttatttgagtaacgta--ttaattcttctatgc-accaaataact--tggctgcagGAAATTTATTCCATTAAATTGCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGC
        |  |||   ||||| || |  ||      |   | | ||     | |   |      ||  | || ||    || |     | |   |  |  ||||||||||| || ||||| |||||||||||  |  |||  ||||| ||||| ||||| ||||||||||| ||||| ||  |||| || |||||| | ||  | |
-------aagttaagcctcatctgccagcagagacccaccgtgacgtcgaaatgtgcaataggtataggtcaactccgaaattctgttgatttgttactatctgcagGAAATCTACTCCATAAAATTGCCTGGAGAAGTTATTCTGGGAGAGGGCAAGCCTGAAAACCAAAACCATGCAATTGTATTTACTCGTGGAGAGGCCATTC

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|33679231|gb|CF307470.1|CF307470
EST:     CAAAGCTTGTTAAAGCTGACATTCATGGAAAGGACAAG                         GAAATTTATTCCATTAAATTGCCTGGCAATTTTAAGCTGGGTGAGGGGAAG
genomic: CAAAGCTTGTTAAAGCTGACATTCATGGAAAGGACAAGgtcagtataa ... ttggctgcagGAAATTTATTCCATTAAATTGCCTGGCAATTTTAAGCTGGGTGAGGGGAAG
EST: gi|29675246|gb|CB671521.1|CB671521
EST:     CCGAGTATTACTCAAAGCTTGTTAAAGCTGACATTCATGGAAAGGACAAG                         GAAATTTATTCCATTAAATTGCCTGGCAATTTTAAGCTGGGTGAGGGGAAG
genomic: CCGAGTATTACTCAAAGCTTGTTAAAGCTGACATTCATGGAAAGGACAAGgtcagtataa ... ttggctgcagGAAATTTATTCCATTAAATTGCCTGGCAATTTTAAGCTGGGTGAGGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttatttgagtaacgtattaattcttctatgcaccaaataacttggctgcagGAAATTTATTCCATTAAATTGCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGC
                                      aaataac  putative branch site (score: 2)
                  tattaattcttctat  TA-rich tract