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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccattctctactttgaccacatgtttaaattattgatcgccagtcttttatgtcacttcgacatttacattagtcttcctttgaattccccgtgacagGTTATGAGCAGACATTCCTGGAAAGACTCAGCTACCCAGCCAAAAGTGAAGTACTTCACTCAGGTGAAAGCACGGCCACCGACGTTCGTTGCCTTTATGA

Basic information

species Oryza sativa
transcript LOC_Os01g12540.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12540.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G848602_T01 (Zea mays), 3'ss of exon 8
tgccattctctactttgaccacatg----tttaaattattgat--cgccagtcttttatgtcacttcgacatttacattagtc-ttcctttgaattccccgtgac--------agGTTATGAGCAGACATTCCTGGAAAGACTCAGCTACCCAGCCAAAAGTGAAGTACTTCACTCAGGTGAAAGCACGGCCACCGACGTTCGTTGCCTTTATGA
               ||||  ||||    |  || ||| |||   | |  | |  | | | || |  | ||| ||  |    | || |||  ||| ||  ||||         |||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||||||||| ||||| ||||| ||||| || || |||||||| ||||
---------------tgactgcatgatgttcaaagttactgactacactggccagtgaagccattgtggcatctatttcgaccattacttctaataccttgtgattgtgctctagGTTATGAGCAGACATTCCTGGAAAGATTCAGCTACTCAGCCAAAAGTCAAGTACTTCACTCAAGTGAAGGCACGACCACCAACATTTGTTGCCTTCATGA

upper sequence: LOC_Os01g12540.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G40160.1 (Glycine max), 3'ss of exon 6
--------tgccattctctactttgaccaca--tgtttaaattattgatcgccagtcttttatgtcacttcgacatttacattagtcttcctttgaattccccgtga-cagGTTATGAGCAGACATTCCTGGAAAGACTCAGCTACCCAGCCAAAAGTGAAGTACTTCACTCAGGTGAAAGCACGGCCACCGACGTTCGTTGCCTTTATGA-----------
         | || |   ||| |  | ||    | |||  |  | | |       | ||  | || | || | | ||   |||  |||  ||||| |||     ||| |||||||||||||| ||||| |||||||||  |||  | ||||| || || ||||| ||||||||||| || || |||||||| || || ||||| ||| ||            
gttgcaaaaggcaattagtacatccatcatcactttttgtaacagtaaaatatgctattggaagtaaatttg-ctttcttatt--tctcactttggattggatttgatcaggttatgagcagGCATTCTTGGAAAGACCAAGCAGCACAGCCTAAGGTTAAGTATTTCACTCAGGTCAAGGCCCGGCCACCTACATTTGTTGCGTTTGTGCGTGGGAAGACT
















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|218496918|gb|FG952342.1|FG952342
EST:     CCGTTGGTTGCGTAAG                         GTTATGAGCAGACATTCCTGGAAAGACTCAGCTACCCAGCCAAAAGTGAAG
genomic: CCGTTGGTTGCGTAAGgtaaacatct ... cccgtgacagGTTATGAGCAGACATTCCTGGAAAGACTCAGCTACCCAGCCAAAAGTGAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttatgtcacttcgacatttacattagtcttcctttgaattccccgtgacagGTTATGAGCAGACATTCCTGGAAAGACTCAGCTACCCAGCCAAAAGTGAAGTACTTCACTCAGGTGAAAGCACGGCCACCGACGTTCGTTGCCTTTATGA
                                          ttccccgt  CT-rich tract
                   atttacatta  TA-rich tract