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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAGGAAGAAAAGGATCAATTACGCAGATACCCATTTTAACCATGCCTAATGATGgttagttatttaaatgtgcttacattttatgataaatctttttgcgaaattgcacttttcctttttttaatttgaagtatgtatgttaattgcacagaaaaacatagtgaatcagttttattaatagaataaatgttacatggataactgatattagatgctgccggcaactttctgactcataagtcgtgctgttgtag

Basic information

species Oryza sativa
transcript LOC_Os01g51380.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51380.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 5'ss of exon 9
ATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAGGAAGAAAAGGATCAATTACGCAGATACCCATTTTAACCATGCCTAATGATGgttagtta-----tttaaatgtgcttacattttatgataaatctttttgcgaaattgcacttttcctttttttaatttgaagtatgtatgttaattgcacagaaaaacatagtgaatcagttttattaatagaataaatgttacatggataactgatattagatgctgccggcaactttctgactcataagtcgtgctgttgtag
|||||||||||| |||| || || ||||| |||||||| || || |||||  | |||||||| ||||| ||||| || ||| |||| ||||| ||||||||| ||||      ||    |||  | |  ||| |  ||     || ||   ||   ||| ||| | || || || | |      | | | || | |||    |       | ||      | |  ||    | |  || | | ||    |   ||  |||   ||| |                                     
ATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAGGCCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgcatccttcctttgtcatcaagtttcagtatttgctttctttgaaatgggcattttactttgttatattatttttgctctttcttgactgcgtgcagtcttcgactgtggacttctccttgtctgtactaa-gcttcacctttg--tggcatttcgtgcag-------------------------------------

upper sequence: LOC_Os01g51380.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 9
ATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAGGAAGAAAAGGATCAATTACGCAGATACCCATTTTAACCATGCCTAATGATGgttagttatttaaatgtgcttacattttatgataaatctttttgcgaaattgcacttttcctttttttaatttgaagtatgtatgttaattgcacagaaaaacatagtgaatcagttttattaatagaataaatgttacatggataactgatattagatgctgccggcaactttctgactcataagtcgtgctgttgtag
|||||||| ||||||||||| || || ||||||||||| || || |||||| |||  |||||||| || || || |||||| | |  ||||| || ||||||  |  || |          | ||  | | |   |  |  | ||                                                                                                                                                           
ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatgtctgatcatcgagatcatct-actgacttactcgcag---------------------------------------------------------------------------------------------------------------------------------------------------------
















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|33811101|gb|CF331441.1|CF331441
EST:     AAGAAAAGGATCAATTACGCAGATACCCATTTTAACCATGCCTAATGATG                         ATATTACACATCCAACTCCTGATCTTACTGGTTATATCACTGAGGGACAGA
genomic: AAGAAAAGGATCAATTACGCAGATACCCATTTTAACCATGCCTAATGATGgttagttatt ... gctgttgtagATATTACACATCCAACTCCTGATCTTACTGGTTATATCACTGAGGGACAGA
EST: gi|58687170|gb|CK075857.1|CK075857
EST:     GATACCCATTTTAACCATGCCTAATGATG                         ATATTACACATCCGACTCCTGATCTTACTGGTTATATCACTGAGGGACAGA
genomic: GATACCCATTTTAACCATGCCTAATGATGgttagttatt ... gctgttgtagATATTACACATCCAACTCCTGATCTTACTGGTTATATCACTGAGGGACAGA
EST: gi|27576717|gb|CA999411.1|CA999411
EST:     AAGAAAAGGATCAATTACGCAGATACCCATTTTAACCATGCCTAATGATG                         ATATTACACATCCAACTCCTGATCTTACTGGTTATATCACTGAGGGACAGA
genomic: AAGAAAAGGATCAATTACGCAGATACCCATTTTAACCATGCCTAATGATGgttagttatt ... gctgttgtagATATTACACATCCAACTCCTGATCTTACTGGTTATATCACTGAGGGACAGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAGGAAGAAAAGGATCAATTACGCAGATACCCATTTTAACCATGCCTAATGATGgttagttatttaaatgtgcttacattttatgataaatctttttgcgaaattgcacttttcctttttttaatttgaagtatgtatgttaattgcacagaaaaacatagtgaatcagttttattaatagaataaatgttacatggataactgatattagatgctgccggcaactttctgactcataagtcgtgctgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT