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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctcttctgttccaactagatgtgcctattcttctttattcattcttctatctctctcctcttttctttctcggtactcgtctgctgctgggcctcagGAAGAACCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGG

Basic information

species Oryza sativa
transcript LOC_Os01g64770.5
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64770.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G08870.1 (Glycine max), 3'ss of exon 5
tttctcttctgttccaactagatgtgcctattcttctttattcattcttctatctctctc-ctcttttctttctcggtactcgtctgctgctggg---cctcagGAAG---AACCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGG------
           |||   ||   | | |  |  ||||| |||| ||||| || |||||||| ||||| ||||||||  | || ||||||||  ||     ||| ||| |   | || || |||||||| ||||| ||  ||||||| ||||| || ||||||||    || ||||| |||||||||||||||||| ||||||||||||      
-----------ttctttctctttat-cacaaacttctctatttattctcctttctctctctctcttctctttctctatgct-gtctgctgtcggcaactctctggatgcacagCCAAATCGAATTCTCTTAGTTACAGTTCATCACATGCTGTATCCTATAACAGCGGATGTGCTACATCAAGTGTTTTCTCCCCATGGATTTGTGGAAAAGA

upper sequence: LOC_Os01g64770.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G43190.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------------------------------------tttctcttctgttccaactagatgtgcctattct----tctttattcattcttctatctctctcctcttttctttctcggtactcgtctgctgctgggcctcag-
                                                                               ||||      ||||  |   |      ||||  |    |||||  |  |  ||||||||   | |  | || | |||   |  | || |||||  ||      |  | | | || ||||| ||||| ||||| || || ||||| ||||| || || || ||  |||| || || |||||||| |||||||||||||||||||| |      
gtttgtaattttattagccgtttgattatataagtagcagtgctagttgtgttattgtcttgttatagaggtacttacatttcgtagtggttcttaaccgtcacttctatattcaattcttttcttttctttctatcttcgttccgtcttttgtctaactggtggt-tgctgtgggatggtggatgtacagCCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGC

upper sequence: LOC_Os01g64770.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 4
---tttctcttctgttccaactagatgtgcctattcttctttattcattcttctatctctctcctcttttctttctcggtactcgtctgctgctgggcctcagGAAGAACCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGG------
   | | ||| || |||        | |  || ||||||| |||| |||||  | |||||||||| | |   | |  |     |||| |   ||   |   |   | | ||||| |||||||| ||||| || ||||||||  |||| |||||||||||  | || ||||| |||||||||||||||||  |||| |||||||      
agttctttctccttttc--------tctatctgttcttctctatttattctcttctctctctcctgtctctatgccggtctaccgtcgggcactct-ctggacacacagCCTAATCGAATTCTCTTAGTTACAATTCATCACCTGCTATACCCTATAACAGTGGAGGTGCTGCATCAAGTGTTTTCTCCTCATGGTTTTGTGGAGAAGA

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|29656748|gb|CB653023.1|CB653023
EST:     ACCAAGAATTGACTACTGATCAGAGCTCTCATGGACGAAATCCTGATCAG                         GAAGAACCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACCCT
genomic: ACCAAGAATTGACTACTGATCAGAGCTCTCATGGACGAAATCCTGATCAGgtatgctttc ... tgggcctcagGAAGAACCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACCCT
EST: gi|33798640|gb|CF325178.1|CF325178
EST:     ACCAAGAATTGACTACTGATCAGAGCTCTCATGGACGAAATCCTGATCAG                         -AA---CCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACCCT
genomic: ACCAAGAATTGACTACTGATCAGAGCTCTCATGGACGAAATCCTGATCAGgtatgctttc ... tgggcctcagGAAGAACCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACCCT
EST: gi|88426086|gb|CI604375.1|CI604375
EST:     ACCAAGAATTGACTACTGATCAGAGCTCTCATGGACGAAATCCTGATCAG                         GAAGAACCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACC
genomic: ACCAAGAATTGACTACTGATCAGAGCTCTCATGGACGAAATCCTGATCAGgtatgctttc ... tgggcctcagGAAGAACCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACC
EST: gi|33798687|gb|CF325201.1|CF325201
EST:     ACCAAGAATTGACTACTGATCAGAGCTCTCATGGACGAAATCCTGATCAG                         -AA---CCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACCCT
genomic: ACCAAGAATTGACTACTGATCAGAGCTCTCATGGACGAAATCCTGATCAGgtatgctttc ... tgggcctcagGAAGAACCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctatctctctcctcttttctttctcggtactcgtctgctgctgggcctcagGAAGAACCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGG
                  ttttcttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctcttctgttccaactagatgtgcctattcttctttattcattcttctatctctctcctcttttctttctcggtactcgtctgctgctgggcctcagGAAGAACCTAACCGAATTCTGTTAGTAACCATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG