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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcacctgaactcctaagttgaactgtgaaatgtgctataaggtgtcctggctctaatgtgttcatttgttattgacaacttgctcatgcttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCTGAGTTTATCAGCTACCCTATCTCTCTATGGACTGAGAAGACCACTGAGA

Basic information

species Oryza sativa
transcript LOC_Os08g39140.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g39140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EDP01972 (Chlamydomonas reinhardtii), 3'ss of exon 1
aatcacctgaactcctaagttgaactgtgaaatgtgctataaggtgtcctggctctaatgtgttcatttgttattgacaacttgct--catgcttcctgcagTTGGA---------ATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCTGAGTTTATCAGCTACCCTATCTCTCTATGGACTGAGAAGACCACTGAGA
| || | || || | | | || | ||| ||| | ||| | | | || | ||| |||| ||| ||||| || ||||| ||| ||||||||||| ||||||||||| ||||| ||| |||||| ||||| || ||||| |||||||
--tgctcttggccatgtgcctgtgttgccccagttaccgcaaagccgcctcctcaccatgggcccatgccgctcggcccttccatttccacccgtcccgcagGAGGACCAGAAGGAGTACCTGGAGGAGCGGCGCATCAAGGACCTGGTCAAGAAGCACAGCGAGTTCATCTCCTACCCCATCTCGCTGTGGACCGAGAAGA---------

upper sequence: LOC_Os08g39140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ22362 (Selaginella moellendorffii), 3'ss of exon 3
aatcacctgaactcctaagttgaactgtgaaatgtgctataaggtgtcctggctctaatgtgttcatttgttattgacaacttgctcatgcttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCTGAGTTTATCAGCTACCCTATCTCTCTATGGACTGAGAAGACCACTGAGA
|| | | || || ||| | || | || || | || || ||| | ||||||||||||||| | |||||||| || |||||||||||||| || ||||||||||| || ||||| | |||| |||||||| ||||| |
--------------------------------------gtaggcgtttctatttcatcgatgtgaaacaagtagttac--tctgattttggttggcacagCTTGAATACCTTGAAGAGAGGAAGCTCAAGGATCTCATCAAGAAGCACTCCGAATTTATCAGCTATCCCATCTCCGTCTGGATCGAGAAGACTACTGACA

upper sequence: LOC_Os08g39140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ25533 (Selaginella moellendorffii), 3'ss of exon 3
aatcacctgaactcctaagttgaactgtgaaatgtgctataaggtgtcctggctctaatgtgttcatttgttattgacaacttgctcatgcttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCTGAGTTTATCAGCTACCCTATCTCTCTATGGACTGAGAAGACCACTGAGA
|| | | || || ||| | || | || ||| | || || ||| | || |||||||||||| | |||||||| || |||||||||||||| |||||||||||||| || ||||| | |||| |||||||| ||||| |
--------------------------------------gtatgcgtttctatttcatcgatgtgaaacaagtacttac--tttgattttggttggcacagCTTGAGTACCTTGAAGAGAGGAAGCTCAAGGATCTCATCAAGAAGCACTCCGAGTTTATCAGCTATCCCATCTCCGTCTGGATCGAGAAGACTACTGACA

upper sequence: LOC_Os08g39140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ17594 (Selaginella moellendorffii), 3'ss of exon 3
aatcacctgaactcctaagttgaactgtgaaatgtgctataaggtgtcctggctctaatgtgttcatttgttattgacaacttgctcatgcttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCTGAGTTTATCAGCTACCCTATCTCTCTATGGACTGAGAAGACCACTGAGA
|||| | | || | || | | | ||| | | ||||| |||| || | ||| | |||||||| || ||| | | |||||||| ||||||||||||||||| ||||| |||||||| || ||||| | ||| ||||||||| || ||||
-------------------------------gtgtgtttttgtgt-ttttgctgtttgagactatccctgtgacta--aactttttcatactgcgc-cagCTTGAATACCTCGAGGAGAGGAGGCTCAAGGATCTGATCAAGAAGCACTCCGAGTTCATCAGCTATCCCATCTCCGTCTGGGTTGAGAAGACGACCGAGA

upper sequence: LOC_Os08g39140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ29061 (Selaginella moellendorffii), 3'ss of exon 3
aatcacctgaactcctaagttgaactgtgaaatgtgctataaggtgtcctggctctaatgtgtt-catttgttattgacaacttgctcatgcttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCTGAGTTTATCAGCTACCCTATCTCTCTATGGACTGAGAAGACCACTGAGA
|||| | | || | | | | || ||| | | ||||| |||| || | ||| | ||||| || || ||| | | |||||||| ||||||||||||||||| ||||| |||||||| || ||||| | ||| ||| ||||| || ||||
-------------------------------gtgtgtttttgtgtttttgctgtttgagactttatccctgtgacta--aactttttcatactgcgc-cagCTTGAATATCTCGAGGAGAGGAGGCTCAAGGATCTGATCAAGAAGCACTCCGAGTTCATCAGCTATCCCATCTCCGTCTGGGTTGAAAAGACGACCGAGA

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|86832248|gb|CI307464.1|CI307464
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|6934863|gb|AU082400.1|AU082400
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|29627082|gb|CB632093.1|CB632093
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         GTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|86596515|gb|CI284826.1|CI284826
EST:     AGCAGCTTGGGAAGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|6934912|gb|AU082449.1|AU082449
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|86894496|gb|CI308249.1|CI308249
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|27921206|gb|CB097014.1|CB097014
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|33655302|gb|CF277916.1|CF277916
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|88830945|gb|CI079379.1|CI079379
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|29628986|gb|CB633997.1|CB633997
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|88217496|gb|CI217345.1|CI217345
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|88236164|gb|CI235366.1|CI235366
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCC
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|33665378|gb|CF296345.1|CF296345
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
EST: gi|86431030|gb|CI083453.1|CI083453
EST:     AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAG                         TTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT
genomic: AGCAGCTTGGGAGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtactaacag ... cttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcctggctctaatgtgttcatttgttattgacaacttgctcatgcttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCTGAGTTTATCAGCTACCCTATCTCTCTATGGACTGAGAAGACCACTGAGA
                          tattgac  putative branch site (score: 2)
 tgcttcct  putative PPT
 atttgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcacctgaactcctaagttgaactgtgaaatgtgctataaggtgtcctggctctaatgtgttcatttgttattgacaacttgctcatgcttcctgcagTTGGAATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCTGAGTTTATCAGCTACCCTATCTCTCTATGGACTGAGAAGACCACTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - -cctgaac
- - - - - - - - - - tgaactg
- - - - - - - - - - - - - - - aatgtgc
- - - - - - - - - - - - - - - - - - - - - - - -cctggct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgctc