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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACTACATACAATTTCTTGGACATGTCACCGCACGTGCTGATTCCAATGCATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatactaattacctctgtagacttcatctatagattacaattattaatctgagaaggtggaatctgtacctcaggattttgtttcttgtcacaatt...

Basic information

species Oryza sativa
transcript LOC_Os01g04200.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04200.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G150866_T02 (Zea mays), 5'ss of exon 10
AAACTACATACAATTTCTTGGACATGTCACCGCACGTGCTGATTCCAATGCATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgat--actaattacctctgtagacttcatctatagattacaattattaatctgagaaggtggaatctgtacctcaggattttgtttcttgtcacaatt
||||||||||||| ||||||||  ||||||| || ||  | ||||||||||||||||| || || |||||||||||  |||||||||||||||||||||||||||    ||||||    ||| || ||    | | ||    | ||  |    | | |     |    ||| |  |||  | | |     ||   |  |   
AAACTACATACAAATTCTTGGAGTTGTCACCACATGTATTAATTCCAATGCATGGAAGGATTAATCTATGGCCCAAGTATATGCTTTGTGGATACCTCAGgtatggagaactaatcgtttctttatacgatttttttaagaaaaaagaaactttatcactgcttcccttctctggctcgtgttctacaggctatacgtac--

upper sequence: LOC_Os01g04200.2 (Oryza sativa), 5'ss of exon 10
lower sequence: AT1G25375.1 (Arabidopsis thaliana), 5'ss of exon 10
AAACTACATACAATTTCTTGGACATGTCACCGCACGTGCTGATTCCAATGCATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatga-tactaat-tacctctgtagac---ttcatctatagattacaattattaatctg---agaaggtggaatctgtacctcaggattttgtttcttgtcacaatt-----------------------------------------------------
|  | ||||| || ||| ||||  | || ||  | ||| ||||||| |||||||||||  ||||  | ||||| ||||| |||||||||||||| |||| |||||| ||  ||| | |    || ||     | || | || |   |  ||| |  | ||   |  || | ||     ||      || |    || ||   | | ||                                                     
AGTCGACATATAAATTCCTGGAGCTTTCTCCAAATGTGGTGATTCCCATGCATGGAAGGGTCAATTTGTGGCCGAAACACATGCTTTGTGGATATCTCAAgtatgaataagaatatgctgtagtggataatctgatgtttaaaaccctgttactgttttgtctatcagtttgatcagataaaagtagagtgaacttattaagatatttgatacattaatatataaaggaattttgatgggaggggtgatcttgttttccag
















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|88226652|gb|CI226568.1|CI226568
EST:     CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAG                         GCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
genomic: CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatact ... tacttttcagGCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
EST: gi|88265269|gb|CI369043.1|CI369043
EST:     ACCTATGGCCCAAACATATGCTTT-TTGATACCTCAG                         GCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
genomic: ACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatact ... tacttttcagGCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
EST: gi|88222973|gb|CI222822.1|CI222822
EST:     CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAG                         GCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
genomic: CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatact ... tacttttcagGCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
EST: gi|86497027|gb|CI139660.1|CI139660
EST:     CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAG                         GCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
genomic: CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatact ... tacttttcagGCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
EST: gi|88227418|gb|CI226898.1|CI226898
EST:     CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGGTACCTCAG                         GCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
genomic: CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatact ... tacttttcagGCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
EST: gi|86854389|gb|CI256511.1|CI256511
EST:     CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAG                         GCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
genomic: CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatact ... tacttttcagGCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
EST: gi|86504455|gb|CI147088.1|CI147088
EST:     CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAG                         GCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
genomic: CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatact ... tacttttcagGCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
EST: gi|88985398|gb|CI002915.1|CI002915
EST:     CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAG                         GCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
genomic: CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatact ... tacttttcagGCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
EST: gi|86497045|gb|CI139678.1|CI139678
EST:     CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAG                         GCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
genomic: CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatact ... tacttttcagGCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
EST: gi|88273399|gb|CI393805.1|CI393805
EST:     CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAG                         GCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC
genomic: CATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatact ... tacttttcagGCACCGAAGGGCAAGGGAAGTGTCCATTCTACAGTCTATAGAGAATGGGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACTACATACAATTTCTTGGACATGTCACCGCACGTGCTGATTCCAATGCATGGAAGAATCAACCTATGGCCCAAACATATGCTTTGTGGATACCTCAGgtatgatactaattacctctgtagacttcatctatagattacaattattaatctgagaaggtggaatctgtacctcaggattttgtttcttgtcacaatt

- - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA