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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGACAGTCACTACACATGTATGTTTTTCCCTCTTCAACAGGACCCTGATCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATGgtatgctttaacattggcatatttgtgatttacttgttcaagttccagtccctatgtagtactgtttctggataacatcaatcttttttattaaaaaacc...

Basic information

species Oryza sativa
transcript LOC_Os02g01030.4
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01030.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA17G14280.1 (Glycine max), 5'ss of exon 10
GATGACAGTCACTACACATGTATGTTTTTCCCTCTTCAACAGGACCCTGATCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATGgtatgctttaacattggcatatttgtgatttacttgttcaagttccagtccctatgtagtactgtttctggataacatcaatcttttttattaaaaaacc-----
                                          |||||||| ||||||||  |||||||||| || ||| ||||||| ||||||||||||||||    | |    |    | || ||    | ||| |||  |||| |  |   || | |   | | |||   | | | |  | |||    ||   ||| |     
------------------------------------------GACCCTGAACTGATGGCGTCATTTGGTGATCCAGAGATTATGGCTGCTCTTCAAGATGgtaattatcagttctaatgt-ttggttccattctttttct-gttcta--cttaatttggacttctctctatttgagaacc-tatttgacgttggcaaagcttgaa

upper sequence: LOC_Os02g01030.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA05G03770.3 (Glycine max), 5'ss of exon 10
GATGACAGTCACTACACATGTATGTTTTTCCCTCTTCAACAGGACCCTGATCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATGgtatgctttaacattggcatatttgtgatttacttgttcaagttccagtccctatgtagtactgtttctggataacatcaatcttttttattaaaaaacc--
                                          |||||||| |||||||| |||||| |||| || ||||||||||| ||||||||||||||||    | |    |   || ||||         | ||    ||  |||   | || | |  | | | |     |    | |     || | |||       
------------------------------------------GACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTTCAAGATGgtaattatcagttcta--atgtttggttccattctttttgtattttagttaatttggacttttctctatttgagaatctatttgacgttgtcaaagcttgaa

upper sequence: LOC_Os02g01030.4 (Oryza sativa), 5'ss of exon 8
lower sequence: AT4G22670.1 (Arabidopsis thaliana), 5'ss of exon 9
GATGACAGTCACTACACATGTATGTTTTTCCCTCTTCAACAGGACCCTGATCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATGgtatgctttaacattggcatatttgtgatttacttgttcaagttccagtccctatgtagtactgtttctggataacatcaatcttttttattaaaaaacc
                                          || ||||| || ||| | |||||| | |||||||| || ||||| |||||||||||||||||| |    || |   | | |||   |||| |  |    |||    |    || |  | |   |  || ||    |     |  | ||  |       
------------------------------------------GATCCTGAGCTAATGACGGCATTTAGCGACCCTGAAGTCATGGCTGCTCTTCAAGATGgtatgatgactcagtt-taaagttgcagtttattaat----gttt---tttgaatatttttcgagtcttgaatgttgtttgaatgctataacag------

upper sequence: LOC_Os02g01030.4 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S9_386V6.1 (Physcomitrella patens), 5'ss of exon 10
GATGACAGTCACTACACATGTATGTTTTTCCCTCTTCAACAGGACCCTGATCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATGgtatgctttaacattggcatatttgtgatttacttgttcaagttccagtccctatgtagtactgtttctggataacatcaatcttttttattaaaaaacc
                                          ||||| || || ||||| ||||||  ||| || || ||||||||||||||||||||||||||| ||   | || || ||    ||    |  | || || |     || ||     | |   |||  |   ||          ||  ||    |||  
------------------------------------------GACCCAGAACTTATGGCTGCATTTTCTGATCCAGAAGTTATGGCAGCTCTTCAAGATGgtatgattactctttcgcttagaactgtgcgatgtttttaattgttgatctctgaactgaaggttttaggtcgaatgctggcgaattcaatccggaaaaa

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|88960903|gb|CI382584.1|CI382584
EST:     TCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATG                         TGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCAAGGTGG
genomic: TCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATGgtatgcttta ... tttttttcagTGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCAAGGTGG
EST: gi|88247902|gb|CI247751.1|CI247751
EST:     TCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATG                         TGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCAAGGTGG
genomic: TCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATGgtatgcttta ... tttttttcagTGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCAAGGTGG
EST: gi|88462993|gb|CI522104.1|CI522104
EST:     TCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATG                         TGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCAAGGTGG
genomic: TCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATGgtatgcttta ... tttttttcagTGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCAAGGTGG
EST: gi|88509469|gb|CI436975.1|CI436975
EST:     TCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATG                         TGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCAAGGTGG
genomic: TCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATGgtatgcttta ... tttttttcagTGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCAAGGTGG
EST: gi|218488113|gb|FG949878.1|FG949878
EST:     GAGGTTATGGCAGCTGCTTCAAGATG                         TGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCANAGGTG
genomic: GAGGTTATGGCAGCT-CTTCAAGATGgtatgcttta ... tttttttcagTGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCA-AGGTG
EST: gi|88907607|gb|CI090401.1|CI090401
EST:     TCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATG                         TGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCAAGGTGG
genomic: TCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATGgtatgcttta ... tttttttcagTGATGAACAATCCTGCCAGCTTTGCGAGGCACCAAGCCAACCCCAAGGTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGACAGTCACTACACATGTATGTTTTTCCCTCTTCAACAGGACCCTGATCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATGgtatgctttaacattggcatatttgtgatttacttgttcaagttccagtccctatgtagtactgtttctggataacatcaatcttttttattaaaaaacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG