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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatatctttgtcatgatgtttatgattgatttagttatcatcactgaccttgtacatttcctttgttcaattggttgcttgaatctgttacatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAAGAAGCGCCACTCGTGGTGGTGGGACAGTCACATTAGCCCTAAGAACTCT

Basic information

species Oryza sativa
transcript LOC_Os01g07360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07360.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G831408_T01 (Zea mays), 3'ss of exon 1
------------------tca--tatctttgtcatgatgtttatgattgatttagttatcatcactgacc-------ttgtacatttcct--ttgttcaattggttgcttgaatctgttac-atttatagTTTT-----GAAGATACCTGAA-CAATGAAGCCACCTTTGGAGAGGAACCCTACCAAGAAGCGCCACTCGTGGTGGTGGGACAGTCACATTAGCCCTAAGAACTCT
                  | |   || ||     | || ||| ||| || | |||| |   || ||  |         ||  ||||||    || ||||  | ||| ||| | || |  ||   || ||| ||      |  |||   |||| | |||||||||||| | ||||||||||| || |||||||||||||||                                    
ctcatttttcgctgtattttaaccattttaactctcatatttgtgactgctatagtcactgtctctctctggtgctgctgcgcatttctgaatttttcagATAGTTTCTTCAGTCCGACACCGCTTCTAGCTTCCCCTCGGCGATCTGTGAAGCTATGAAGCCACCTCTCGAGAGGAACCCGACTAAGAAGCGCCACTCG------------------------------------
















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|88412588|gb|CI690330.1|CI690330
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|58666269|gb|CK054955.1|CK054955
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|58672522|gb|CK061208.1|CK061208
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|58653981|gb|CK042661.1|CK042661
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|88407696|gb|CI607830.1|CI607830
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|33677737|gb|CF305976.1|CF305976
EST:     AGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: AGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|58671469|gb|CK060155.1|CK060155
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|88350143|gb|CI622074.1|CI622074
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|58606505|gb|CK034538.1|CK034538
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|88389714|gb|CI603213.1|CI603213
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|58606805|gb|CK034838.1|CK034838
EST:     TTTGGGGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|58663083|gb|CK051769.1|CK051769
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|33797289|gb|CF324507.1|CF324507
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|58662899|gb|CK051585.1|CK051585
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|163925758|gb|EG714594.1|EG714594
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
EST: gi|58664309|gb|CK052995.1|CK052995
EST:     TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAG                         TTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA
genomic: TTTGGTGCAGGATCCTCACCTCCGGTTCTGAAAGAACCCCTGTTTCCCAGgtgagattat ... acatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaccttgtacatttcctttgttcaattggttgcttgaatctgttacatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAAGAAGCGCCACTCGTGGTGGTGGGACAGTCACATTAGCCCTAAGAACTCT
 cactgac  putative branch site (score: 2)
                                           ttacatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatatctttgtcatgatgtttatgattgatttagttatcatcactgaccttgtacatttcctttgttcaattggttgcttgaatctgttacatttatagTTTTGAAGATACCTGAACAATGAAGCCACCTTTGGAGAGGAACCCTACCAAGAAGCGCCACTCGTGGTGGTGGGACAGTCACATTAGCCCTAAGAACTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC