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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttcaaggcatgataattactggaaatagaatttgatgtgtatttatgttaatgtttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT

Basic information

species Oryza sativa
transcript LOC_Os03g01150.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G374779_T04 (Zea mays), 3'ss of exon 5
tttcttcaaggcatgataattactg-gaaatagaatttgatgtgtatttatgttaatgtttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT----------
            || | | ||     | |||| | ||| ||     | ||||  ||||||||   |    ||||||||  |||| |     |   | |||||||||  |||||||| | ||| ||||||| ||||||||||| |||||||||||  | |||| | ||||||||||||||||||||||||| || || ||||          
-------gtacaattaaatttgtcatgtaatatagtttcata---gtatatgagaatgtttctggtgcacgaagtttgtctaac-taaaagtatgtatcaggatatggcagATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCTTAGAGAATTT

upper sequence: LOC_Os03g01150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G374779_T03 (Zea mays), 3'ss of exon 9
---tttcttcaaggcatgataattactg-gaaatagaatttgatgtgtatttatgttaatgtttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT
    || ||      || | | ||     | |||| | ||| ||     | ||||  ||||||||   |    ||||||||  |||| |     |   | |||||||||  |||||||| | ||| ||||||| ||||||||||| |||||||||||  | |||| | ||||||||||||||||||||||||| || || ||||
ttgattattagtacaattaaatttgtcatgtaatatagtttcata---gtatatgagaatgtttctggtgcacgaagtttgtctaac-taaaagtatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCT

upper sequence: LOC_Os03g01150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA01G41570.1 (Glycine max), 3'ss of exon 9
-tttcttcaag-gcatgataattactggaaatagaatttgat-gtgtatttatgtt-aatgt-ttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT
   | | |||     | |||||  ||    ||  |  ||  |  |  ||||   || ||| |  || |     |||  ||   ||||  ||        |||||||  ||  | ||||||||  ||   |||||||||||||||  ||||||||||||  |||||| | | |||||| | || ||||||||||| ||||| ||||
cactgtgcaattatgtaataatccctattcatgtatcttagttattcatttgctttcaatatgctcaaaaccttgacattgatataaaatttg-----atttcagGCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAATGAAATACCAGATAAGAGAAATTCTACTTACAAGGAAAGATTTAGTAGCT

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|29619263|gb|CB624275.1|CB624275
EST:     GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
EST: gi|29661632|gb|CB657907.1|CB657907
EST:     GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
EST: gi|58585728|gb|CF984036.1|CF984036
EST:     GCGCGTCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCAGATTATTTAAAGGGTTGTAGATTTNCTTCCAAAGCTTAACAA
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTT-CTTCCAAAGCTTAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgttaatgtttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT
                                     ccttcctatgcttttc  CT-rich tract
      ttaatgttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttcaaggcatgataattactggaaatagaatttgatgtgtatttatgttaatgtttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT