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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattttaagttgaggcatgtcttgttatctttgcttaaaatgctattacttttctgaaagaccaatgattcttgaacttatggatatgataatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAACTGTGGCATGAAGAGCTGGAGCCCCAGAACTCGTTGCTGGACATACTTG

Basic information

species Oryza sativa
transcript LOC_Os02g53060.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 7
aattttaagttgaggcatgtcttgttatctttgcttaaaatgctattacttttctgaaagaccaatgattcttg-----aacttatggatatgataatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAACTGTGGCATGAAGAGCTGGAGCCCCAGAACTCGTTGCTGGACATACTTG
     ||  |      |    ||  ||| |||||||    |    |    | |   | |||||  |  || | |     |||  |      ||   ||  |||||||||| || ||||| ||   |||||| ||| ||||||| ||||| ||||  |||||||| || |||||||| ||||||||||||||||| || || ||||
-----tatctcttactaccatttcctatgtttgcttgtgttctcttcctctgtggcatagacccttttttgtggttcaaaacaaactctcttggctatgctgcagATAAATGCGGATGGCGTGAAGAGGAACTTTTACCCTGGCGACAAGCTACCCCTGTGGCACGACGAGCTGGAACCCCAGAACTCGTTGCTTGATATTCTTG

upper sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 7
------aattttaagttgaggcatgtcttgttatctttgcttaaaatgctattacttttctgaaagaccaatgattcttgaacttatggatatgataatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAACTGTGGCATGAAGAGCTGGAGCCCCAGAACTCGTTGCTGGACATACTTG
         | | | | | |       |  || | | ||||      |  ||     ||     ||  ||   |      |||  |   || || | ||   ||||||||| || ||||| ||   |||||| ||  ||||||| ||||| ||||  |||||||| || |||||||||||||||||||||||||| || || ||||
atacttgcctcttactggcgtttccaatatttgtttgtgctctctgcggcatggacctttccttagttcagaaa------aacaaactcatttggttatgccgcagATAAATGCGGATGGCGTGAAGAGGAACTTCTACCCTGGCGACAAGCTACCCCTGTGGCACGACGAGCTGGAGCCCCAGAACTCGTTGCTTGATATTCTTG
















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|88281960|gb|CI403356.1|CI403356
EST:     TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
genomic: TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
EST: gi|88271757|gb|CI387810.1|CI387810
EST:     TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAACGCAGATGGTGTTTCGAGGAAATTTCAGCCCTGGAGACAAACTACA
genomic: TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCA-CCCTGGAGACAAACTACA
EST: gi|88503126|gb|CI430632.1|CI430632
EST:     TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
genomic: TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
EST: gi|11233281|gb|AU164713.1|AU164713
EST:     TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
genomic: TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
EST: gi|88551157|gb|CI481189.1|CI481189
EST:     TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
genomic: TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
EST: gi|88320707|gb|CI525649.1|CI525649
EST:     TGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAACCCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
genomic: TGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
EST: gi|88671264|gb|CI723184.1|CI723184
EST:     TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
genomic: TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
EST: gi|163920296|gb|EG710592.1|EG710592
EST:     TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCT
genomic: TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCT
EST: gi|88318949|gb|CI510744.1|CI510744
EST:     TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAACGCAGATGGTGTTTCGAGGAAATTTCAGCCCTGGAGACAAACTACA
genomic: TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCA-CCCTGGAGACAAACTACA
EST: gi|88677292|gb|CI729950.1|CI729950
EST:     TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
genomic: TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
EST: gi|88379765|gb|CI503964.1|CI503964
EST:     TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
genomic: TTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAA
EST: gi|3761046|gb|C98300.1|C98300
EST:     TGCTATAGCCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT                         ATAAAACGCAGATGGTGTTTCCGAGGAAATTTCACCCTGGAGACAAACTAC
genomic: TGCTATAG-CCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACTgtaagtgctc ... aatcttgcagAT-AAACGCAGATGGTGTTT-CGAGGAAATTTCACCCTGGAGACAAACTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttttctgaaagaccaatgattcttgaacttatggatatgataatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAACTGTGGCATGAAGAGCTGGAGCCCCAGAACTCGTTGCTGGACATACTTG
                                      atatgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattttaagttgaggcatgtcttgttatctttgcttaaaatgctattacttttctgaaagaccaatgattcttgaacttatggatatgataatcttgcagATAAACGCAGATGGTGTTTCGAGGAAATTTCACCCTGGAGACAAACTACAACTGTGGCATGAAGAGCTGGAGCCCCAGAACTCGTTGCTGGACATACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA