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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttttttttttcgcgcagctaaaagcatgatatgtgctctctttttgtgcatcacttatgtttaactgtactattcttacgtacacaactgtaatgtgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTCACCCAGATGGCAGAGCAGCTGCAGAAGAGTGCTCATGTGACCGGGGAAC

Basic information

species Oryza sativa
transcript LOC_Os09g33810.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33810.5 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G800734_T02 (Zea mays), 3'ss of exon 2
-----------gtaagttcttt------tttttttcgcgcagctaaaa-----gcatgatatgtgctctctttt------tgtgcatcacttatgtttaactg----tactattcttacgtacacaactgtaa---tgtgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTCACCCAGATGGCAGAGCAGCTGCAGAAGAGTGCTCATGTGACCGGGGAAC
           |  | | | ||      ||||  |   | |  ||| |        |  ||  |  | | || |      ||  |  || | |  || |  ||    |  || | |||| || |    ||||     || |||||||||| ||||| ||||  |||||||| ||||| |||||||| ||||||||||||| ||||||||| || ||||| ||||| |||||||| |   | || ||||
gtatctctcttgctattgccttaatatgttttgattaagaatttaagatgcttatgttgtacatagttttttctgccggctgaaccacattcagattcatttggaattgttaattttac-tatagtgttgtatgctcgtcatgtgcagGACCCATCGATAAGAGAGATGGCTGAGCAAATTGCAAGTGACCCTGTGTTCAACCAGATGGCTGAACAGCTTCAGAAAAGTGCTCAGGGTGCTGGAGAAC
















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|55828232|gb|AU068959.2|AU068959
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|58608747|gb|CK036780.1|CK036780
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|29662509|gb|CB658784.1|CB658784
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88760364|gb|CI769920.1|CI769920
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGG
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGG
EST: gi|1631432|gb|C19161.1|C19161
EST:     CAGGCCTTGCCAATCCTTTTGATTTTTCTCAGTTTAGCAANTTGCTCAAT                         GATCCATCTATAAAGGAGAT
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGAT
EST: gi|88358556|gb|CI617642.1|CI617642
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGGAGATTG-AAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|27554079|gb|CA997979.1|CA997979
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88720913|gb|CI744212.1|CI744212
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAA
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAA
EST: gi|29670241|gb|CB666516.1|CB666516
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|29613548|gb|CB618561.1|CB618561
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88313743|gb|CI597374.1|CI597374
EST:     CAGGC-TTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88690767|gb|CI734846.1|CI734846
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATNCATCTATAAAGGAGATGGCAGAGCAG
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAG
EST: gi|29658731|gb|CB655006.1|CB655006
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88360017|gb|CI608531.1|CI608531
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|33684353|gb|CF312592.1|CF312592
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|218480322|gb|FG970039.1|FG970039
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88395378|gb|CI611295.1|CI611295
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATC-ATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88358223|gb|CI605148.1|CI605148
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|569734|gb|D40583.1|D40583
EST:     CAGGCCTTNCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGG
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGG
EST: gi|29617932|gb|CB622944.1|CB622944
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|29627631|gb|CB632642.1|CB632642
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88356737|gb|CI619223.1|CI619223
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCA
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCA
EST: gi|117234746|gb|CT847861.1|CT847861
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|218481521|gb|FG960926.1|FG960926
EST:     CAGGCCTTCCCAATCCTTGTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88731883|gb|CI753393.1|CI753393
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTG
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTG
EST: gi|88329332|gb|CI653246.1|CI653246
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|58675502|gb|CK064189.1|CK064189
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|29636054|gb|CB641063.1|CB641063
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|58592381|gb|CF990689.1|CF990689
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|8859951|gb|AU097269.1|AU097269
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|86901754|gb|CI310516.1|CI310516
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATNAAGGAGATGGCAGAGCAGATTGCAAGCGACCCT
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCT
EST: gi|29688694|gb|CB684969.1|CB684969
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88356902|gb|CI620790.1|CI620790
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88762075|gb|CI771631.1|CI771631
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGC
EST: gi|88411125|gb|CI606344.1|CI606344
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttatgtttaactgtactattcttacgtacacaactgtaatgtgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTCACCCAGATGGCAGAGCAGCTGCAGAAGAGTGCTCATGTGACCGGGGAAC
                      ttcttac  putative branch site (score: 2)
     tatgtttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcttttttttttcgcgcagctaaaagcatgatatgtgctctctttttgtgcatcacttatgtttaactgtactattcttacgtacacaactgtaatgtgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTCACCCAGATGGCAGAGCAGCTGCAGAAGAGTGCTCATGTGACCGGGGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG