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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAGAGGGGTCTTCTGGCTCGCAAAGGGGAGCTCCCCCGGCACCTGATGCAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttcttttttttttcgcgcagctaaaagcatgatatgtgctctctttttgtgcatcacttatgtttaactgtactattcttacgtacacaactgtaatgtgatgtgcag

Basic information

species Oryza sativa
transcript LOC_Os09g33810.5
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33810.5 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G800734_T02 (Zea mays), 5'ss of exon 2
ACCAGAGGGGTCTTCTGGCTCGCAAAGGGGAGCTCCCCCGGCACCTGATGCAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttcttt----tttttttcgcgcagctaaaagcatgatatgtgct-ctctttttgtgcatcacttatgtt--taactgtactattcttacgtacac----aactgtaatgtgatgtgcag-----------------------
|  ||||      |        | |  |    |  |  | ||| ||| ||||||||| |||||||| ||||||||||||    | ||||||||||||||||||  |   ||    ||   ||        |  |   |  || |  | | ||  | |||| |||   || |  |     ||| || |   | |  | ||     || ||| |  |    |  ||                       
ATGAGAGCAAAAATTCAAA--ACCAGAGAAGCCATCTTCAGCAGCTGGTGCAGGCCTCCCCAATCCGTTTGATTTTTCTTCTATGAGCAACTTGCTCAATgtatctctcttgctattgccttaatatgttttgattaagaatttaagatgcttatgttgtacatagttttttctgccggctgaaccacattcagattcatttggaattgttaattttactatagtgttgtatgctcgtcatgtgcag
















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|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|29636054|gb|CB641063.1|CB641063
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|218480322|gb|FG970039.1|FG970039
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88360017|gb|CI608531.1|CI608531
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|58608747|gb|CK036780.1|CK036780
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88395378|gb|CI611295.1|CI611295
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATC-ATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|569734|gb|D40583.1|D40583
EST:     CAGGCCTTNCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGG
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGG
EST: gi|29688694|gb|CB684969.1|CB684969
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88356737|gb|CI619223.1|CI619223
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCA
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCA
EST: gi|29688695|gb|CB684970.1|CB684970
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88731883|gb|CI753393.1|CI753393
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTG
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTG
EST: gi|58675502|gb|CK064189.1|CK064189
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|88329332|gb|CI653246.1|CI653246
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|58592381|gb|CF990689.1|CF990689
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTC
EST: gi|86901754|gb|CI310516.1|CI310516
EST:     CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAAT                         GATCCATCTATNAAGGAGATGGCAGAGCAGATTGCAAGCGACCCT
genomic: CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCT
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 68 (downstream exon)
Score: 80

ACCAGAGGGGTCTTCTGGCTCGCAAAGGGGAGCTCCCCCGGCACCTGATGCAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATgtaagttctt ... tgatgtgcagGATCCATCTATAAAGGAGATGGCAGAGCAGATTGCAAGCGACCCTGTGTTCACCCAGATGGCAGAGCAGCTGCAGAAGAGTGCTCATGTGACCGGGGAAC




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