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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcaatgccttgattactactttctgttaaaatctttggtcatctcagcaacatcatacttatatatctcttaacatgccatcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAAGACAGCTACTGATTCTTATGAAAACCCGGGCTTTGAGTTCCTTTCTGCA

Basic information

species Oryza sativa
transcript LOC_Os12g05650.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G109785_T02 (Zea mays), 3'ss of exon 8
--------------gtattgcaatgccttgattactactttctgttaaaatctttggtcatctcagcaacatcatacttatatatctcttaacatgccatc-atatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAAGACAGCTACTGATTCTTATGAAAACCCGGGCTTTGAGTTCCTTTCTGCA
                |||  |    | | || || | || || | |   | |||  |  | ||  |    |  |   |||  |    |||   |||  |  ||||||| |||    |||||| |||||||||| ||||| ||||| |||||||||||||||||||| ||||| || ||     |    |||    |       |  |
gtctacttccttggtcattcgagcaacatcataaccatttcct-taacgttatttttttctgtcttcgttgtgttcactatgcacactttattttgctttttatatagGCGCTGACCAATTGCCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAAGACAGCTATTGATTGTTGTGTTTGTCGAACCTTCCTATAGTGCATTAGA

upper sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G066496_T01 (Zea mays), 3'ss of exon 9
--------------gtattgcaatgccttgattactactttctgttaaaatc--tttggtcatctcagcaacatcatacttatatatctcttaacatgccatcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAAGACAGCTACTGATTCTTATGAAAACCCGGGCTTTGAGTTCCTTTCTGCA
                ||| ||          || |  |||||  ||||     |||  || | ||  || |||  |   | |  |    |     |||  |  || ||||| |  | |||||  |||||||||| ||||| ||||| |||||||||||||||||||| ||| | || ||           |   ||| |     |  |
gtctagttccttggtcatttcagcaaacatcataatcgtttctactaaatgtgattttttcctgtcctcatcattttcgctttgcacacttcgttttgcttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAAGACAGCTATTGACTGTTGTGTTGTTGAACCTTGCTAGTACTACATTAAA

upper sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G825902_T02 (Zea mays), 3'ss of exon 9
--------------gtattgcaatgccttgattactactttct-gttaaaatctttggtcatctcagcaacatcatacttatatatctcttaacatgccatc-atatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAAGACAGCTACTGATTCTTATGAAAACCCGGGCTTTGAGTTCCTTTCTGCA
                |||  |    | | || || | || ||   |   || |||     |||  |     |   |||| |  |    |||   |||  |  ||||||| |||    |||||| |||||||||| ||||| ||||| |||||||||||||||||||| ||||| || ||     |    |||    |       |  |
gtctacttccttggtcattcgagcaacatcatgaccatttccttaatgttatttttttctgtcttcgttgtgtt-cactt-tgcacactttattttgctttttatatagGCGCTGACCAATTGCCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAAGACAGCTATTGATTGTTGTGTTTGTCGAACCTTCCTATAGTGCATTAGA

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|88476276|gb|CI413547.1|CI413547
EST:     AGGTGCCAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|27577338|gb|CB000033.1|CB000033
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88509817|gb|CI437323.1|CI437323
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGGTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88552099|gb|CI482219.1|CI482219
EST:     GAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: GAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88490918|gb|CI428190.1|CI428190
EST:     ATTCCATGTGAGTTACAGAGGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: ATTCCATGTGAGTTACAGA-GGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88506169|gb|CI433675.1|CI433675
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88508659|gb|CI436165.1|CI436165
EST:     AATTCCATGTGAGTTACAGAGGTGCCGAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGANACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|86255014|gb|CI017134.1|CI017134
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88279515|gb|CI400515.1|CI400515
EST:     CAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: CAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|87026460|gb|CI252414.1|CI252414
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88241583|gb|CI241432.1|CI241432
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|14192305|gb|AU184516.1|AU184516
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|86823074|gb|CI253990.1|CI253990
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|86823113|gb|CI254016.1|CI254016
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88547845|gb|CI478173.1|CI478173
EST:     TGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: TGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88661073|gb|CI449923.1|CI449923
EST:     GGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: GGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88240853|gb|CI238704.1|CI238704
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|55408732|gb|CV721108.1|CV721108
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|86599021|gb|CI355638.1|CI355638
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88516411|gb|CI444065.1|CI444065
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|86540849|gb|CI181055.1|CI181055
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATGATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|8335146|gb|BE040130.1|BE040130
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|5900741|gb|AU078396.1|AU078396
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|89188397|gb|CI115646.1|CI115646
EST:     AATTCCATGTGAGTTACAGAGGTGCTAAATTGAACAGCTCATTATCTCAG                         GTGCTCGAGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|86259447|gb|CI008124.1|CI008124
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88205440|gb|CI205289.1|CI205289
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88277171|gb|CI397973.1|CI397973
EST:     GCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: GCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88526843|gb|CI454933.1|CI454933
EST:     GCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: GCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|89165417|gb|CI102507.1|CI102507
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|86251590|gb|CI016879.1|CI016879
EST:     AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: AATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
EST: gi|88469811|gb|CI407082.1|CI407082
EST:     TGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG                         GTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA
genomic: TGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAA

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: 52 (upstream exon), 70 (downstream exon)
Score: 15

GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAGgtattgcaat ... catcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAAGACAGCTACTGATTCTTATGAAAACCCGGGCTTTGAGTTCCTTTCTGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtcatctcagcaacatcatacttatatatctcttaacatgccatcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAAGACAGCTACTGATTCTTATGAAAACCCGGGCTTTGAGTTCCTTTCTGCA
                                  tcttaac  putative branch site (score: 15)
                  atcatacttatatat  TA-rich tract