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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtcatctctgcctttacctatacatatgatgccagagtgcgtgcaaaataagtttccttggcgggctgtaggctgcacaattttgccgctagac...

Basic information

species Oryza sativa
transcript LOC_Os04g59040.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59040.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G104918_T03 (Zea mays), 5'ss of exon 3
GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtcatctctgccttt----acctatacatatgatgccagagtgcg--tgcaaaataagtttccttggcgggctgtaggctgcacaattttgccgctagac
| ||||||||||||||||| ||||| |||||||||  ||||  ||| ||     | ||   ||| | ||      |  |   || || ||  | | |     |    |   || | ||  | | ||  |      
GTCCTGGTGCTCCTGCTGTATTCAATGTTgtaagtaccatcattgctttctaacagcttggcatgttatatgtttgctctgctgaaacatttgatgcacctacaacatactgg-tacatgagtctgttga-----
















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|87023771|gb|CI288124.1|CI288124
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|55433781|gb|CV730004.1|CV730004
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|3768324|gb|AU032351.1|AU032351
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|33794379|gb|CF323075.1|CF323075
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|88423146|gb|CI613447.1|CI613447
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|33681023|gb|CF309262.1|CF309262
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|88732604|gb|CI755781.1|CI755781
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|88300646|gb|CI587450.1|CI587450
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|88427290|gb|CI586838.1|CI586838
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|88721865|gb|CI743377.1|CI743377
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|33686066|gb|CF314305.1|CF314305
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|58602895|gb|CK013423.1|CK013423
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|286879|gb|D15686.1|D15686
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|66915284|gb|CX102132.1|CX102132
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTAGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAACGAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAA-GAA
EST: gi|88726501|gb|CI750156.1|CI750156
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|27554006|gb|CA997906.1|CA997906
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|55433023|gb|CV729535.1|CV729535
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|86907275|gb|CI292840.1|CI292840
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|32948454|gb|BP185026.1|BP185026
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|218494174|gb|FG955165.1|FG955165
EST:     GCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|58599062|gb|CK009590.1|CK009590
EST:     GGCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|55409712|gb|CV722088.1|CV722088
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|33693190|gb|CF321429.1|CF321429
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|58671895|gb|CK060581.1|CK060581
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|88742766|gb|CI766274.1|CI766274
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|163927162|gb|EG710251.1|EG710251
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCA
EST: gi|88405920|gb|CI591315.1|CI591315
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGACATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|25799147|gb|CA755108.1|CA755108
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGA
EST: gi|55434349|gb|CV730296.1|CV730296
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|163925905|gb|EG712281.1|EG712281
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGCGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
EST: gi|86848615|gb|CI293930.1|CI293930
EST:     GCCCTGGTGCTCCTGCTGTCTTCAACGTT                         GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA
genomic: GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAA

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: 73 (upstream exon), 66 (downstream exon)
Score: 112

GCCCTGGTGCTCCTGCTGTCTTCAACGTTgtaagtgtca ... cacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG




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