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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatcaatcactgtttcccaccactcttgactaccatgatattaaataatatttgcgttggcattggtgcggtacag

Basic information

species Oryza sativa
transcript LOC_Os11g17610.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g17610.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G840928_T01 (Zea mays), 5'ss of exon 9
TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatcaatcactgtttcccaccactcttgactaccatgatattaaataatatttgcgttggcattggtgcggtacag
||| ||||||||||||||||||||||| |||||| || |||| || ||  | ||||||||||| |||| | | |  || ||  || ||   |||        |  |||  |       | |||    ||||  ||| | |    |||
TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctggataacc-ttccctttcac--------agaatggaaacccgggagattcaatttggttttgtttcaacgcag
















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|88530840|gb|CI459265.1|CI459265
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|88271211|gb|CI387264.1|CI387264
EST:     TCATGGACACGTCACTTTCTCCTGACTAATGAGTACCCTACAGAAAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|86427132|gb|CI072229.1|CI072229
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|86485836|gb|CI128469.1|CI128469
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|88506305|gb|CI433811.1|CI433811
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|88485472|gb|CI422743.1|CI422743
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|88901816|gb|CI374424.1|CI374424
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|86598669|gb|CI355286.1|CI355286
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATTATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|86490045|gb|CI132678.1|CI132678
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTTTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|88540023|gb|CI470031.1|CI470031
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|86883137|gb|CI314316.1|CI314316
EST:     TCATGGGCACGTCACTTTCTCCTTACGAATGAGTACCCTACACAGAAGAG                         CGTTAATCCGATGATGCTTGGGTGCATTGCTGGCTCTGTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|88488080|gb|CI425351.1|CI425351
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|86887072|gb|CI325887.1|CI325887
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTTTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
EST: gi|218499213|gb|FG962191.1|FG962191
EST:     TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG                         CGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA
genomic: TCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAA

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: 55 (upstream exon), 75 (downstream exon)
Score: 5

TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAGgttatgatca ... tgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAAAGCTGCATCACATGCTTTTGAGAAGAACAAGAGATCAACTGTCACCACT




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