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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgtaattctattcccaacttatgttcaggaccatcaatatttctaagcatttatcatgcctacagtacatttttataccaatctcactgtcacttagggca...

Basic information

species Oryza sativa
transcript LOC_Os03g05280.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05280.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv13s0019g05280.t01 (Vitis vinifera), 5'ss of exon 4
CTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgta----attctat-tcccaacttatgttcaggaccatcaatatttctaagcatttatcatgcctacagtacatttttataccaatctcactgtcacttagggca
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CTGGACAGGAGAGGTTTGGAACATTGACAAACACTTACTACAGAGGTGTCCATGGCATTATTCTAGgtatgtgattggatattctaacttctttcttcttcttccacttcttttta----ttgataggctcactatatgtgcaaaccctttttttctccaaattcataga-
















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|33654291|gb|CF276905.1|CF276905
EST:     TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG                         TGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGG
genomic: TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgtaattctat ... cttctgttagTGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGG
EST: gi|86592468|gb|CI253149.1|CI253149
EST:     TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG                         TGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGG
genomic: TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgtaattctat ... cttctgttagTGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGG
EST: gi|58592544|gb|CF990852.1|CF990852
EST:     TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG                         TGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGG
genomic: TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgtaattctat ... cttctgttagTGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGG
EST: gi|33691502|gb|CF319741.1|CF319741
EST:     TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG                         TGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGG
genomic: TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgtaattctat ... cttctgttagTGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGG
EST: gi|86910401|gb|CI293056.1|CI293056
EST:     TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG                         TGTATGATGTCACAAA
genomic: TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgtaattctat ... cttctgttagTGTATGATGTCACAAA
EST: gi|33693314|gb|CF321553.1|CF321553
EST:     TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG                         TGTATGATGTCACAAAGAGAAAAAGTTTCACAAATTTGGCTGATGTATGGG
genomic: TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgtaattctat ... cttctgttagTGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGG
EST: gi|58589049|gb|CF987357.1|CF987357
EST:     AGGGGAATCACAAGTTCTTACTACAGAGTGTGCCCATGGCATCATTCTAG                         TGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGG
genomic: AGGGGAATCACAAGTTCTTACTACAGAG-GTGCCCATGGCATCATTCTAGgtaattctat ... cttctgttagTGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGG
EST: gi|88401815|gb|CI591142.1|CI591142
EST:     TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG                         TGTATGATGTCACAAAGAGAGAAAG
genomic: TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgtaattctat ... cttctgttagTGTATGATGTCACAAAGAGAGAAAG
EST: gi|88401813|gb|CI591140.1|CI591140
EST:     TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG                         TGTATGATGTCACAAAGAGAGAAAGTT
genomic: TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgtaattctat ... cttctgttagTGTATGATGTCACAAAGAGAGAAAGTT
EST: gi|88451481|gb|CI565534.1|CI565534
EST:     TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG                         TGTATGATGTC-CAAAGAGAGAAAGTTTCA-AAATTTGGGTGATG
genomic: TAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgtaattctat ... cttctgttagTGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATG

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: 65 (upstream exon), 72 (downstream exon)
Score: 29

CTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAGgtaattctat ... cttctgttagTGTATGATGTCACAAAGAGAGAAAGTTTCACAAATTTGGCTGATGTATGGGCCAAGGAAATAGAATTGCATTCGACAAATAAAGAGTGCATCAAAATGCT




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