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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCAACGGAGCCGATAAGGAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaattttgcgattaacatattgtctcatcgtcatcatttaatcatttgttattttcgccacacttagctttcgtccagcaatgcagacaagtaacatttcaccaaactgatcttttttcctctgcccattgtgcttgctctctttggcag

Basic information

species Oryza sativa
transcript LOC_Os07g48410.1
intron # 6
splice site 5'
intron type U2

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|86253323|gb|CI058248.1|CI058248
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|58603862|gb|CK014390.1|CK014390
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGA
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGA
EST: gi|58657427|gb|CK046107.1|CK046107
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|58676590|gb|CK065277.1|CK065277
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCA
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCA
EST: gi|58607975|gb|CK036008.1|CK036008
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|29666734|gb|CB663009.1|CB663009
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGAACAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|88325268|gb|CI675062.1|CI675062
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|88851800|gb|CI675002.1|CI675002
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|86257029|gb|CI061792.1|CI061792
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|58659889|gb|CK048569.1|CK048569
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|88221815|gb|CI221771.1|CI221771
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|58612737|gb|CK040449.1|CK040449
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|88268546|gb|CI378481.1|CI378481
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|29681057|gb|CB677332.1|CB677332
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC

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), 74 (downstream exon)
Score: 17

GAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCAACGGAGCCGATAAGGAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGCGGGATTTGCTCGCGATCCTTTCGCTCCCACTGAGGCGGAGATCTCCGCC




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