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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtgtttgcaacctttatttagttttgcagctgtctctagattctacacaaaatcatgtctttctgattgaccatctgatgatgacatgtgaca...

Basic information

species Oryza sativa
transcript LOC_Os01g11370.1
intron # 3
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|29625175|gb|CB630186.1|CB630186
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
EST: gi|88362444|gb|CI623784.1|CI623784
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAG
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAG
EST: gi|88388923|gb|CI592811.1|CI592811
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
EST: gi|58691453|gb|CK080140.1|CK080140
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
EST: gi|29658869|gb|CB655144.1|CB655144
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
EST: gi|88312143|gb|CI580308.1|CI580308
EST:     AGGGTGGTCGAATTATAGGCTGCACTCAACCAAGACGATTGGGCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGA
EST: gi|88411265|gb|CI564386.1|CI564386
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAAC-AAGAC-ATTGGC-GTGCAG                         T---T-GCATCAAGAGTAGCGGAAGAAGTAG-TGTGAGACTCGGAGAACAA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
EST: gi|88727156|gb|CI750811.1|CI750811
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
EST: gi|88366515|gb|CI610734.1|CI610734
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGA
EST: gi|58674693|gb|CK063380.1|CK063380
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
EST: gi|29626953|gb|CB631964.1|CB631964
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
EST: gi|29636300|gb|CB641309.1|CB641309
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTG
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTG
EST: gi|88441713|gb|CI599618.1|CI599618
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
EST: gi|29624813|gb|CB629824.1|CB629824
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
EST: gi|88324258|gb|CI566071.1|CI566071
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCCTCAAGAGTAGCGGAAGAAGTA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTA
EST: gi|88430331|gb|CI567350.1|CI567350
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAAGAGTAGCGGAAGAAGTCGGTGTGAGACTCGGAGAAGAA
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAA
EST: gi|88430530|gb|CI569553.1|CI569553
EST:     AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG                         TCAGTTGCATCAATGAGTAGCGGAAGAAGTATGTGTGAGACTCGGAGGAAG
genomic: AGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAA-GAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAG-AAG

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: 49 (upstream exon), 46 (downstream exon)
Score: 12

TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAGgtatccagtg ... atttgaacagTCAGTTGCATCAAGAGTAGCGGAAGAAGTAGGTGTGAGACTCGGAGAAGAAGTTGGTTACACAATCCGATTTGAGGATCAAACAAATCCA




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