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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctcaagtcattcttggcatacttttttactactttctttatgagcaggaaaaaaaagaggaaaggctaaactattactagcccatatcgctatg...

Basic information

species Oryza sativa
transcript LOC_Os03g63020.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G045241_T07 (Zea mays), 5'ss of exon 1
----------GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctcaagtcattcttggcatacttttttactactttctt-tatgagcaggaaaaaaaagaggaaaggctaaactatta--ctagcccatatcgctatg
          || ||||| |||||   ||| || |||||||||||| | ||||| ||||| |||||||| || ||| |||||||||| |||||| ||||||||     |  |  |    | ||||  ||||||||||  || || ||| |     |  || |  |  |||||||||   |  |  |||  || ||  ||    
TTTTCTGCAGGCCCTTCAGAAACTATTTCACCCTAACATTGTGAAGCTGAAGGAAGTGACGATGGAAAACCATGAGCTGTTCTTCATCTTTGAACACATGgtttagtccttgctacatctagcatg-ttttttactatatttttgtataaattaaaggaagagaaaaaaaggctaattcaccatgctattccctaaggcac--

upper sequence: LOC_Os03g63020.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G045241_T01 (Zea mays), 5'ss of exon 6
GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctcaagtcattcttggcatacttttttactactttctt-tatgagcaggaaaaaaaagaggaaaggctaaactatta--ctagcccatatcgctatg
|| ||||| |||||   ||| || |||||||||||| | ||||| ||||| |||||||| || ||| |||||||||| |||||| ||||||||     |  |  |    | ||||  ||||||||||  || || ||| |     |  || |  |  |||||||||   |  |  |||  || ||  ||    
GCCCTTCAGAAACTATTTCACCCTAACATTGTGAAGCTGAAGGAAGTGACGATGGAAAACCATGAGCTGTTCTTCATCTTTGAACACATGgtttagtccttgctacatctagcatg-ttttttactatatttttgtataaattaaaggaagagaaaaaaaggctaattcaccatgctattccctaaggcac--
















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|29656191|gb|CB652466.1|CB652466
EST:     AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG                         GAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
EST: gi|25798660|gb|CA754621.1|CA754621
EST:     AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG                         GAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
EST: gi|58694135|gb|CK082822.1|CK082822
EST:     AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG                         GAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
EST: gi|29663526|gb|CB659801.1|CB659801
EST:     AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG                         GAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
EST: gi|58656490|gb|CK045170.1|CK045170
EST:     AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG                         GAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
EST: gi|88324687|gb|CI587656.1|CI587656
EST:     AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG                         GAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
EST: gi|29644978|gb|CB649985.1|CB649985
EST:     AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG                         GAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
EST: gi|58692426|gb|CK081113.1|CK081113
EST:     AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG                         GAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
EST: gi|29613119|gb|CB618132.1|CB618132
EST:     AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG                         GAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
EST: gi|58675001|gb|CK063688.1|CK063688
EST:     AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG                         GAATGCACTTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
EST: gi|29613394|gb|CB618407.1|CB618407
EST:     AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG                         GAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: AGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
EST: gi|33381171|gb|CF196514.1|CF196514
EST:     TTGTTCTTCATTTTTGAAAACATG                         GAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA
genomic: TTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAA

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: 70 (upstream exon), 69 (downstream exon)
Score: 36

GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATGgttggtctca ... cttttcacagGAATGCAATTTGTATGATGTCATAAGAGAAAGGCAAGCTGCTTTCTCAGAAGAGGAGATACGGAACTTTATGGTGCAGATACTGCAAGGTCTTGCATATA




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