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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGCGGGCGGCGGAAGCAATCGTAGTTAGCAGAGGCCGGCGAGCGAGCCGCCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctaccctctctctctcttttccggcggagatcgggagcatattggtctctgacgcgctcgtgtggcttccgttccgctgctgcag

Basic information

species Oryza sativa
transcript LOC_Os03g26970.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g26970.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S2_595V6.1 (Physcomitrella patens), 5'ss of exon 1
TCGCGGGCGGCGGAAGCAATCGTAGTTAGCAGAGGCCGGCGAGCGAGCCGCCACCGGCG---ATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctaccctctctctctcttttccggcggagatcgggagcatattggtctctgacgcgc---tcgtgtggcttccgttccgctgctgcag--------
 |  | || ||    |   ||  |  ||       |  | |||  ||     | | ||    ||||| |||||||||||||| ||||| || |||||||||||||  |    | ||  ||   |||||  | |   |  |   |   | | |   ||   |       |||   |     | | |  |   |||          
ACCGGTGCAGCTTCGGTCTTC-CAACTATTTCC--CTCGTGAGTAAGTTTTAAGCTGCAGCCATGGGGGACAGCCAGTACTCGTTCTCGCTTACCACCTTCAGgttagtgcacatcagtcgg-cttttgtgacacggtcccttaatttctcgacatcgatcagaggtatcgatagatagtcatgcaacgattgcgcggagttta
















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|58673780|gb|CK062466.1|CK062466
EST:     CCGCCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|33681297|gb|CF309536.1|CF309536
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|218490861|gb|FG966652.1|FG966652
EST:     CCGCCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88313637|gb|CI671766.1|CI671766
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|569227|gb|D40076.1|D40076
EST:     CACCGG-GAATGGGCGACAG-CAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CACCGGCG-ATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88580311|gb|CI697228.1|CI697228
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88570436|gb|CI661809.1|CI661809
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88727790|gb|CI749592.1|CI749592
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|4880857|gb|AU065156.1|AU065156
EST:     CACCGG-GATTGGGCGACAGCAAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CACCGGCGA-TGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88342989|gb|CI641515.1|CI641515
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|33808224|gb|CF330001.1|CF330001
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88580702|gb|CI697646.1|CI697646
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88329883|gb|CI651559.1|CI651559
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|58669010|gb|CK057696.1|CK057696
EST:     CCGCCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|58656409|gb|CK045089.1|CK045089
EST:     CCGCCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88740256|gb|CI763764.1|CI763764
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|58597692|gb|CK008220.1|CK008220
EST:     CCGCCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88591382|gb|CI707412.1|CI707412
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88827968|gb|CI778533.1|CI778533
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|55435846|gb|CV731059.1|CV731059
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|33662862|gb|CF293829.1|CF293829
EST:     CCACCGGCGATGGGCGACAGCCAGTACCCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88406056|gb|CI593836.1|CI593836
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCCCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|40486330|gb|BX897911.1|BX897911
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|33691028|gb|CF319267.1|CF319267
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88351773|gb|CI617498.1|CI617498
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|58683283|gb|CK071970.1|CK071970
EST:     CCGCCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88390466|gb|CI607502.1|CI607502
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88959392|gb|CI685873.1|CI685873
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|33654277|gb|CF276891.1|CF276891
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|33815449|gb|CF333578.1|CF333578
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88574120|gb|CI665889.1|CI665889
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|33677213|gb|CF305452.1|CF305452
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
EST: gi|88728844|gb|CI752354.1|CI752354
EST:     CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC
genomic: CCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTC

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: 64 (upstream exon), 70 (downstream exon)
Score: 7

TCGCGGGCGGCGGAAGCAATCGTAGTTAGCAGAGGCCGGCGAGCGAGCCGCCACCGGCGATGGGCGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtgcgctacc ... gctgctgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTGACGGCGGTCGGGTCCGGCCAGACCTCCCTCGGGATCAAAG




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