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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAAAAACTGCTTATGTTGGTCTCGCAAGTGCAGAGGTTCCTTTGGCTAAAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcattggatgttttctcatttcgtcaccgacagtactattttttcttgaaaattgcatgttcttatttgtgacaattatactttctttactatgt...

Basic information

species Oryza sativa
transcript LOC_Os11g38900.1
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|88219521|gb|CI219081.1|CI219081
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|87038208|gb|CI192830.1|CI192830
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|218493534|gb|FG958321.1|FG958321
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGCTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|58678636|gb|CK067323.1|CK067323
EST:     AAATGCGAACCCTGCAACATAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|86482418|gb|CI125051.1|CI125051
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|58677534|gb|CK066221.1|CK066221
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|87040861|gb|CI195483.1|CI195483
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|86479324|gb|CI121957.1|CI121957
EST:     AATGCGAACCCGTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AATGCGAACCC-TGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|29622757|gb|CB627768.1|CB627768
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|87038570|gb|CI193192.1|CI193192
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|88236205|gb|CI235407.1|CI235407
EST:     AAATGCGAACCCTGCAACTAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|88198118|gb|CI197968.1|CI197968
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|86477847|gb|CI120480.1|CI120480
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|89176010|gb|CI043031.1|CI043031
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|86518191|gb|CI158397.1|CI158397
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|86540420|gb|CI180626.1|CI180626
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|86513659|gb|CI156292.1|CI156292
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|29638593|gb|CB643602.1|CB643602
EST:     AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
EST: gi|86435681|gb|CI106914.1|CI106914
EST:     AAATGCGAACCCTGCAACGAATACATTAAAGCATAATCTGCCATTGCAAG                         AAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT
genomic: AAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTT

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: 74 (upstream exon), 71 (downstream exon)
Score: 32

TCCAAAAACTGCTTATGTTGGTCTCGCAAGTGCAGAGGTTCCTTTGGCTAAAATGCGAACCCTGCAACAAAAACATTAAAGCATAATCTGCCATTGCAAGgtgagtcatt ... ttacctacagAAGTAGGCGATTGTTGTAGAACTATGAAGCAGCAGGGTGCATTCAGTGTTTCAAGATGCCATGTAATAAGGTTGGCCTTCGTCTGGATGAGAATGCAAAA




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