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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttatagttcatccttccaaacccttttaaagtaaagaaaatttatgaaaactgtcataattataagaattggtgtgtttggagttgagcatttccccccctgccatttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTTGAAAAGTTGGGTTCACCAATGTCATGGGAACATATCACTAATCAG

Basic information

species Oryza sativa
transcript LOC_Os06g35540.1
intron # 7
splice site 3'
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|88960529|gb|CI006490.1|CI006490
EST:     CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|86415209|gb|CI069612.1|CI069612
EST:     CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|86521313|gb|CI161519.1|CI161519
EST:     CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCGTTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|88958600|gb|CI096116.1|CI096116
EST:     AGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: AGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|157650051|gb|EX449685.1|EX449685
EST:     CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|89182827|gb|CI045585.1|CI045585
EST:     AGTTTATGGCTGAAAGAGGTCAAG                         GGTATGTCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: AGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|88849517|gb|CI089425.1|CI089425
EST:     CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|86428294|gb|CI074975.1|CI074975
EST:     CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|86855856|gb|CI271075.1|CI271075
EST:     CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|88245868|gb|CI245717.1|CI245717
EST:     ATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: ATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|88507917|gb|CI435423.1|CI435423
EST:     GTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: GTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|86601803|gb|CI258479.1|CI258479
EST:     CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|3760200|gb|C97458.1|C97458
EST:     CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
genomic: CTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT
EST: gi|89188646|gb|CI115895.1|CI115895
EST:     TATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAG                         GGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCGAAGAGAACCTT
genomic: TATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTT

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), 71 (downstream exon)
Score: 17

TAGACCTTTGTACAGCAACCCACCCGTTCATGGTGCATTAATTGTTTCAACTATTCTTGGTGATCCGGAGTTGAAAAGTTTATGGCTGAAAGAGGTCAAGgtagttatag ... tttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTTGAAAAGTTGGGTTCACCAATGTCATGGGAACATATCACTAATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataagaattggtgtgtttggagttgagcatttccccccctgccatttgtctcagGGTATGGCTGATCGTATCATTGGAATGCGAACAGCACTCAAAGAGAACCTTGAAAAGTTGGGTTCACCAATGTCATGGGAACATATCACTAATCAG
                              tttccccccctgccat  CT-rich tract