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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT

Basic information

species Oryza sativa
transcript LOC_Os12g27520.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 5
gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT
||||||||||  |||||||||| |||||||| ||| ||| ||| | ||||||  |||  |||||||| |||||||||||| ||  |||||| |||||||| ||||| |||||||||||||||||||||||||||| ||||||||| |||||||||||||||||||||||||||||||||| |||||||||||||||
gtaagtacattgttagattatgacaattatgcactgacccaaaaatataaccatatggtgcttaaacgttggtgaatttggattaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G179308_T01 (Zea mays), 3'ss of exon 5
gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT
||||||||||  ||||||| ||||||||||||||| ||| ||| ||||||||   ||  ||||||||||||||||||||| ||  |||||| |||||||| ||||| ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||
gtaagtacattgttagattgtggcaattatgaactgacccaaaaagataaccatgtggtgcttaaacattggtgaatttggatcaatggtgagcagGTCTTTGAGAGGCTTGGACCAAGCTTATATGATTTTCTGCGGGAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGATTGCCAAACAACTGT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G02740.3 (Glycine max), 3'ss of exon 4
gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT
|||||||  | ||| | | |||| ||| ||    |  ||||   | | |       |  | | | |||  ||||||||| ||||| |  |   ||||| | |||||| ||||||||||||||||| |||||||| |||||||||| ||| |||||||| || ||||  || || || ||| ||| ||||||||| |
gtaagtatttaatttg-tgatgg-aatcat---ttccccaatttacaaataatttgggggttaagacaacggtgaatttaaatggtt--ttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAAACAACTAT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 4
gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT
|||||||  | |||   || ||     | |||  |  |||| | | ||||     ||  | ||||     ||||||||  ||||| ||     ||||| | |||||| ||||||||||||||||| |||||||| |||||||||||||| || ||||| || ||||  || || || ||| ||| |   ||||| |
gtaagtatttgattgatttgtgatggat-tgatttccccaatatacataa-----tgggggttaag----ggtgaattcaaatggttgc--aacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTAT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 4
gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT
|||||||  | |||   || ||     | |||  |  |||| | | ||||     ||  | ||||     ||||||||  ||||| ||     ||||| | |||||| ||||||||||||||||| |||||||| |||||||||||||| || ||||| || ||||  || || || ||| ||| |   |||||||
gtaagtatttgattgatttgtgatggat-tgatttccccaatatacataa-----tgggggttaag----ggtgaattcaaatggttgc--aacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTGT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G13440.2 (Glycine max), 3'ss of exon 4
gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT
|||||||  | ||| | | |||| ||| ||    |  ||||   | | |       |  | | | |||   |||||||| ||||| |  |   ||||| | |||||| ||||||||||||||||| |||||||| |||||||||| ||| |||||||| || ||||  || || || ||| ||| || |||||| |
gtaagtatttaatttg-tgatgg-aatcat---ttccccaatttacaaataatttgggggttaagacaacagtgaatttaaatggtt--ttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtacatcattagatt-atggcaattatgaactaaccaaaagagataaccccatgaagcttaaac--attggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT
|||||||  |  | |  ||  ||     |||||  |  ||      |  ||     ||  | | ||     | | |||| || ||  | | |    ||||| | ||||||||||||| | || ||||| |||||||| |||||||||| ||| ||||| || || ||||  || || || ||| ||| |   ||||| |
gtaagtatttagtcaattttgtgatgtctatgattttccccggtttgggaaatagttggggttgaattttgtggatgaacttaaaatggttgcta-cagGTATTTGAGAAGCTTGGATCGAGTTTATACGATTTTCTTCGGAAAAACAATTATCGCTCCTTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTCT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacatt----ggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT
||||||| |  |||  ||||||     | |||  |  ||||       ||     ||  | ||||   ||    | ||||||  ||||| |  |   ||||| | |||||||||||||||||||||||| |||||||| |||||||||| ||| |||||||| || ||||  || || || ||| ||| || ||||||||
gtaagtataaaattgaattatgatggct-tgatttccccaatttcacgaatattttgggggttaagactttgtggatgaattcaaatggtt--tcaacagGTGTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTACGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTGT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaa---cattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT
||||||| || | |   ||| |   || ||||  |  ||||       ||     ||  |||||||     || |||||||| |||||    |   ||||| | ||||| |||||||||||||||||| |||||||| |||||||||| ||| |||||||| ||| |||  ||||| || ||| ||| || ||||||||
gtaagtatatgactgatttacgatgat-atgatttccccaacttcatgaatattttggggcttaaaacttgttagtgaatttaaatggtc--ttaacagGTATTTGAGATGCTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGT

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|29668017|gb|CB664292.1|CB664292
EST:     TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT                         GTCTGTGAGAAGCTTGGACCA-GCTTATATGATTTTCTGCGGAAAAACAGT
genomic: TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacat ... tggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGT
EST: gi|29689119|gb|CB685394.1|CB685394
EST:     TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT                         GTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGT
genomic: TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacat ... tggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGT
   agataac  putative branch site (score: 3)
                    ttaaacatt  TA-rich tract