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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCACATCTACCACAAGCTCCTTGCCCCTCTTCTTCCTCTTCTGTTTCCTGCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtacccctttgcatcagattgatatcttgtcttttcttctgttctcctgcatctattaactgtgatttaggttgacatgataaaacctatgtatttaaatgtttcaatttcatatgatgtcaag

Basic information

species Oryza sativa
transcript LOC_Os01g68598.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68598.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G170975_T01 (Zea mays), 5'ss of exon 1
CCCACATCTACCACAAGCTCCTTGCCCCTCTTCTTCCTCTTCTGTTTCCTGCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgta-------------cccctttgcatcagattgatatcttgtct-tttcttctgttctcctgca------------tctattaactgtgatttaggttgacatgataaaacctatgtatttaaatgtttcaatttcatatgatgtcaag
||||||||||||||||||||| ||||||||||||||||  ||| || ||||||  || | |||||||  ||||  ||||  ||| ||||||| |  |||||||             || | || ||    |    |  ||||| | |||| ||| | ||    |             ||| |    ||    ||   ||    |        ||   |||| |    ||||||| | || |||  | |||
CCCACATCTACCACAAGCTCCCTGCCCCTCTTCTTCCTTCTCTCTTGCCTGCTTATCGGCCATGCTCTCTGCAGCCAAGCCCACAATGGCAGAACATCAGgtattcaggcccttcccctccttacacacaaaccctgacttgtttatttcctctttccttgcacgagactagtcccttctttcttttggcccttgctttttgtttgctttcactgcttattcactcatttcaatctaatttgagttgaag
















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|88330965|gb|CI638373.1|CI638373
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAG                         GTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... tgatgtcaagGTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
EST: gi|86908163|gb|CI300654.1|CI300654
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAG                         GTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... tgatgtcaagGTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
EST: gi|88674912|gb|CI729025.1|CI729025
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTC--                         --AC--ACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... tgatgtcaagGTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
EST: gi|163927814|gb|EG712526.1|EG712526
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAG                         GTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... tgatgtcaagGTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
EST: gi|88671875|gb|CI725817.1|CI725817
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCA--TC--                         -T-CAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... tgatgtcaagGTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
EST: gi|88962880|gb|CI025366.1|CI025366
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAG                         GTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... tgatgtcaagGTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA
EST: gi|89169984|gb|CI039261.1|CI039261
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAG                         GTACAGACTATGGAGAACGATATCCTCACCGAACATTACCTGAAGAACATA
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... tgatgtcaagGTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATA

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: 68 (upstream exon), 65 (downstream exon)
Score: 3

CCCACATCTACCACAAGCTCCTTGCCCCTCTTCTTCCTCTTCTGTTTCCTGCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... tgatgtcaagGTACAGACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATATACATTTGCAGGAGAACATCAAG




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