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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCACATCTACCACAAGCTCCTTGCCCCTCTTCTTCCTCTTCTGTTTCCTGCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtacccctttgcatcagattgatatcttgtcttttcttctgttctcctgcatctattaactgtgatttaggttgacatgataaaacctatgtatttaaatgtttcaatttcatatgatgtcaaggtacag

Basic information

species Oryza sativa
transcript LOC_Os01g68598.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68598.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G170975_T01 (Zea mays), 5'ss of exon 1
CCCACATCTACCACAAGCTCCTTGCCCCTCTTCTTCCTCTTCTGTTTCCTGCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgta-------------cccctttgcatcagattgatatcttgtct-tttcttctgttctcctgca------------tctattaactgtgatttaggttgacatgataaaacctatgtatttaaatgtttcaatttcatatgatgtcaaggtacag
||||||||||||||||||||| ||||||||||||||||  ||| || ||||||  || | |||||||  ||||  ||||  ||| ||||||| |  |||||||             || | || ||    |    |  ||||| | |||| ||| | ||    |             ||| |    ||    ||   ||    |        ||   |||| |    ||||||| | || |||  | |||      
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|88671875|gb|CI725817.1|CI725817
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAG                         ACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATATACATT
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... caaggtacagACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATATACATT
EST: gi|88962880|gb|CI025366.1|CI025366
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGGTACAG                    
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCA--TC---T-CAGgtaccccttt ... caagg
EST: gi|86908163|gb|CI300654.1|CI300654
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAG                         G
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... caaggtacag-
EST: gi|86908163|gb|CI300654.1|CI300654
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAG                         G
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... caaggtacag-
EST: gi|86908163|gb|CI300654.1|CI300654
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAG                         G
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... caaggtacag-
EST: gi|89169984|gb|CI039261.1|CI039261
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGGTACAG                    
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCA--TC---T-CAGgtaccccttt ... caagg
EST: gi|88330965|gb|CI638373.1|CI638373
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGGTACAG                    
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCA--TC---T-CAGgtaccccttt ... caagg
EST: gi|88674912|gb|CI729025.1|CI729025
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAC                         ACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATATACATT
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... caaggtacagACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATATACATT
EST: gi|88665843|gb|CI715999.1|CI715999
EST:     GCTCTTCACTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAG                         ACTATGGAGAACAATATCCTCACCAAACATTACCTGAACAACATATACATT
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... caaggtacagACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATATACATT
EST: gi|163927814|gb|EG712526.1|EG712526
EST:     GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGGTACAG                    
genomic: GCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCA--TC---T-CAGgtaccccttt ... caagg

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: 32 (upstream exon), 53 (downstream exon)
Score: 3

CCCACATCTACCACAAGCTCCTTGCCCCTCTTCTTCCTCTTCTGTTTCCTGCTCTTCAGTCATGCTCGTTGCAATCAAGGGCACCATGGCAGCATCTCAGgtaccccttt ... caaggtacagACTATGGAGAACAATATCCTCACCAAACATTACCTGAAGAACATATACATTTGCAGGAGAACATCAAG




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