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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGTCTAGCTGAAAAGACAGCTGTTTTGTTTACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTGgtatttgctctcatcctagtatcccccctcctctctatcctcccctgtctgatcttatttcttgatctttatatccttgaag

Basic information

species Oryza sativa
transcript LOC_Os01g43030.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43030.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G047093_T01 (Zea mays), 5'ss of exon 16
GTTGGTCTAGCTGAAAAGACAGCTGTTTTGTTTACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTGgtatttgctctcatcctagtatcccccctcctctctatcctcccctgtctgatcttatttcttgatctttatatccttgaag
||||| || || || ||||| ||||| |||||||| || || || ||||| ||||||||||| |||||||||||||||||||||||| ||||||    |   |     |  ||   | | | |   |   ||| |||| | | | |||| |  |||||  | |||
GTTGGCCTTGCCGAGAAGACTGCTGTCTTGTTTACAAAAGATGGTGATCAACACAATAATCTTCATGACATGCAGTGCATGTGgtatgtgctctttctcctctgctatctatctgttatgttcattc---tct-atctaactacatgatat--atatcacttaag

upper sequence: LOC_Os01g43030.1 (Oryza sativa), 5'ss of exon 16
lower sequence: EFJ27872 (Selaginella moellendorffii), 5'ss of exon 15
-----------------GTTGGTCTAGCTGAAAAGACAGCTGTTTTGTTTACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTGgtatttgctctcatcctagtatcccccctcctctctatcctcccctgtctgatcttatttcttgatctttatatccttgaag
                 ||||  || || || || || || |   | || || ||||| |||||||| ||||| |||||  ||||||||||||||||||||||  |  |       | || |  |   | ||||  |    | |   |  |                               
TGTTGCAAGCCGACCAGGTTGAACTTGCCGAGAAAACTGCCGCGCTCTTCACCAAGGATGGCGATCAACACAACAATCTGTATGACATGCAGTGCATGTGgtaagtatttg---ttttgtgtttcagatgctctaaaagtcctcgccttag-------------------------------

upper sequence: LOC_Os01g43030.1 (Oryza sativa), 5'ss of exon 16
lower sequence: EFJ36800 (Selaginella moellendorffii), 5'ss of exon 15
-----------------GTTGGTCTAGCTGAAAAGACAGCTGTTTTGTTTACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTGgtatttgctctcatcctagtatcccccctcctctctatcctcccctgtctgatcttatttcttgatctttatatccttgaag
                 ||||  || || || || || || |   | || || ||||| |||||||| || || |||||  ||||||||||||||||||||||  |  | |     | || |      | ||||  |    | |   |  |                               
TGTTGCAAGCCGACCAGGTTGAACTTGCCGAGAAAACTGCCGCGCTCTTCACCAAGGATGGCGATCAACATAACAATCTGTATGACATGCAGTGCATGTGgtaagtatttt---ttttgtgttttagatgctctaaaagtcctcgccttag-------------------------------

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|29635309|gb|CB640318.1|CB640318
EST:     ACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTG                         GTATGAGCTTGCTTCTGGTGAGAGTTACTATCGTCAAGGTGATCTCGGCAG
genomic: ACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTGgtatttgctc ... atccttgaagGTATGAGCTTGCTTCTGGTGAGAGTTACTATCGTCAAGGTGATCTCGGCAG
EST: gi|3761437|gb|C98685.1|C98685
EST:     ACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTG                         GTATGAGCTTGCTTCTGGTGAGAGTTACTATCGTCAAGGTGATCTCGGCAG
genomic: ACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTGgtatttgctc ... atccttgaagGTATGAGCTTGCTTCTGGTGAGAGTTACTATCGTCAAGGTGATCTCGGCAG
EST: gi|29643975|gb|CB648982.1|CB648982
EST:     ACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTG                         GTATGAGCTTGCTTCTGGTGAGAGTTACTATCGTCAAGGTGATCTCGGCAG
genomic: ACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTGgtatttgctc ... atccttgaagGTATGAGCTTGCTTCTGGTGAGAGTTACTATCGTCAAGGTGATCTCGGCAG
EST: gi|29635310|gb|CB640319.1|CB640319
EST:     ACTAAGGACGGCGATCAGCTCAATAATCTCCATGACATGCAGTGCATGTG                         GTATGAGCTTGCTTCTGGTGAGAGTTACTATCGTCAAGGTGATCTCGGCAG
genomic: ACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTGgtatttgctc ... atccttgaagGTATGAGCTTGCTTCTGGTGAGAGTTACTATCGTCAAGGTGATCTCGGCAG

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: 73 (upstream exon), 71 (downstream exon)
Score: 16

GTTGGTCTAGCTGAAAAGACAGCTGTTTTGTTTACTAAGGACGGCGATCAGCACAATAATCTCCATGACATGCAGTGCATGTGgtatttgctc ... atccttgaagGTATGAGCTTGCTTCTGGTGAGAGTTACTATCGTCAAGGTGATCTCGGCAGGGCTCTCAAAAATTTCTTGGCTGTTGAGAAGCATTATGCTGACATGACT




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