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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTAGGGTTTCCTCCCAATCCCCTCCATGGCCAAGACCAAGCAGGGCAAGAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAGgtacgggccgcttctcgctttcttcatttccggccaagatttgggtctctttagtttcttcatgagggtttgtggtggtggtgtggaag

Basic information

species Oryza sativa
transcript LOC_Os09g21770.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G091265_T06 (Zea mays), 5'ss of exon 2
CTCTAGGGTTTCCTCCCAATCCCCTCCATGGCCAAGACCAAGCAGGGCAAGAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAGgtacgggccgcttctc-gctttcttcatt---tccggccaagatttgggtctctttagtttcttcatgagggtttgtggtggtg-gtgtggaag------
                    | |   |||||||||||| ||||| || |||  ||| |||||  |||| |||||||||||||||| |||| | |||||||||| |  | ||   || |   |||| ||     ||| |      |   ||||    | ||      ||| |  |  || || |  | ||| |        
-----------------CCCCTCTGTCATGGCCAAGACGAAGCAAGGGAAGCGGGATGTCGACGCCTATACCATCAAGGGCACCAACAAGGTGGTCCGAGgtaagccctgccagtccgtgctcttgatcgagcccgtcgcgtgctctagtctaaagatttgagctctgacgtctcttgttgctctgcgtgaaccgtgaag

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G091265_T05 (Zea mays), 5'ss of exon 1
CTCTAGGGTTTCCTCCCAATCC----CCTC---CATGGCCAAGACCAAGCAGGGCAAGAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAGgtacgggccgcttctc-gctttcttcatt---tccggccaagatttgggtctctttagtttcttcatgagggtttgtggtggtg-gtgtggaag------
       |||| ||| ||||||    ||||   |||||||||||| ||||| || |||  ||| |||||  |||| |||||||||||||||| |||| | |||||||||| |  | ||   || |   |||| ||     ||| |      |   ||||    | ||      ||| |  |  || || |  | ||| |        
-------GTTTTCTCGCAATCCAGCCCCTCTGTCATGGCCAAGACGAAGCAAGGGAAGCGGGATGTCGACGCCTATACCATCAAGGGCACCAACAAGGTGGTCCGAGgtaagccctgccagtccgtgctcttgatcgagcccgtcgcgtgctctagtctaaagatttgagctctgacgtctcttgttgctctgcgtgaaccgtgaag

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv12s0059g01180.t01 (Vitis vinifera), 5'ss of exon 1
CTCTAGGGTTTCCTCCCAATCCCCTCCATGGCCAAGACCAAGCAGGGCAAGAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAGgtacgggccgcttctcgctttcttcatt------tccggccaagatttgggtctct--ttagtttcttcatgagggtttgtggtggtggtgtggaag----
 |||  |     ||  ||| ||| | |||||||||||||||||  ||||| |||||| | || || ||||||||||||||||||| |||| | ||  |||||   |||  ||| |   ||| |   ||      | |       || ||  |||||  ||  | | || ||     |    | |||| |    ||      
TTCTTTGTGAATCTTACAACCCCATTCATGGCCAAGACCAAGCCTGGCAAAAAGGACTTGGATTCTTACACCATCAAGGGCACCAACAAGGTTGTTAGAGgtg-aggcttcttttttttttttctgttggcttgtgcatgtggaatctgaatctctggtttttgttttgatttacctgctggttggttgctccgagaactg

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|58601090|gb|CK011618.1|CK011618
EST:     GAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAG                         TGGGGGATTGCGTGCTGATGC-GGNGTCGGACACGGAGAAGGCGCCGTACG
genomic: GAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAGgtacgggccg ... ggtgtggaagTGGGGGATTGCGTGCTGATGCGGGCGTCGGACACGGAGAAGGCGCCGTACG
EST: gi|33663380|gb|CF294347.1|CF294347
EST:     GAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAG                         TGGGGGATTGCGTGCTGATGCGGGCGTCGGACACGGAGAAGGCGCCGTACG
genomic: GAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAGgtacgggccg ... ggtgtggaagTGGGGGATTGCGTGCTGATGCGGGCGTCGGACACGGAGAAGGCGCCGTACG
EST: gi|66916749|gb|CX103597.1|CX103597
EST:     GAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAG                         TGGGGGATTGCGTGCTGATGCGGGCGTCGGACACGGAGAAGGCGCCGTACG
genomic: GAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAGgtacgggccg ... ggtgtggaagTGGGGGATTGCGTGCTGATGCGGGCGTCGGACACGGAGAAGGCGCCGTACG
EST: gi|86851116|gb|CI311334.1|CI311334
EST:     GAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAG                         TGGGGGATTGCGTGCTGATGCGGGCGTCGGACACGGAGAAGGCGCCGTACG
genomic: GAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAGgtacgggccg ... ggtgtggaagTGGGGGATTGCGTGCTGATGCGGGCGTCGGACACGGAGAAGGCGCCGTACG
EST: gi|29638118|gb|CB643127.1|CB643127
EST:     GAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAG                         TGGGGGATTGCGTGCTGATGCGGGCGTCGGACACGGAGAAGGCGCCGTACG
genomic: GAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAGgtacgggccg ... ggtgtggaagTGGGGGATTGCGTGCTGATGCGGGCGTCGGACACGGAGAAGGCGCCGTACG

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: 70 (upstream exon), 64 (downstream exon)
Score: 24

CTCTAGGGTTTCCTCCCAATCCCCTCCATGGCCAAGACCAAGCAGGGCAAGAAGGACGTCGAATCCTACACCATCAAGGGCACCACCAAGATCGTCCGAGgtacgggccg ... ggtgtggaagTGGGGGATTGCGTGCTGATGCGGGCGTCGGACACGGAGAAGGCGCCGTACGTGGGGAGGGTGGAGAGGCTGGAGACGGACGGGAGGGGGAGCGTGCGGGT




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