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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCTTGGTAACATCCAAGCGATGCTTCTTGTTGGCTGGCGACTATGCAAGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaatactagctggcaaaggctgcctttcttcctctgtaactagaactttgtgttcctttgatatatcagtgattttaacttttgattcctcgctcccatttag

Basic information

species Oryza sativa
transcript LOC_Os01g06600.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G862219_T03 (Zea mays), 5'ss of exon 10
AATGCTTGGTAACATCCAAGCGATGCTTCTTGTTGGCTGGCGACTATGCAAGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaatactagctggcaaaggctgcctt--tcttcctctgtaactagaactttgt-gttcctttgata---tatcagtgattttaacttt----tgattcctcgctcccatttag-----------
 ||||| |||||| ||||  ||||| | || || |||||||| || |||||||| || ||||| ||||||||||| || || || |||||  |||||||||| |||    |  |     |    ||||| |     | ||    |     | ||||  || | ||  | ||     |||   || |  |  || |    |||   | || | | | |              
GATGCTCGGTAACGTCCAGTCGATGGTCCTCGTCGGCTGGCGTCTCTGCAAGCTCTACGAGTCGGGGAAAATGACGCCGGGCCACGCTAGCCTAGGGAAGgtctgtagtgtgttttgcagactcggctggcacggccgtctctcgctttgataactcagtcgctcgctcgacgctttattcctggtcctggctgtgatgtgacgacgcgtttctaatgtttttttgtttag

upper sequence: LOC_Os01g06600.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA18G43240.1 (Glycine max), 5'ss of exon 11
AATGCTTGGTAACATCCAAGCGATGCTTCTTGTTGGCTGGCGACTATGCAAGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgt--ttgtgaaatactagctggcaaag--gctgcctttcttcctctgtaactagaactttgtgttcctttgatatatcagtgattttaacttttgattcctcgctcccatttag------------------
|||||| |||||||| ||||| ||| |||||||||| ||||| || |||||| | ||||||   || |||||||||||||| |||||||| || ||||||||  ||   ||  ||    |  ||||      |    | |  |   ||||  | | |||| ||||   |   | | |   || |  ||| ||  | |   |  ||     | |                   
AATGCTAGGTAACATTCAAGCAATGATTCTTGTTGGTTGGCGCCTGTGCAAGTTGTATGAGAGTGGTAAAATGACACCAGGTCATGCTAGCTTGGGGAAGgtaattcctaaccacctattcacaaaataaaagaaaatatcaccaagtaataaaagctttatgttggct-attttgttgttgttaataaattgaggtagataactggtgataaaatgtcaatcatgtttcag
















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|29658082|gb|CB654357.1|CB654357
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|86504925|gb|CI147558.1|CI147558
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGCCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGNTGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|33683999|gb|CF312238.1|CF312238
EST:     GCTTTATGAGTCAGGGAAAATGACACCAGGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATT
genomic: GCTTTATGAGTCAGGGAAAATGACACCA-GGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTT-CCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATT
EST: gi|44666104|gb|CR279538.1|CR279538
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGATGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|4715706|gb|AU056822.1|AU056822
EST:     GCTTTATGAGTCAGGGAAAATGACCACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: GCTTTATGAGTCAGGGAAAATGA-CACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|7839222|gb|AU090633.1|AU090633
EST:     CTTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: C-TTTATGAGTCAGGGAAAATGACACCAGGGCATGC-TAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|29668419|gb|CB664694.1|CB664694
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|29660317|gb|CB656592.1|CB656592
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|29660291|gb|CB656566.1|CB656566
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG

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: 58 (upstream exon), 52 (downstream exon)
Score: 13

AATGCTTGGTAACATCCAAGCGATGCTTCTTGTTGGCTGGCGACTATGCAAGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG




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