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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGCCTCGGTCCAGATCAACATTGGGCATGTGGATGAGAATGGGCTGTACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatcattgtaaacttttgtttatttacatgtgcctgaatttctctttgtgaactgtctcattgctgtattgctctatttcctgcatgatcatgaa...

Basic information

species Oryza sativa
transcript LOC_Os03g46490.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g46490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G125300_T02 (Zea mays), 5'ss of exon 3
CCATGCCTCGGTCCAGATCAACATTGGGCATGTGGATGAGAATGGGCTGTACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatcattgtaaacttttgtttatttacatgtgcctgaatttctctttgtgaactgtctcattgctgtattgctct--atttcctgcatgatcatgaa
||||||||| ||||||||||||||||| ||  |||||| |||||| ||||| ||||| | |||||| ||||||||||||||||||||  ||||||||||||| |   |   ||  |  |||  |  ||||   |   ||  ||  | |     |  | |||          |   ||| |  | |  ||   || |      
CCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCCTGTATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttcatgatatgtttattgcatttgtctagcccataaaatttaaagcttgagtgtaaagcctacatgaggctttttactgtctatgtgtttcct--

upper sequence: LOC_Os03g46490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G134109_T01 (Zea mays), 5'ss of exon 3
CCATGCCTCGGTCCAGATCAACATTGGGCATGTGGATGAGAATGGGCTGTACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatcattgtaaacttttgtttatttacatgtgcctga-atttctctttgtgaactgtctcattgctgtattgctctatttcctgcatgatcatgaa-
 |||||||| ||||||||||||||||| ||  |||||| |||||| ||||||||||| | |||||||||||||||||||||||||||  ||||||||||||| ||  ||      |  |  ||  ||  | ||  |  ||        ||  |||  | ||  |        |    |   |     || ||||        
TCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCCTGTACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtc--caggatgtgatgcctacatgcaactttctactgcaattccgtgtttattgagttcacatgttggcacctgacacagtgaatgactgaatgg

upper sequence: LOC_Os03g46490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G093574_T01 (Zea mays), 5'ss of exon 3
CCATGCCTCGGTCCAGATCAACATTGGGCATGTGGATGAGAATGGGCTGTACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatcattgtaaacttttgtttatttacatgtgcctgaatttctctttgtgaactgtctcattgctgtattgctctatttcctgcatgatcatgaa
||||||||| ||||||||||||||||| ||  |||||| |||||| ||||| ||||| | |||||| ||||||||||||||||||||  ||||||||||||| ||  |   ||  |  |||  |  ||||   |   ||  ||  | |     |  | |||          |   ||| | |    |   || |      
CCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCCTGTATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagttcatgatatgtttattgcatttgtctagcccataaagtttaaagcttgagtgtaaagcctacatgaggctttttactgtctgtgtttcctgt

upper sequence: LOC_Os03g46490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G05030.1 (Glycine max), 5'ss of exon 2
CCATGCCTCGGTCCAGATCAACATTGGGCATGTGGATGAGAATGGGCTGTACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatcattgtaaacttttgtttatttacatgtgcctgaatttctct-ttgtgaactgtc--tcattgctgtattgctctatttcctgcatgatcatgaa
|||||| ||||| ||| | ||||||||||||||||||||||||||  | ||| ||||||  ||| |||| ||||||||||  || ||||| |||||||||||    ||  || | |  |||| ||||||    ||| |  |||||||| | ||||  | | |   |  ||  ||| ||  | |     ||     |  ||  |
CCATGCTTCGGTTCAGGTTAACATTGGGCATGTGGATGAGAATGGCGTCTACAATGGCCATTTCTCCACTTTTGCTCTCTGCGGCTTCATACGTGCTCAGgtctaaatttttttcactttttttttattc---tgttctggaatttctttcttgtttatttttattatttattgttttatttttgcctctatgcaagtataca

upper sequence: LOC_Os03g46490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G37700.1 (Glycine max), 5'ss of exon 2
CCATGCCTCGGTCCAGATCAACATTGGGCATGTGGATGAGAATGGGCTGTACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgta-attatcattgtaaacttttgtttatttacatgtgcctgaatttctctttgtgaactgtctcattgctgtattgctctatttcctgcatgatcatgaa
|||||||||||| ||||| |||||||| ||| |||||||||||||  | ||  |||| |  ||  |||| | |||||||||||| ||| | || || |||||  |  ||  ||  ||    ||  |||||    | ||  | | | |   || | | | || |   ||   |  |      |   |   |||   | |   
CCATGCCTCGGTTCAGATAAACATTGGCCATTTGGATGAGAATGGTATCTATAATGGTCATTTTTCCACTTCTGCTCTCTCTGGCTTCGTTCGAGCACAGgtttaccatttttcaaatacattacttattgcattatggtttactattatttagagtattggcaacttagagcttccaatgacagcacacattgcctttt-

upper sequence: LOC_Os03g46490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G15800.1 (Glycine max), 5'ss of exon 3
CCATGCCTCGGTCCAGATCAACATTGGGCATGTGGATGAGAATGGGCTGTACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatcattgtaaacttttgtttatttacatgtgcctgaatttct-ctttgtgaactgtctcattgctgtattgctctatttcctgcatgatcatgaa---
|||||| ||||| ||||||||||||||||||||||||||||||||  | ||| ||||||  ||| |||| ||||| ||||  || ||||||||||||||||||  |||  || |  |||||| ||||| | |  || |  |||||||| | ||||  | |   | |||  ||| ||  | ||    ||     |  |       
CCATGCTTCGGTTCAGATCAACATTGGGCATGTGGATGAGAATGGCGTCTACAATGGCCATTTCTCCACTTTTGCCCTCTGCGGATTCATCCGTGCTCAGgtatctattttttttcactttt-tttatattcg-gttctggaatttctgccttgtttatt--tttattattgttttattttagcctctatgcaagtaacccttt

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|89175738|gb|CI042759.1|CI042759
EST:     ACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAG                         GGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
genomic: ACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatca ... atttcgacagGGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
EST: gi|88556380|gb|CI486701.1|CI486701
EST:     ACGATGGCCGCTTCACCACGTTTGCTCTCTGTGGGTTCATCCGTGCTCAG                         GGAGACNCCGACAGTNCTCTGGATAGGCTGTGGCAGAAGAGGAAGNCTGAG
genomic: ACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatca ... atttcgacagGGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
EST: gi|88991865|gb|CI035003.1|CI035003
EST:     TGGGTTCATCCGTGCTCAG                         GGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
genomic: TGGGTTCATCCGTGCTCAGgtaattatca ... atttcgacagGGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
EST: gi|88348854|gb|CI653898.1|CI653898
EST:     ACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAG                         GGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
genomic: ACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatca ... atttcgacagGGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
EST: gi|88490968|gb|CI428240.1|CI428240
EST:     ACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAG                         GGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
genomic: ACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatca ... atttcgacagGGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
EST: gi|88546853|gb|CI477105.1|CI477105
EST:     ACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAG                         GGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
genomic: ACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatca ... atttcgacagGGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
EST: gi|112787237|gb|EE592316.1|EE592316
EST:     ACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAG                         GGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG
genomic: ACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatca ... atttcgacagGGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAG

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: 66 (upstream exon), 46 (downstream exon)
Score: 18

CCATGCCTCGGTCCAGATCAACATTGGGCATGTGGATGAGAATGGGCTGTACGATGGCCGCTTCACCACGTTTGCTCTCTCTGGGTTCATCCGTGCTCAGgtaattatca ... atttcgacagGGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAGGTCAAGCAGCAGTAGATGTTGCTACTAGTTTTACCTGTAAGAACTCGTT




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