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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttcttgttcaccatgctaatatgttgaaaacttgtatactttcttatacgtcttgtttactaacctgttccatttttcag

Basic information

species Oryza sativa
transcript LOC_Os02g11830.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttctt-gttcaccatgctaatatgttgaaaacttgtatactttcttatacgtcttgttta-----ctaacctgttccatttttcag
||||||||||||||||||||| |||||||||||||| |||||| |||| ||||||||||||||||||||||||||||||| | ||||||||||||||||||||  ||| ||||||||||||  |  | || ||||||    |  || |||||    || | |      || | ||||| ||||||| ||
AGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAGCATAATGAAATCCAAACTGTTAATATCAAGAGTGTTGGTGCAGACAATGAGgttgcctttgttcaccatgctgctgcgatgtaaacttagtaagcttgttataaagtttctctgtggtccttaactgtttcattttttag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttctt-gttcaccatgctaatatgttgaaaacttgtatactttcttatacgtcttgttta-----ctaacctgttccatttttcag
||||||||||||||||||||| |||||||||||||| |||||| |||| ||||||||||||||||||||||| ||||||| | ||||||||||||||||||||  ||| ||||||||||||| |||| || ||||||    |  || ||||| |  || | |      || |  |||| ||||||| ||
AGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAGCATAATGAAATCCAAACTGTTAACATCAAGAGTGTTGGTGCAGACAATGAGgttgcctttgttcaccatgctattatgatgtaaacttagtaagcttgttataaggtttctctgtggtccttaattgtttcattttttag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttcttgttcaccatgctaatatgttgaaaacttgtatactttctta-tacgtcttgtttactaacctgttccatttttcag------------------------
||||||||| ||||||||||||| ||| || ||||| || ||||| || ||||||||||| || ||||| ||||| || | | | || |||||    ||||| |     |     || |   | | ||       |||||| |||   |  | |   |||| | |   || |    ||  | |                         
AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggc-tctgttattcctttttttttttgggctgtataatttgcgagcaagaagtgttaagttctctttatttttagtgacatgtgcaagtactatgcttcttag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgt------tttcttgttcaccatgcta-----atatgttg-----aaaacttgtatactttcttatacgtcttgtttacta---acctgttccatttttcag
||| ||||| ||||||||||||| |||||| ||||| || ||||| || ||||||||||| || ||||| ||||| || | | | || |||||    |||||      | | || ||||   |  |      |||  |||     || |  |||  | ||   | ||  | | ||    |    |  |  |    || | ||
AGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctattattcatttttttggctgtataatttgcgagcaagaagtgttaagttctctttatttttagtgagatgtgtaagtactatgcttcttag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 10
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttt---tcttgttcaccatgctaatatgttga---aaacttgtatactt-tcttatacgtcttgtttactaacctgttcc-atttttcag-----
| ||||||| |||||||||||||  |  ||||||||||||||| | || ||||||||||| |||||||  || ||||| | ||||||||||||  | |||||      | |  |    |  || |||   ||    |   |    || || | || |   | | |  |  | |   |||    || |  |      
AATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAGCATAATGAAATTCAAACTGCAAACATCAAAAGTATTGGTGCAGATTACGAGgtacacgccatacttgtaactcttatactgtggcataggatgacctatttgttttttgtttttcgcctgatgataagtttttgttctgtaacttag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 10
lower sequence: AT3G15980.5 (Arabidopsis thaliana), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttt---tcttgttcaccatgctaatatgttgaaaacttgtatactttcttatacgtcttgtttactaacctgttccat--ttttcag
| ||||||| |||||||||||||| || ||||||||||||||| | || ||||||||||| ||||| |  || ||||| | |||||||||||   | ||||| |   || |  |    |  ||  |||  ||  |      |  ||   | |  |  ||  ||   |   |||    ||  |||| ||
AATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAGCATAATGAAATTCAAACCGCAAACATCAAAAGTATTGGTGCAGGTTACGAGgtctagctcctaattgtaactcttgtattctggcatgggaaaacctgcgtgactcagctatttatttgtactgcctgatgattttaag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 10
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttt---tcttgttcaccatgctaatatgttg-------aaaacttgtatacttt-----cttatacgtcttgtttactaacctg----ttccatttttcag------
| ||||||| |||||||||||||| || ||||||||||||||| | || ||||||||||| ||||| |  || ||||| | |||||||||||   | ||||| |   || |  |    |  ||  |||  ||       ||||| ||  |   |       ||||  ||  ||  |  | |  |     || ||| | ||        
AATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAGCATAATGAAATTCAAACCGCAAACATCAAAAGTATTGGTGCAGGTTACGAGgtctagctcctaattgtaactcttgtattctggcatgggaaaacctgcgtgactcagctatttatttgtactgcctgatgattttaagctttcatctctctaccttag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttt----tcttgttcaccatgctaatatgttgaaaacttgtatactttcttatacgtcttgtttactaacctgttccatttttcag-----------------
||| ||||| || || ||||||| |||||||||||| |||||| | || ||||||||||| || ||||| ||||| |||| | | || |||||   ||||||||    |    |||| | |  |   || |||   || || | | |      || ||      | || |    |  ||||| |                    
AGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAGCATAATGAAATTCAGACTGTGAATATAAAGAGTGTGGGAGCAGATTTTGAGgtttgaacttaaattcagcttattctcattttggttacatg-acattgaagcttaagtgagaaatccttaaggttcacatttctttcttgccatgccttctcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S79_180V6.2 (Physcomitrella patens), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgtt-------ttcttgttcaccatgctaatatgttgaaaacttgtatactttcttatacgtcttgtttactaacctgttccatttttcag------------------------------------------------------------------------------
 |  || ||||||||||||||  | ||||| |||||||||||| ||||||| |||||||| || ||||| ||| ||||| |  ||||||| ||    |||||         || |||| |  |     ||      |||  | ||    ||| || ||    || ||| ||   |  |   | || |||                                                                               
GGCACCAGTTGCTAGCATGGATGGTAGTGGTAAAATCATATGGGCAAAACACAATGAAATACAGACTGTCAATGTCAAGGCAGTTGGTGCTGATTTCGAGgtggcgcctactcctgtttaaaaattagattcaaataaagttagttgtatttgttttatactttctttcctgtgcaatgttagttatcattagctatatttagaactatcatgtagtaatatcaaataactgaagctttttcatgtttttatttttatttttgtgcag

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|300215876|gb|HO088502.1|HO088502
EST:     ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAG                         ATTGCAGATGGTGAACGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGT
genomic: ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttcttgt ... catttttcagATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGT
EST: gi|29680637|gb|CB676912.1|CB676912
EST:     ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAG                         ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGT
genomic: ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttcttgt ... catttttcagATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGT
EST: gi|29671007|gb|CB667282.1|CB667282
EST:     ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAG                         ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGT
genomic: ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttcttgt ... catttttcagATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGT
EST: gi|29613910|gb|CB618923.1|CB618923
EST:     ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAG                         ATTGCAGATGGCGAGCGCTTACCCTTGGCTGTGAAGGAGTTGGGAACCTGT
genomic: ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttcttgt ... catttttcagATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGT

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: 75 (upstream exon), 74 (downstream exon)
Score: 16

AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttcttgt ... catttttcagATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA




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