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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAATTATATGGGCATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttcttatgttatattcatccttgtagattcatgaccatccttatttatacgttaactaagccacagttcatcgtgatggataatattactctgacactttccatgtag

Basic information

species Oryza sativa
transcript LOC_Os02g44510.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g44510.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM5G846198_T02 (Zea mays), 5'ss of exon 5
ATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAATTATATGGGCATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctta-tgttatattcatc--cttgtag---attcatgaccatc-cttatttatacgttaactaagccacagttcatcgtgatggataatattactctgacactttccatgtag
||||||||||||||| ||||| ||||||||||||||  | |||||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||||    |    || | |  | |||  |||||      | ||   ||||| ||  ||| ||    |   ||   |     |  |||  |  | | | || |  ||| ||| ||  |||||
ATGGCCAACATGGTTACACAAGCAGAAAGAGAAGCAAAGGATTATATGGGCATATAAGATCTTATTTCTGGATGTCATTTTTCCACTTTCACTGAGGAAGgtaccccccccctgctgttctaatcagcttgtgatgtgtgcaattccatcactcttttttagaacattaaaataatctgaccacgttctaaaaacttttcccatgatactctctgtgtag

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA08G20020.1 (Glycine max), 5'ss of exon 32
ATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAATTATATGGGCATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtat------tttcttatgttatattcatccttgtagattcatgaccatccttatttatacgttaactaagccacagttcatcgtg----atggataatatt-actctgacactttccatgtag---------------------------------
|||||| ||||||||||| || |||||||| ||||||||||| || |||||||| || || || || || |||||||| ||||| |||||  ||  ||||||||      |||||| |  |  ||  |  |   |   || ||     | ||  | |  ||  | | |  | ||  ||    | ||    |   ||   ||| ||   ||  ||    ||| |                                  
ATGGCCTACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAATAATTTGGGCATATAAAATTTTATTCCTTGATGTCATCTTTCCCCTTTCCTTGGAGAAGgtatcatgattttcttcttctgcatcaaatcccatgcttttatt-ttgttctcttctgcactcttaat--gtcatggtgtcacatgcaccacacatggcattgacaaggatgctggtaatgaaaagaaaatttttacttaaaaatttgtgtttgcag

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA05G30230.1 (Glycine max), 5'ss of exon 33
ATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAATTATATGGGCATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttcttatgttatattcatccttgtagattcatgaccatccttatttatacgttaactaagccacagttcatcgtgatggataatattactctgacactttccatgtag
 ||||| ||||||||||| || |||||||| ||||||||||| || |||||||| || ||||| || ||||||||||| || || |||||  ||  |||||||   ||  |  || |  |  | | |  || | |||| |  |   | ||| |   ||    ||   |   ||||  ||    ||  | |  ||||| | | | |        
GTGGCCCACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAATAATTTGGGCATATAAAATCTTATTCCTAGATGTCATTTTCCCCCTTTCTTTGGAGAAGgta---tcacagtttcttcttctgcatcaagttccatg-cttttggtttttgtcttttgcacaattaat--ttcaatgt--cagactacacaactcttagaatgttgg-----

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA08G13400.1 (Glycine max), 5'ss of exon 35
ATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAATTATATGGGCATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttcttatgttatattcatccttgtagattcatgaccatccttatttatacgttaactaagccacagttcatcgtgatggataatattactctgacactttccatgtag----------------------------------------------------
 ||||| ||||||||||| || |||||||| ||||||||||  || |||||||| || ||||| || ||||||||||| || || |||||  ||  |||||||      | | || |  |  | | |  || | ||||    |  || ||| |   ||    |      | ||||  || |      | | | || |||||      ||| ||                                                    
GTGGCCCACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAAGAATTTGGGCATATAAAATCTTATTCCTAGATGTCATTTTCCCCCTTTCTTTGGAGAAGgtaccacagtttcttcttcttctgcatcaagttccatg---ctttttgtttttgtcttttgcactattaatttcaatgtcacactacacaatgctgtgacaaagataatgaagaattaaaatcccttacaggaaaatctgtctaaaatctaccaatattatgcag

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 32
ATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAATTATATGGGCATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttcttatgttatattcatccttgtagattcatgaccatccttatttatacgttaactaagccacagttcatcgtgatggataatattactctgacactttccatgtag
||||||  | |||||||| ||||||||||| ||||| |||||||| ||||| ||||| ||  | || || |||||||||||||| || ||| ||   ||||||     | ||  ||| |||||   |     ||| || | ||  | ||   |     |  | |     || |  |||  |||  |  | |                      
ATGGCCGTCCTGGTTGCATAAACAGAAAGAAAAGCAACGAATTATTTGGGCCTACAAAATTCTTTTCCTTGATGTCATATTTCCTCTCTCATTGGAAAAGgtacaga-tgatcatattttcatttct-----ttcttg-cgattttgatgcttggaagatgtcactataaggtattcgacatgtgttctgtag--------------------

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 5'ss of exon 33
ATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAATTATATGGGCATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtatttt---cttatgttatattcatccttgtagattcatgaccatccttatttatacgttaactaagcca---cagttcatcgtg-atggataatattactctgacactttccatgtag--------
|||||||||||||||||| || |||||||| |||||||||||||| |||||||| || ||| |||| || ||||| || || ||||||||  ||   |||||| |||    | | ||  |  | |  | |  ||           | |   || || | |   || |  |    ||  |   | || ||| |||   || | |   |  |     ||||         
ATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAATTATCTGGGCATATAAAATCCTGTTCCTTGATGTTATTTTCCCACTTTCTTTGGAAAAGgtaatttggtttcaagtcctgcttaaacatagagtgctgccttgtttccatttcattcatcttcttatgctttccaacttcacatgcatgtatagcttttcacaatctatcaatgtgtatatctgcag

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|58609426|gb|CK037459.1|CK037459
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58658861|gb|CK047541.1|CK047541
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58678387|gb|CK067074.1|CK067074
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|218480649|gb|FG956875.1|FG956875
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58692422|gb|CK081109.1|CK081109
EST:     CATA-TTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58605088|gb|CK033121.1|CK033121
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58687397|gb|CK076084.1|CK076084
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACT
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTA-TTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACT
EST: gi|428777|gb|D24933.1|D24933
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58658473|gb|CK047153.1|CK047153
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG

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: 74 (upstream exon), 70 (downstream exon)
Score: 60

ATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAATTATATGGGCATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTGTATGACATGAATCTGAAGGGTCGTCCCCTTGCGTATACTCCATTCTGCG




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