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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcag

Basic information

species Oryza sativa
transcript LOC_Os05g03820.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 8
CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaa-acctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcag
|||||| ||||| |||||||| || || ||  |||||||||| |||||||| || || ||||||||||||||||  |||    || |    | ||  ||    |||||||||   |      | ||| ||||||||   |||||| ||  |   | | ||           ||| |  |||||  | |    |   | | |                         
CCATATCTGGACAGATACTGATAATAATCGTGCAGGGATGCTCCCTTTTGTCTTTGACGACTCATTTGGgttagc-tctccttttga----actc--cctctctcccccacctttagtgtcagtaatttgattgaattgcctcatatttcctttaaagatgaagcggtcctaatcatagtttctgtttg---ggggtgcag-------------------------

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 8
CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcag
|||||| ||||| ||||| || ||||||||  |||||||||| |||||||| || ||  ||||||||||||||| || | |  ||   ||       |||   |||||||||  ||   |  | ||| |||||||   | ||||| |    |||||| ||||  |  |||||                      || || |||||||||  |||    | |||||
CCATATCTGGACAGATACCGATAACAACCGTGCAGGGATGCTCCCTTTTGTCTTTGACAACTCATTTGGgttagcatttct--tttgaact------ccccactcccccaccttgagtgccagtaatttgattgattgcttcattctctttaaagatgttttcaatgtgaaa--------------------gcatcctaattatagtttcttttgggggtgcag

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 9
CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatctataattcataccattcgaccctcttcccccacccagaacact--ggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcag
||||||||||||||||||||| ||  ||||| |||| ||||| |||||||| || |||||||| ||||||| ||    | |  |    |  ||       |    |   | |            ||  | ||| |  |  | ||||| |   |      |||| | | | |                                                        
CCATATTTGGACTGATACTGATAAGGACCGCACAGGCATGCTGCCTTTTGTTTTTGATGACTCTTTTGGgtaagagattct--tctgaattatgaagaattaagactgaagctgttgtttctaagccttttgactctaggcttcattgttttcctgtgaatttaaaagaag--------------------------------------------------------

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA08G01750.1 (Glycine max), 5'ss of exon 9
CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttag---tatctataattcat--accattcgaccctcttcccccacccagaacactggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcag
||||||||||||||||||||||||  | ||| |||| ||||| |||||||| || |||||||| ||||||| ||   | | | | | | ||  |  |||    |     |          ||  ||     | ||||   |  | ||| | |   |      |||| | | | |                                                        
CCATATTTGGACTGATACTGACAAGGATCGCACAGGCATGCTGCCTTTTGTTTTTGATGACTCTTTTGGgtaagagatttttctgaattatgaataattaagactgaaactattgtttctaagcct-----tctgatgctaggcttcactgttttcgtgtgaatttaaaagaag--------------------------------------------------------

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 9
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 9
CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcag
||| || ||||| || ||||||||  ||||| |||| ||||| || ||||| ||||||||||| ||||||| |||||| ||  || || | ||   |  |  || |   ||   |     |||   ||  ||   || | ||       |||| ||   | | | |      |                                                    
CCACATATGGACAGACACTGACAAGGACCGCACAGGAATGCTACCATTTGTTTTCGATGACTCTTTTGGgtgagtatcgatgtttaat-ctatgaaaaacaattacattacattgg---ttggtt-tggtatgagaagcttctcaaaaaccaatgactctgtct-cgcattcttg--------------------------------------------------

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|55411431|gb|CV723807.1|CV723807
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|11442624|gb|BF430527.1|BF430527
EST:     GCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|58663354|gb|CK052040.1|CK052040
EST:     GACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|58695197|gb|CK083884.1|CK083884
EST:     TGACTCA-TTGG                         A-TTGAGCGATATGTGGACTACGCATTA-ATGTCCCGATGTATTTTGTCTA
genomic: TGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|58658531|gb|CK047211.1|CK047211
EST:     GACAACAAACGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         GTTTGAGCGATATGTGGACTATGCATT
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATT
EST: gi|218498945|gb|FG948066.1|FG948066
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|58663415|gb|CK052101.1|CK052101
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|218500233|gb|FG945122.1|FG945122
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTAAGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|33676123|gb|CF304362.1|CF304362
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|29679436|gb|CB675711.1|CB675711
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         GTTTGAGCGATATGTGGACTATGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA

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: 69 (upstream exon), 74 (downstream exon)
Score: 111

CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG




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