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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGGAATCCAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattaccagatttgatcttatggacatgattgaccaatgaatattatatatgtccaacatctgttattttctgctgattggaggactgttaaacactcacttatttaatctttgatgcattaaacag

Basic information

species Oryza sativa
transcript LOC_Os03g61810.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G840909_T02 (Zea mays), 5'ss of exon 2
TTGTGGAATCCAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattatt---------------accagatttgatcttat---ggacatgattgacca-atgaatattatatatg----------tccaacatctgttattttctgctgattggagg-----actgttaaaca---ctcacttatttaatctttgatgcattaaacag
||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||||   |||               || | | |  || || |   |  |    || | |  ||| ||   ||  | |          | |||| | ||   |  | | |  | ||         ||||| ||| |   ||  ||||||| | ||||| |  || ||||||
TTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtgacattgttgcttcctcgtccactaaactctatattgtcttgtccccatttcatcgcatgcatggcattcaagattcaactaatacaacctatgcattcctgtacacactgttattccttactgtgaaaaaggacttgcttatttgagctttggtttatcaaacag

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA17G04720.1 (Glycine max), 5'ss of exon 1
----------------------------------------TTGTGGAATCCAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattaccagatttgatcttatggacatgattgaccaatgaatattatatatgtccaacatctgttattttctgctgattggaggactgttaaacactcacttatttaatctttgatgcattaaacag
                                        |||||||| | ||||| |||||  ||||||| ||| | || |||||||||||||||||||||| |  | |   ||   |  | |      |  |||  |||||  | |  |||  ||    |||  | |  ||| |  |||||         ||  |  |   |||||||| |                  
TATTTATGTTTTTTTTTTCTTTTCTTTTTTATTACTTCAGTTGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttctgcat---agttcagatttcttgttg--caatgt-tttcttattagttatccatg-gctgatttttattgatt-------cattttaggccatcttatttattg-----------------

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G37210.1 (Glycine max), 5'ss of exon 2
TTGTGGAATCCAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattaccagatttgatcttatggacatgattgaccaatgaatattatatatgtccaacatctgttattttctgctgattggaggactgttaaacactcacttatttaatctttgatgcattaaacag
|  ||||| |||| || || || || || ||||||||||||||| |||||||||| |||||||| || |  |   |||||| | |     | ||   | |   |   |   | || |    ||   |||||||||| ||  ||  |  |                                          
TATTGGAAGCCAAAGATGGTACTATTTCTGTTGCTTCAGCATTTCCTGGTCATCAAGAAGgtatgataataa---ttgatcatttctgtttcatctgcaacccaccctcccacatttttttcaaacgttattttct-cttgttataccag-----------------------------------------

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA17G04720.2 (Glycine max), 5'ss of exon 2
TTGTGGAATCCAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattaccagatttgatcttatggacatgattgaccaatgaatattatatatgtccaacatctgttattttctgctgattggaggactgttaaacactcacttatttaatctttgatgcattaaacag
|||||||| | ||||| |||||  ||||||| ||| | || |||||||||||||||||||||| |  | |   ||   |  | |      |  |||  |||||  | |  |||  ||    |||  | |  ||| |  |||||         ||  |  |   |||||||| |                  
TTGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttctgcat---agttcagatttcttgttg--caatgt-tttcttattagttatccatg-gctgatttttattgatt-------cattttaggccatcttatttattg-----------------

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|88375374|gb|CI681142.1|CI681142
EST:     CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG                         CCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
genomic: CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattac ... cattaaacagCCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
EST: gi|88338152|gb|CI677144.1|CI677144
EST:     CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG                         CCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
genomic: CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattac ... cattaaacagCCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
EST: gi|27547275|gb|CA765405.2|CA765405
EST:     GGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG                         CCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
genomic: GGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattac ... cattaaacagCCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
EST: gi|66916794|gb|CX103642.1|CX103642
EST:     CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG                         CCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
genomic: CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattac ... cattaaacagCCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
EST: gi|88733312|gb|CI756489.1|CI756489
EST:     CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG                         CCGTACAAGACAGGGATCACAAATTTTTGTCTAA-GCAGTTGAAGAAGCTT
genomic: CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattac ... cattaaacagCCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
EST: gi|88587458|gb|CI705204.1|CI705204
EST:     CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG                         CCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
genomic: CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattac ... cattaaacagCCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
EST: gi|88588249|gb|CI706054.1|CI706054
EST:     CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG                         CCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT
genomic: CAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattac ... cattaaacagCCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTT

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), 52 (downstream exon)
Score: 10

TTGTGGAATCCAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattac ... cattaaacagCCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTTACCAAGGAGTAGATTGTGGCCATGGAGGTCCATTTGGTGCAGTTGTTGT




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