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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCAAGCTTTCTGGATGCCACTGTTTGCATATTTAATGCATCGAGTTTGAGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctacaaaaactcaacaggacacaatatatcctttatatattctaacttactggattaaattggtactcttgcttctgaaaacattttgtcttgct...

Basic information

species Oryza sativa
transcript LOC_Os03g14980.1
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 26
ATGCAAGCTTTCTGGATGCCACTGTTTGCATATTTAATGCATCGAGTTTGAGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctacaaaaactcaacaggacacaatatatcctttatatattctaacttactggattaaattggtactcttgct---tctgaaaacattttgtcttgct
||||||||||| |||||||||||||| ||||||||||||  |||||||||||||| |||||||| ||||||||||| || ||||||||||  |||||||||||||||| |||||   || ||     |  ||     |||   ||  |  ||  || |||| |||||| | ||||| |   | |  |||  |    ||  | |
ATGCAAGCTTTATGGATGCCACTGTTGGCATATTTAATGGGTCGAGTTTGAGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctataaaaa---aaaagtttttagcattgttgttaggaatgatgtctgtctagattgaattggcattcttgttgagtttataaaattaagatcaagtt

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G550865_T02 (Zea mays), 5'ss of exon 10
ATGCAAGCTTTCTGGATGCCACTGTTTGCATATTTAATGCATCGAGTTTGAGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctacaaaaactcaa--caggacacaatatatcctttatatattctaact-tactggattaaattggtactcttgcttctgaaaacattttgtcttgct
||||||||||| |||||||||||||| |||||||||||||||||||||||||||| |||||||| ||||||||||| || ||||| || |  |||||||||||||||| ||||    ||    |     |  ||    || |   ||     || |  | |||| |||||  | ||||| |||||| |  ||    |   |  
ATGCAAGCTTTATGGATGCCACTGTTGGCATATTTAATGCATCGAGTTTGAGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctataaaacacaaaatttgtttttagcattgttttcaggaatgacgtctgtcttcgattgaattgacattcttg-ttctgagattataaaattaag--
















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|29676284|gb|CB672559.1|CB672559
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|27554431|gb|CA998331.1|CA998331
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTNCAA-TGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATC
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCT-CAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATC
EST: gi|58585882|gb|CF984190.1|CF984190
EST:     GACTCCAATGTCGAATTCTTGCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: GACTCCAATGTCGAATTCTT-CCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|58694783|gb|CK083470.1|CK083470
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|29672341|gb|CB668616.1|CB668616
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|86851209|gb|CI312610.1|CI312610
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGAAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|29629470|gb|CB634479.1|CB634479
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|29680681|gb|CB676956.1|CB676956
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|58694029|gb|CK082716.1|CK082716
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|218501279|gb|FG957977.1|FG957977
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|89167843|gb|CI021542.1|CI021542
EST:     TCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: TCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|218487225|gb|FG954419.1|FG954419
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|29622175|gb|CB627186.1|CB627186
EST:     AGACTCCAATGTGGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|88975023|gb|CI023274.1|CI023274
EST:     TCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: TCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|163925572|gb|EG713389.1|EG713389
EST:     CCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: CCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|29666551|gb|CB662826.1|CB662826
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|29673861|gb|CB670136.1|CB670136
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
EST: gi|29628403|gb|CB633414.1|CB633414
EST:     AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAG                         CTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA
genomic: AGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCA

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: 70 (upstream exon), 75 (downstream exon)
Score: 77

ATGCAAGCTTTCTGGATGCCACTGTTTGCATATTTAATGCATCGAGTTTGAGACTCCAATGTCGAATTCTTCCAGCATCCTATCTTCCTCAGAATATCAGgtattctaca ... tgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCAGTTTGCTCTAGGCCTGACTGATGGTGGTGTTTATGTATTGGAACCCTTG




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