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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGAGGGGAGAGGCGGCGCTGGCAAGGCTGAAGGCGTACGAGGGCGTGCCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcggattcgcttgttgtttggatttttttttgtgtaattgtgcgcgagcgagtagtctaatggtgtttgtttggtgccgaattgtag

Basic information

species Oryza sativa
transcript LOC_Os03g54890.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g54890.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G072315_T03 (Zea mays), 5'ss of exon 2
CCAAGAGGGGAGAGGCGGCGCTGGCAAGGCTGAAGGCGTACGAGGGCGTGCCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcggattcgcttgttgtttggatttttttttgtg-----taattgtgcgcgagcgagtagtctaatggtgtttgtttggtgccgaattgtag
|||||||||| |||||||| ||||| ||||| ||| ||||||||||||| |||||||||||||||| |||||||||| |||||||||| ||||| || |||||||| |  |||| ||||  |  |||||||  |   ||     | ||  | |         | |||| ||| | ||   ||| ||  |    ||||
CCAAGAGGGGGGAGGCGGCTCTGGCGAGGCTCAAGACGTACGAGGGCGTCCCGCCGCCGTACGACAAGACCAAGCGCCTGGTCATCCCTGACGCTCTTAAgtacgt-gtcttcgtttgtattagggattttcctgattgatggctgatcttaccttgtgttcttgtctgatgatattctgttgttgt-ggtccgtag

upper sequence: LOC_Os03g54890.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G090422_T01 (Zea mays), 5'ss of exon 2
CCAAGAGGGGAGAGGCGGCGCTGGCAAGGCTGAAGGCGTACGAGGGCGTGCCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcggattcgcttgttgtttggatttttttttgtgta-----attgtgcgc-gagcgagtagtctaatggtgtttgtttggtgccgaattgtag
|||||||||| |||||||| ||||| ||||| ||| ||||||||||||| |||||||||||||||| ||||||||| ||||||||||| ||||| || |||||||| |  | |    ||  || |||||| | |   || |     ||  |||   | |  | | || |  || || |  | | ||   |  |  |||
CCAAGAGGGGGGAGGCGGCTCTGGCGAGGCTCAAGACGTACGAGGGCGTCCCGCCGCCGTACGACAAGACCAAGCGTATGGTCATCCCTGACGCTCTTAAgtacgt-gtttccatccgtatttgggatttatctgattgcaggcagatcttgctttgtgacattcgtgtc-tgatgctattcttgttgtggttcttag
















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|27577828|gb|CB000523.1|CB000523
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGACAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|58599534|gb|CK010062.1|CK010062
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGGCTCCT
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCT
EST: gi|58597252|gb|CK007780.1|CK007780
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|58664019|gb|CK052705.1|CK052705
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|86888621|gb|CI305689.1|CI305689
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|58695434|gb|CK084121.1|CK084121
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|218480584|gb|FG964922.1|FG964922
EST:     CTGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|218498099|gb|FG967283.1|FG967283
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|218502993|gb|FG964681.1|FG964681
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCT
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCT
EST: gi|58594149|gb|CF992457.1|CF992457
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|58691553|gb|CK080240.1|CK080240
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|58597148|gb|CK007676.1|CK007676
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGT
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGT
EST: gi|27577829|gb|CB000524.1|CB000524
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCAGCCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|58677624|gb|CK066311.1|CK066311
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGGCTCCTCGGGCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|218484320|gb|FG953179.1|FG953179
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACCAGTACTGCCTCCTCGGCCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
EST: gi|58595748|gb|CK006276.1|CK006276
EST:     CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAA                         GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC
genomic: CCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTC

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), 75 (downstream exon)
Score: 81

CCAAGAGGGGAGAGGCGGCGCTGGCAAGGCTGAAGGCGTACGAGGGCGTGCCGCCGCCGTACGACAGGACCAAGCGCATGGTCATCCCCGACGCGCTCAAgtacgtcgga ... cgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTCCAAGGAGGTTGGCTGGAACTACTATGACACCATCAGG




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