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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcgccttatgtcctaaatcttttctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatttcttatctaaatacataattttgtaatctgattccaatattcatctatggtatgttcatgtgtttggtaatag

Basic information

species Oryza sativa
transcript LOC_Os09g07510.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 5
GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcgccttatgtcctaaatcttttctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatttcttatctaaatacataattttgtaatctgattccaatattcatctatggtatgttcatgtgtttggtaatag
|| || || ||||| || ||||| |||||||| ||||||||||||||||| || || || || || ||||||| | | |||||||||     |||| |  ||   || || | |        ||   | || ||      |||      |  | | || |     | | || | | |||| ||  | ||                                                   
GATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAGgtattattattattat-tattactactattattttgctgattattgcacatgctgcatatctt------tctatgatagtgc---tatgttgtgtgaatatattgtatta--------------------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 5
GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcgccttatgtcctaaatcttttctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatttcttatctaaatacataattttgtaatctgattccaatattcatctatggtatgttcatgtgtttggtaatag
|| || || ||||| || ||||| |||||||| ||||||||||||||||| ||||| || || || ||||||| | | |||||||||                ||  ||  | | |      || || | || |||| |  |||  | |  || | |   || | ||||| |||  | | |    || ||| |    |||  |                                     
GATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGCGAAGCTGTAGGCCCTGAACCTACCAGgtattatt---------------attattattatta----ttattattattattttgctgatta--ttgcacatgctgc-atatctttct-atcatagtgctatgttatgtgaatatattgta-------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G10000.1 (Glycine max), 5'ss of exon 4
GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcgccttatgtcctaaatcttttctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatt--tcttatctaaatacataattttgtaatctgattccaatattcatctatggtatgttcatgtgtttggtaatag
|| || |||||||| |||||||| |||||||| |||||| | |||||||| || || || ||||||||||| |   | |||||       |||| ||| |          |||  ||||       | | |  || | |    | ||  |   || | || |  |||  |  ||||| || |  |  |||  |    | ||   |||                                   
GATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAGgta------accttttgtac----------ctgctaaaa-------tgattggttggttgtcaagattttctgagcttttttccattggtgctatctgaaaatctgttttcat----taatattaat-----------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA09G31760.1 (Glycine max), 5'ss of exon 5
GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcgccttatgtcctaaatcttt--tctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatttcttatctaaatacataattttgtaatctgattccaatattcatctatggtatgttcatgtgtttggtaatag
|| || |||||||| |||||||| |||||||| |||||| | |||||||| || || || ||||||||||| |   | |||||  |       ||  | |||||   ||  |  ||       | |     | |   |  |  |  | |||||| |  |   | |   || ||||  | |                                                              
GATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAGgtaaaaccttttgtacctgctaaacgattgattggttgttgtgattttctgacaagctttttttccattggtgctatctgaaaatctgtttttattaata--------------------------------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 6
GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtat-tatgcgccttatgtcctaaatcttttctgtca---aaaccaatcataaa----tactttggtccttaaatggtgcaagttattatttatttcttatctaaatacataattttgtaatctgattccaatattcatctatggtatgttcatgtgtttggtaatag
|| || || ||||| ||||| ||||||||||| |||||||| |||||||| || || || ||||||||||| | | | |||||  ||| | |||  ||     || ||  | |||     |   |  ||||  |     | ||   |  ||||||  ||  || | | || | ||||||                                                                     
GATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGgtaaatattcccctgttgatgataagctactgtgttttgcatttctttcatgtaaccccaattctattgttaaatcctgtgagct-taatatttttcttga-------------------------------------------------------------------

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|300215963|gb|HO088589.1|HO088589
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCTGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58654414|gb|CK043094.1|CK043094
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|86904336|gb|CI306754.1|CI306754
EST:     CAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: CAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58652709|gb|CK041389.1|CK041389
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|38474762|gb|CF958895.1|CF958895
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|33654809|gb|CF277423.1|CF277423
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58593044|gb|CF991352.1|CF991352
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCTGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|33796143|gb|CF323937.1|CF323937
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|29635602|gb|CB640611.1|CB640611
EST:     GGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58598714|gb|CK009242.1|CK009242
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|218487576|gb|FG960599.1|FG960599
EST:     GAGCTCTGCGAGGCAGGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GAGCTCTGCGAGGCA-GTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|300215769|gb|HO088395.1|HO088395
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCTGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|3768380|gb|AU032407.1|AU032407
EST:     GGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58655438|gb|CK044118.1|CK044118
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|33676187|gb|CF304426.1|CF304426
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58678838|gb|CK067525.1|CK067525
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA

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), 74 (downstream exon)
Score: 169

GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGAAGTGCGGATAGCGGCTGCAGGGAAAGTTACTAAGTTCTGTAGGATTTTA




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