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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTGAAGGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAGgtaatgttgtgctcctttgttttgtttgatgtcttcagatcaacttttatttactatatgtgccatcttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g36790.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g36790.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA17G01820.1 (Glycine max), 5'ss of exon 2
CTTTTGAAGGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAGgtaatgttgtgctcctttgttttgtttgatgtcttcagatcaacttttatttactatatgtgccatcttgcag-----------
          |||||||| | ||||||||  |  |||| ||||| | |||||||||||| |||||| |||| ||||| ||||||||  |||| ||||||||| |  |     | |||  |  | |  | |   ||| |     ||||     | | | | |    | ||               
---------ATTCAATTGGTTAGAATTCAAGTTAGAGTACCTGAGTATGGTTGGACTACTCAGAAGATTTTTCATCTCATGAACTTCATTGTCAACGGAGgttagctctcaattcttcctcatttcaggttctttctgtgtttctttcgcccatttttttttattttttatttttatattccag

upper sequence: LOC_Os03g36790.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA17G01820.3 (Glycine max), 5'ss of exon 1
CTTTTGAAGGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAGgtaatgttgtgctcctttgttttgtttgatgtcttcagatcaacttttatttactatatgtgccatcttgcag---------------------------
  | || || |||||||| | ||||||||  |  |||| ||||| | |||||||||||| |||||| |||| ||||| ||||||||  |||| ||||||||| |  |     | |||  |  | |  | |   ||| |     ||||     | | | | |    | ||                               
GCTCTGTAGATTCAATTGGTTAGAATTCAAGTTAGAGTACCTGAGTATGGTTGGACTACTCAGAAGATTTTTCATCTCATGAACTTCATTGTCAACGGAGgttagctctcaattcttcctcatttcaggttctttctgtgtttctttcgcccatttttttttattttttatttttatattccagtgcgtgcagtggtgtt

upper sequence: LOC_Os03g36790.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA17G01820.2 (Glycine max), 5'ss of exon 1
CTTTTGAAGGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAGgtaatgttgtgctcctttgttttgtttgatgtcttcagatcaacttttatttactatatgtgccatcttgcag-----------
  | || || |||||||| | ||||||||  |  |||| ||||| | |||||||||||| |||||| |||| ||||| ||||||||  |||| ||||||||| |  |     | |||  |  | |  | |   ||| |     ||||     | | | | |    | ||               
GCTCTGTAGATTCAATTGGTTAGAATTCAAGTTAGAGTACCTGAGTATGGTTGGACTACTCAGAAGATTTTTCATCTCATGAACTTCATTGTCAACGGAGgttagctctcaattcttcctcatttcaggttctttctgtgtttctttcgcccatttttttttattttttatttttatattccag

upper sequence: LOC_Os03g36790.3 (Oryza sativa), 5'ss of exon 1
lower sequence: AT4G21790.1 (Arabidopsis thaliana), 5'ss of exon 2
CTTTTGAAGGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAGgtaat-gttgtgctcctttgtt--ttgtttgat---gtcttcagatcaacttttatttactatat-gtgccatcttgcag---------------------
         |||||| |||| || || ||  || |||||||||| | |||||||||||| |||||||| || ||||| ||||||||||| || || |||||| ||  |||||    | | ||      |||||   || ||    |        |  |     ||  ||   | ||| |                      
---------GTTCAACTGATAAGGATCCAAATGAGAGTGCCTGAGTATGGTTGGACTACTCAGAAGGTGTTTCATCTTATGAACTTTGTCGTCAATGGAGgtgattattgtgtgtttctattgaccaattgatagggtttttgtgtttgtcagcacctttgggattatgttttgttgaatttctctgttgtgtgtgtgcag

upper sequence: LOC_Os03g36790.3 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv10s0116g00020.t01 (Vitis vinifera), 5'ss of exon 2
CTTTTGAAGGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAGgt--aatgttgtgctcctt--tgttttgtttgatgtcttcagat-----caacttttatttactatatgtgccatcttgcag-------
          ||||| |||| || ||| |  || ||||||| || | ||||||||| || ||||||||||||||||| ||||||||  | || || ||||||  ||| | ||| | |||  | ||||| ||  |   |||   |         | ||||||  | | || |  |  |||          
---------ATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAGgtgaaatatagtgttgcttgatattttggttatttctttcttgtgtggatgtttattatttggtttttgggtgaatttgtgtattgcag

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|218497390|gb|FG957738.1|FG957738
EST:     TTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAG                         TTCGTGCTGTCGTGTTTGGATTTCATGCTCAAGTGTTCCTTTTTCAAACAA
genomic: TTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAGgtaatgttgt ... catcttgcagTTCGTGCTGTCGTGTTTGGATTTCATGCTCAAGTGTTCCTTTTTCAAACAA
EST: gi|58677241|gb|CK065928.1|CK065928
EST:     TTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAG                         TTCGTGCTGTCGTGTTTGGATTTCATGCTCAAGTGTTCCTTTTTCAAACAA
genomic: TTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAGgtaatgttgt ... catcttgcagTTCGTGCTGTCGTGTTTGGATTTCATGCTCAAGTGTTCCTTTTTCAAACAA

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: 72 (upstream exon), 67 (downstream exon)
Score: 34

CTTTTGAAGGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAGgtaatgttgt ... catcttgcagTTCGTGCTGTCGTGTTTGGATTTCATGCTCAAGTGTTCCTTTTTCAAACAAAA




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