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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCGGACTGGCCAAAGATGGGCCTCAAGAAGACGAGACACATGTCTCCACTAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgtactaaaattgtcacacatatagtctacctagctagctagttttgtaaacgagtagtggcgaagtttaacataatatacctttcatgtaccctaaagaaataaaaatatatacctttcatgtttcaactaattggctattaatattacttcatgttattgcag

Basic information

species Oryza sativa
transcript LOC_Os10g25550.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g25550.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G110968_T01 (Zea mays), 5'ss of exon 4
TTCGGACTGGCCAAAGATGGGCCTCAAGAAGACGAGACACATGTCTCCACTAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgtactaaaattgtcacacatatagtctacctagctagctagttttgtaaacgagtagtggcgaagtttaacataatatacctttcatgtaccctaaagaaataaaaatatatacctttcatgtttcaactaattggctattaatattacttcatgttattgcag
||||| || || || | ||| |||  |||||||||||| || || || ||  |||| |||||||| |||||||| |||||||| || ||||||||||| ||||      |  | |  || | | | |        |   |     | |  | || |||| |||  | ||   | |   |  |||  ||      |||  |  |                                                             
TTCGGGCTAGCGAAGGCTGGACCTGGAGAAGACGAGACCCACGTGTCGACCCGAGTCATGGGCACGCAGGGCTACGCCGCACCCGAGTACATCATGACAGgtat----gtacttaggcaaaaaatattatggaacatgcatgcgcgcactc-agcagtgacga--tctactgtta---attttttctgcgtta-aaattagcag------------------------------------------------------------

upper sequence: LOC_Os10g25550.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G110968_T02 (Zea mays), 5'ss of exon 4
TTCGGACTGGCCAAAGATGGGCCTCAAGAAGACGAGACACATGTCTCCACTAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgtactaaaattgtcacacatatagtctacctagctagctagttttgtaaacgagtagtggcgaagtttaacataatatacctttcatgtaccctaaagaaataaaaatatatacctttcatgtttcaactaattggctattaatattacttcatgttattgcag
||||| || || || | ||| |||  |||||||||||| || || || ||  |||| |||||||| |||||||| |||||||| || ||||||||||| ||||      |  | |  || | | | |        |   |     | |  | || |||| |||         || | |   |||  | | |  ||||   |  |    || || |   || |    |  |     |                            
TTCGGGCTAGCGAAGGCTGGACCTGGAGAAGACGAGACCCACGTGTCGACCCGAGTCATGGGCACGCAGGGCTACGCCGCACCCGAGTACATCATGACAGgtat----gtacttaggcaaaaaatattatggaacatgcatgcgcgcactc-agcagtgacga-------tctactgttaattttttctgcgttaaaattagcagggcatctaacgaccaagagcgacgtgtacag----------------------------

upper sequence: LOC_Os10g25550.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA13G17050.1 (Glycine max), 5'ss of exon 4
TTCGGACTGGCCAAAGATGGGCCTCAAGAAGACGAGACACATGTCTCCACTAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgtactaaaattgtcacacatatagtctacctagctagctagttttgtaaacgagtagtggcgaagtttaacataatatacctttcatgtaccctaaagaaataaaaatatatacctttcatgtttcaactaattggctattaatattacttcatgttattgcag
|| ||  |||| |||||||| ||  ||| ||| || ||||| || || |||||||| ||||||||||| |||||||| || ||||||||||||||||| ||||  || | | |||| || | |||  |   |   |   |       | | |  ||     | | |||||  | ||  |    |     |      | |  |  | |  | |  |||     | |                                       
TTTGGCTTGGCAAAAGATGGTCCCGAAGGAGATGACACACACGTTTCAACTAGAGTCATGGGCACACAAGGCTATGCGGCCCCAGAATACATCATGACAGgta--aataatttcactcaaaaagtaaaaaaaaacaatga------cacatggttaact-tggactttaatttgattcattgctagctcaattctcacatgtgtacacttttttcttcttcatatag-------------------------------------

upper sequence: LOC_Os10g25550.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA17G05660.1 (Glycine max), 5'ss of exon 4
TTCGGACTGGCCAAAGATGGGCCTCAAGAAGACGAGACACATGTCTCCACTAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgtactaaaattgtcacacatatagtctacctagctagctagttttgtaaacgagtagtggcgaagtttaacataatatacctttcatgtaccctaaagaaataaaaatatatacctttcatgtttcaactaattggctattaatattacttcatgttattgcag
|| ||  ||||||||||||| ||| ||| ||| || ||||| || || |||||||| ||||||||||| |||||||| || ||||||||||||||||| ||||    |||  |  |||||  ||       |  ||   |    ||   ||  || |    | |||||||  |  |  ||   |      | | ||    | |    || ||   |||| | || |   ||                                 
TTTGGCTTGGCCAAAGATGGTCCTGAAGGAGATGACACACACGTTTCAACTAGAGTCATGGGCACACAAGGCTATGCGGCCCCAGAATACATCATGACAGgta----aataatttcacatcaag-------aagtaaaaaacaatg---acaggttgacttggagtttaattt--ttaactcattgctagctcaaatctcacacgtgtacatttttttcttcttccgtatag--------------------------------

upper sequence: LOC_Os10g25550.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv04s0008g02070.t01 (Vitis vinifera), 5'ss of exon 4
TTCGGACTGGCCAAAGATGGGCCTCAAGAAGACGAGACACATGTCTCCACTAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgta--ctaaaattgtcacacatatagtctacctagctagctagttttgtaaa-cgagtagtggcgaagtttaacataatatacctttcatgtaccctaaagaaataaaaatatatacctttcatgtttcaactaattggctattaatattacttcatgttattgcag
||||| || || || || || ||  |||  |||||||| || || || ||  || | ||||||||||| ||||||||||| || || || |||||||||||||   |   ||    |||| || |   |  |  |  | |||       ||| | |||| |    |   ||    | | |||| | |||                                                                              
TTCGGGCTAGCGAAGGACGGTCCAGAAGGCGACGAGACTCACGTATCAACCCGAATAATGGGCACACATGGCTATGCCGCTCCTGAGTATATCATGACTGgtaaattttgatcaaaacacttagaaaatctcctgagacctaaccccaaaaatctagtacttctaatactt----tta-atacttctcag-----------------------------------------------------------------------------

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|87034443|gb|CI189067.1|CI189067
EST:     TAGAGTGATGGGCACACAGGGCTATTCCGCACCAGAATACATCATGACTG                         GTCATCTAACGACAAAGAGCGATGTGTATAGCTATGGTGTGGTGCTGCTGG
genomic: TAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgtactaaaat ... gttattgcagGTCATCTAACGACAAAGAGCGATGTGTATAGCTATGGTGTGGTGCTGCTGG
EST: gi|87015000|gb|CI273398.1|CI273398
EST:     TAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTG                         GTCATCTAACGACAAAGAGCGATGTGTATAGCTATGGTGTGGTGCTGCTGG
genomic: TAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgtactaaaat ... gttattgcagGTCATCTAACGACAAAGAGCGATGTGTATAGCTATGGTGTGGTGCTGCTGG
EST: gi|86546505|gb|CI186711.1|CI186711
EST:     TAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTG                         GTCATCTAACGACAAAGAGCGATGTGTATAGCTATGGTGTGGTGCTGCTGG
genomic: TAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgtactaaaat ... gttattgcagGTCATCTAACGACAAAGAGCGATGTGTATAGCTATGGTGTGGTGCTGCTGG
EST: gi|88846241|gb|CI373009.1|CI373009
EST:     GGCACACAGGGCTATGCCGCACCAGAATACATCATGACTG                         GTCATCTAACGACAAAGAGCGATGTGTATAGCTATGGTGTGGTGCTGCTGG
genomic: GGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgtactaaaat ... gttattgcagGTCATCTAACGACAAAGAGCGATGTGTATAGCTATGGTGTGGTGCTGCTGG
EST: gi|86545535|gb|CI185741.1|CI185741
EST:     TAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTG                         GTCATCTAACGACAAAGAGCGATGTGTATAGCTATGGTGTGGTGCTGCTGG
genomic: TAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgtactaaaat ... gttattgcagGTCATCTAACGACAAAGAGCGATGTGTATAGCTATGGTGTGGTGCTGCTGG

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: 55 (upstream exon), 33 (downstream exon)
Score: 2

TTCGGACTGGCCAAAGATGGGCCTCAAGAAGACGAGACACATGTCTCCACTAGAGTGATGGGCACACAGGGCTATGCCGCACCAGAATACATCATGACTGgtactaaaat ... gttattgcagGTCATCTAACGACAAAGAGCGATGTGTATAGCTATGGTGTGGTGCTGCTGGAGCTACTAACCGGACGGAAAGCCGTGGATAAGAAGAGACCGCCGCGAGA




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