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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcaaatttctatgggtatgttcttttatgatggtagtgtactagtatagtcctgaactcctgatggtcgattttttttcttctaagcattatgcaatcatattttatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTTCTTCAGTATGGTGCTCGTACGTTGAATGAAGGTGGTTTTCAA

Basic information

species Oryza sativa
transcript LOC_Os10g37210.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G032222_T03 (Zea mays), 3'ss of exon 9
gttagtcaaatttctatgggtatgttcttttatgatggtagtgtactagtatagtcctgaactcctgatggtcgattttttttcttctaagcattatgcaatcatattttatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTTCTTCAGTATGGTGCTCGTACGTTGAATGAAGGTGGTTTTCAA
       ||  ||      |  | |  |   |   ||   |  | |   |  | |  | ||      |   |  |  |  |||  |||||  ||| |||||||||||||       |||||||| ||||| ||||||||||| || | | ||||||| |||||||||| | ||||||||||||| |||||  | |||||||||||||| || 
-------aagattaaggatgggtatattagaagactgactgatttcctatgaattaataaat-----agaatgaacctagttttctctaaatattgtgcaatcatattt-------cagAAATTTAAGCAGCACCCTGCTGTTAGAAAACTTTTGGAAGGTGGAACAGCTATTCAGTATGGTGCACGTACTCTCAATGAAGGTGGTTTCCAG

upper sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA15G03360.1 (Glycine max), 3'ss of exon 9
gttagtcaaatttctatgggtatgttcttttatgatggtagtgtactagtatagtcctgaactcctgatggtcgattttttttcttctaagcattatgcaatcatattttatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTTCTTCAGTATGGTGCTCGTACGTTGAATGAAGGTGGTTTTCAA
        |  ||  ||    || ||||    |  || |      |||  ||       |    ||  |  | | |  ||  |  |||   | || ||      | | ||      |||||| | ||||| || |||||  | |   || || |||| |||||||||||| | |||||||| ||||| || || ||||||||||||||||| 
--------aggttacatta-catattctgaattcgtgat----ccctaacatttattcaattatcttct--ttgctccttccttctctctcccttgtgtc----tgtcttggtcaccagAAACTAAAGCATCATCCTGCAATTAAATCATTTCTGGAAGGTGGAACAGTTATCCAGTATGGAGCTCGCACTTTAAATGAAGGTGGTTTTCAG

upper sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G43400.1 (Arabidopsis thaliana), 3'ss of exon 9
gttagtcaaatttctatgggtatgttcttttatgatggtagtgtactagtatagtcctgaactcctgatggtcgattttttttcttctaagcattatgcaatcatattttatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTTCTTCAGTATGGTGCTCGTACGTTGAATGAAGGTGGTTTTCAA
                   ||||||   ||| | ||     |  |||          | | |   |  |   | | |   |||||   |  ||| ||    | ||  |  | ||   ||||| |||| || || |||||| | |     || ||||| ||||| || || ||||||||||| |||||||| || ||||||||||||||||| 
-------------------gtatgtcaatttctcataacgatagact--------tttcagcggttacta--caaatacatttctaaaacccatcattt--ttatcctccaaat---agAAACTCAAACACCATCCTGCTATTAAAGGCATCTTGGAAGGTGGTACCGTGCTTCAGTATGGAGCTCGTACTTTAAATGAAGGTGGTTTTCAG

upper sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv05s0102g01110.t01 (Vitis vinifera), 3'ss of exon 9
gttagtcaaatttctatgggtatgttcttttatgatggtagtgtactagtatagtcctgaactcctgatggtcgattttttttcttctaagcattatgcaatcatattttatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTTCTTCAGTATGGTGCTCGTACGTTGAATGAAGGTGGTTTTCAA
            |  | | |||   ||| |  | ||     ||||    | ||  | ||   | ||  || |   ||  || ||||        ||||  ||  |   || || |  ||||| | || || || |||||  |||   |  || |  | ||||| || ||||| |||||||||||||| || |||||||| || |||||||| 
-----------ctggaagtgtagtgtctatcttaatttgcttgtaagcatttatccatgttttgctcgtgatttcttgcttatctttc------tatgttatgtttccttctaat--agAAACTTAAACATCATCCTGCCATCAAACCTCTTCTCAAAGGTGGGACTGTTCTCCAGTATGGTGCTCGCACTTTGAATGAGGGCGGTTTTCAG

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|218502645|gb|FG955089.1|FG955089
EST:     CCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAG                         AAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT
genomic: CCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAGgttagtcaaa ... tatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT
EST: gi|218483729|gb|FG951541.1|FG951541
EST:     TTGCCTTGAACTATCAAAATCCTTTCATGAGCCCATATGATGAATTCCAG                         AAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT
genomic: TTGCCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAGgttagtcaaa ... tatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT
EST: gi|88385296|gb|CI630397.1|CI630397
EST:     TTGCCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAG                         AAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT
genomic: TTGCCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAGgttagtcaaa ... tatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT
EST: gi|29615150|gb|CB620163.1|CB620163
EST:     TTGCCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAG                         AAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT
genomic: TTGCCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAGgttagtcaaa ... tatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT
EST: gi|88345653|gb|CI629914.1|CI629914
EST:     TTGCCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAG                         AAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT
genomic: TTGCCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAGgttagtcaaa ... tatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT
EST: gi|88337643|gb|CI632145.1|CI632145
EST:     TTGCCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAG                         AAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT
genomic: TTGCCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAGgttagtcaaa ... tatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTT

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: 68 (upstream exon), 73 (downstream exon)
Score: 35

TTAGCGATAGGTCTGGTTGTTGCCTTGAACTATCAAAATCCTTTCATGAGCCCATACGATGAATTCCAGgttagtcaaa ... tatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTTCTTCAGTATGGTGCTCGTACGTTGAATGAAGGTGGTTTTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatggtcgattttttttcttctaagcattatgcaatcatattttatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTTCTTCAGTATGGTGCTCGTACGTTGAATGAAGGTGGTTTTCAA
 tcctgat  putative branch site (score: 35)
                            attatgcaatcatatt  TA-rich tract