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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGATGACACAAATTATGTTTGAGACATTCAGCGTTCCAGCCATGTATGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaacaaagaataagcattttcatttgtaaattctgttttgctactctggaatctcaatagagcaggaacaaaccgggtgatgttcaaatcaaat...

Basic information

species Oryza sativa
transcript LOC_Os10g36650.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g36650.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G030169_T02 (Zea mays), 5'ss of exon 3
GAGAAGATGACACAAATTATGTTTGAGACATTCAGCGTTCCAGCCATGTATGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaacaaagaataagcattttcatttgtaaat-tctgttttgctactctggaatctcaatagagcaggaacaaaccgggtgatgttcaaatcaaat
|| |||||||||||||| |||||||| || ||||| ||||| || |||||||| ||||||||||| ||||||||||| ||||||||||| ||||| |||||||||||| |||| ||| | |||||| ||||||     |   | ||| | ||||||| |||  |      |  | | | | |       || |       |
GAAAAGATGACACAAATCATGTTTGAAACCTTCAGTGTTCCTGCTATGTATGTTGCTATTCAAGCTGTGCTTTCCCTATATGCTAGTGGCCGTACCACTGgtaagtgatcaaataatcatcatttt-atttgtgtgcattcatcttgttgctctggagtctggaatcttaatcatccagcagaactgaattgaccaatggt

upper sequence: LOC_Os10g36650.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G082484_T01 (Zea mays), 5'ss of exon 3
GAGAAGATGACACAAATTATGTTTGAGACATTCAGCGTTCCAGCCATGTATGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaacaaagaataagcattttcatt-tgtaaattctgtttt---gctactctggaatctcaatagagcaggaacaaaccgggtgatgttcaaatcaaat
|| |||||||||||||| |||||||| || ||||| ||||| || |||||||| ||||||||||| || |||||||| ||||||||||| ||||| |||||||||||| |||| ||| ||||||||  |  |||| ||||| ||||   ||| ||||||||||| |||  || |  ||| |   |    | | | ||||     
GAAAAGATGACACAAATCATGTTTGAAACTTTCAGTGTTCCTGCTATGTATGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatcaaataatcagcattttattcatgtacattctttttttttgctgctctggaatcttaatctagtataaactagttgaccaaaggtgaaata----

upper sequence: LOC_Os10g36650.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G19420.1 (Glycine max), 5'ss of exon 3
GAGAAGATGACACAAATTATGTTTGAGACATTCAGCGTTCCAGCCATGTATGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaacaaagaataagcattttcatttgtaaattctgttttgctac---tctggaatctcaatagagcaggaacaaaccgggtgatgttcaaatcaaat
||||||||||| ||||||||||||||||| ||||  || || ||||||||||| || ||||| || ||  | || || ||||| |||||| | ||||| |||  ||   |   || | | |  ||  ||||   |||| |  | | ||       ||  || ||||| |    ||  ||         ||         |  |
GAGAAGATGACCCAAATTATGTTTGAGACTTTCAATGTGCCTGCCATGTATGTTGCAATTCAGGCTGTCTTGTCTCTGTATGCCAGTGGAAGAACTACAGgtttgttt-ctgtgattgatc--ttggatttaccaattttactatactgtggtcatgtgatttcaattggattgggccagttatttgaataaatgctgtatgt

upper sequence: LOC_Os10g36650.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G05570.1 (Glycine max), 5'ss of exon 3
GAGAAGATGACACAAATTATGTTTGAGACATTCAGCGTTCCAGCCATGTATGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaacaaagaataagcattttcatttgtaaatt-ctgttttgctactctggaatctcaatagagcaggaacaaaccgggtgatgttcaaatcaaat-------
||||||||||| ||||||||||||||||| ||||  || || ||||||||||| || ||||| || ||  | || || ||||| |||||||||||||| |||  ||   |   || | | |  ||  ||||   | || || |   |      ||  || ||||| |     ||  |   | | | ||  ||  | |||||       
GAGAAGATGACCCAAATTATGTTTGAGACTTTCAATGTGCCTGCCATGTATGTTGCAATTCAGGCTGTCTTGTCTCTGTATGCCAGTGGACGTACTACAGgtttgttt-ctgtgattgatc--ttggatttactatttactataccgtggacatgtgatttcaattg-----gattaggtcagcttattatctgagcaaattcctgta

upper sequence: LOC_Os10g36650.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
GAGAAGATGACACAAATTATGTTTGAGACATTCAGCGTTCCAGCCATGTATGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaacaaagaataagcattttcatttgtaaattctgttttgctact-ctggaatctcaatagagcaggaacaaaccgggtgatgttcaaatcaaat
||||||||||| || || ||||||||||||||||  || || ||||||||||| || ||||| ||||| ||||| |||||||| ||||| ||||| || ||| |||    ||    ||| |||   ||  | | | || | || |  |  | || | || |   || ||  |   |       || |              
GAGAAGATGACTCAGATCATGTTTGAGACATTCAATGTCCCTGCCATGTATGTTGCCATTCAGGCCGTTCTTTCTCTCTATGCCAGTGGTCGTACAACCGgttagttcttaactc-taaacat--ccaagtctgagttatattatcttcttacttgtatttacttaaagtcgtt-ctctttttgtaacag-----------

upper sequence: LOC_Os10g36650.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 5'ss of exon 4
GAGAAGATGACACAAATTATGTTTGAGACATTCAGCGTTCCAGCCATGTATGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaacaaagaataagcattttcatttgtaaattctgttttgctactctggaatctcaatagagcaggaacaaaccgggtgatgttcaaatcaaat
|| |||||||| ||||| ||||||||||| || |  || || ||||||||||| || ||||| || || ||||| || ||||| ||||| ||||| ||||||  ||      |  | || | ||||   ||| || ||   |||| ||  ||||   |     |||     |  | |||    || |  |   |  |   
GAAAAGATGACTCAAATCATGTTTGAGACTTTTAATGTGCCTGCCATGTATGTTGCCATTCAGGCTGTTCTTTCTCTATATGCCAGTGGGCGTACAACTGgttcgt------attaaaatctttttggattggaattttcatttttcttttctgttgttagtgtagcctgagttctaact---tgctcctttgactag--

upper sequence: LOC_Os10g36650.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 5'ss of exon 2
GAGAAGATGACACAAATTATGTTTGAGACATTCAGCGTTCCAGCCATGTATGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaacaaagaataagcattttcatttgtaaattctgttttgctactctggaatctcaatagagcaggaacaaaccgggtgatgttcaaatcaaat------
||||| ||||| || |||||||||||||| |||| ||| || ||||||||||| ||||| ||||| ||||| || || ||||| ||||| ||||| || |||  |||  ||||| |     | ||  |   | ||| |          ||  |    | |   |      |  |     |   | ||  |  || |          
GAGAAAATGACCCAGATTATGTTTGAGACCTTCAACGTACCTGCCATGTATGTTGCTATCCAAGCTGTGCTGTCTCTGTATGCCAGTGGTCGTACAACAGgtttgtgt-caaagcactgcaagttgtagaagcaaaatacaag-----acctttttgtgtgtgtgtgtgtgtcattgttcatattattcttgaaccgttagccatt

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|33675014|gb|CF303253.1|CF303253
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
EST: gi|58685588|gb|CK074275.1|CK074275
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
EST: gi|163920040|gb|EG709834.1|EG709834
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGA
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGA
EST: gi|58677488|gb|CK066175.1|CK066175
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
EST: gi|58672834|gb|CK061520.1|CK061520
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTC
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTC
EST: gi|58591066|gb|CF989374.1|CF989374
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
EST: gi|58675018|gb|CK063705.1|CK063705
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
EST: gi|58679576|gb|CK068263.1|CK068263
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
EST: gi|58680564|gb|CK069251.1|CK069251
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
EST: gi|58686486|gb|CK075173.1|CK075173
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
EST: gi|58680396|gb|CK069083.1|CK069083
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
EST: gi|58665180|gb|CK053866.1|CK053866
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
EST: gi|58664066|gb|CK052752.1|CK052752
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACG
EST: gi|58678348|gb|CK067035.1|CK067035
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTAC
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTAC
EST: gi|58656556|gb|CK045236.1|CK045236
EST:     TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTG                         GTATTGTCTTGGATTCTG
genomic: TGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTG

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: 70 (upstream exon), 74 (downstream exon)
Score: 32

GAGAAGATGACACAAATTATGTTTGAGACATTCAGCGTTCCAGCCATGTATGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaac ... ttgtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACGAAGGTTATGCCCTTCCGCATGCCATTCTCCGTCTTGATCTTGCTGGTAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGATGACACAAATTATGTTTGAGACATTCAGCGTTCCAGCCATGTATGTCGCTATTCAAGCCGTGCTTTCCCTCTATGCTAGTGGACGTACTACTGgtaagtgaacaaagaataagcattttcatttgtaaattctgttttgctactctggaatctcaatagagcaggaacaaaccgggtgatgttcaaatcaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA