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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaaccctcacaagtttttgttccctatgcactcaatgctgttataaaatgattactagtttgttgaagcattacaaaggtaactgtttccccgaaattgcag

Basic information

species Oryza sativa
transcript LOC_Os05g51790.1
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51790.2 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G440916_T01 (Zea mays), 5'ss of exon 26
GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaaccctcacaagtttttgttccctatgcactcaatgctgttataaaatgattactagtttgttgaagcattacaaaggt---aactgtttccccgaaattgcag
|||||||| || || |||||| |||| ||||| |||||||||||||||||||||||||| |||||||| |||||||||||||||||||| ||  ||||  | |   | ||   ||| | |           ||||      |||| | |||  ||||  | | |||     |||   |    ||   |||||  |||||
GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac--tgaattgcttcatttctcca----------actgt------atgactgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcag

upper sequence: LOC_Os05g51790.2 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA20G34020.1 (Glycine max), 5'ss of exon 27
GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaaccctcacaagtttttgttccctatgcactcaatgctgttataaaatgattactagtttgttgaagcattacaaaggtaactgtttccccgaaattgcag
|| || ||||||||||| ||  | || ||||| || |||||||||||||| |||||||| ||| | |||||||||||||| || |||||   |  |    |   |     || || ||  ||    ||   ||  || | | ||  |   | | ||||     || |                             
GAACGCTCAGTTTCAACTATTGTTTATCTTGTTTCCCTTCAAGATCTTACAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAGgtgtgttactgtttgaagaaaattctttccattgacaccagctct-ctaaagactgtctttgactgtgtttt--tatcag----------------------------

upper sequence: LOC_Os05g51790.2 (Oryza sativa), 5'ss of exon 26
lower sequence: AT5G15920.1 (Arabidopsis thaliana), 5'ss of exon 2
------------GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaaccctcacaagtttttgttccctatgcactcaatgctgttataaaatgattactagtttgttgaagcattacaaaggtaactgtttccccgaaattgcag
            ||||| || || ||||| ||||| ||||| || || ||||||||||| || ||||| || ||  |||| ||||||||||| |||||||| ||   ||     | | |||||| ||    ||| |   ||  ||||    |||          || ||  |||  |   |||  ||    ||| |  |    |||||
CAATCTGGAGGAGAGCGTTCTGTCTCAACTATCCTTTACCTCGTCTCTCTTCAAGATCTGACAAACTGTCCTTTCAGGGTTGTTGATGAGATTAATCAAGgtaa---aaagtgtaaatgttttt-tttttaatgta---aaaactgtctcgaaaca--------ttagtcaaagtctcttaaaaatatacatttgcttg----tgcag

upper sequence: LOC_Os05g51790.2 (Oryza sativa), 5'ss of exon 26
lower sequence: Vv13s0064g00180.t01 (Vitis vinifera), 5'ss of exon 26
GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaaccctcacaagtttttgttccctatgcactcaatgctgttataaaatgattactagtttgttgaagcattacaaaggtaactgtttccccgaaattgcag
||||| |||||| |||| || ||||| ||||| || || |||||||| || |||||||| ||| |||| ||||||||||||||||||||  ||  ||     | | | | || || | |           |   ||  |||||   |||| |  | |  |          |  |   | || |||| |        
GAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACAAACTGCCCTTTTAGGGTGGTTGATGAGATAAATCAAGgtgagttaaaatata-atggtgttattgctt----------cgtcattgcaaaatatatact-gcctttcaagatgacttttattttgtttttccccctag-------

upper sequence: LOC_Os05g51790.2 (Oryza sativa), 5'ss of exon 26
lower sequence: PP1S274_85V6.1 (Physcomitrella patens), 5'ss of exon 27
GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaaccctcacaagtttttgttccctatgcactcaatgctgttataaaatgat-tactagtttgttgaagcattacaaaggtaactgtt-tccccgaaattgcag
|| || ||||| || || || |||||||| || || ||||||||||| ||  ||||||||||||| || || |||||||| ||||| || ||     | ||||  ||  | || || || ||   | | |      |||   | ||  | |  || ||  |||   ||  ||   |  |||| | | || |       
GAACGCTCAGTATCGACAATACTGTACCTCGTCTCCCTTCAAGATCTGACACACTGCCCCTTTCGTGTGGTGGATGAGATCAATCAGGgtaa-ttttctctcagcagactctgctcact-tgggtttattcgaagaatatgttaatgcaattattggtacaagtgatatgaaaa-atttgttgtgcacgca-------

upper sequence: LOC_Os05g51790.2 (Oryza sativa), 5'ss of exon 26
lower sequence: EFJ24458 (Selaginella moellendorffii), 5'ss of exon 25
GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaaccctcacaagtttttgttccctatgcactcaatgctgttataaaatgattactagtttgttgaagcattacaaaggtaactgtttccccgaaattgcag
|| || || || ||||| || || |||||||| ||||| ||||| |||||| |||| || ||||| || || ||||||||||| ||||| |  |  ||      |  ||| || |  | |  |  | |  | | | || |                                                        
GAACGCTCGGTGTCAACTATACTCTACCTTGTCTCACTCCAAGACCTTACCCACTGTCCGTTTCGTGTTGTGGATGAGATAAACCAAGgtatcctgactg----agatttctggttgcgaatctttaacaggtttgatcag-------------------------------------------------------

upper sequence: LOC_Os05g51790.2 (Oryza sativa), 5'ss of exon 26
lower sequence: EFJ13183 (Selaginella moellendorffii), 5'ss of exon 24
GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaaccctcacaagtttttgttccctatgcactcaatgctgttataaaatgattactagtttgttgaagcattacaaaggtaactgtttccccgaaattgcag
|| || || || ||||| || || |||||||| ||||| ||||| |||||| |||| || ||||| || || ||||||||||| ||||| |  |   |      |  ||| || |  | |  |  | |  | | | || |                                                        
GAACGCTCGGTGTCAACTATTCTCTACCTTGTCTCACTCCAAGACCTTACCCACTGTCCGTTTCGTGTTGTGGATGAGATAAACCAAGgtatcctggctg----agctttctggttgcgaatctttaacaggtttgatcag-------------------------------------------------------

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|86844639|gb|CI338619.1|CI338619
EST:     TCTTACCAACTGCCCCTTTCGGGTCGTTTATGAGATAAATCAAG                         GAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG
genomic: TCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaac ... gaaattgcagGAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG
EST: gi|25798012|gb|CA753973.1|CA753973
EST:     TCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG                         GAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG
genomic: TCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaac ... gaaattgcagGAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG
EST: gi|66914986|gb|CX101834.1|CX101834
EST:     TCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG                         GAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG
genomic: TCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaac ... gaaattgcagGAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG
EST: gi|218486434|gb|FG966621.1|FG966621
EST:     TCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG                         GAATGGATCCCATCAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG
genomic: TCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaac ... gaaattgcagGAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG
EST: gi|88845942|gb|CI084672.1|CI084672
EST:     TCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG                         GAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG
genomic: TCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaac ... gaaattgcagGAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG
EST: gi|29628420|gb|CB633431.1|CB633431
EST:     TCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG                         GAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG
genomic: TCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaac ... gaaattgcagGAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAG

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: 71 (upstream exon), 70 (downstream exon)
Score: 20

GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaac ... gaaattgcagGAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAGCCAGTCAGCCAAACACTCCACA




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