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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaagatgtgatatatcctactgataaaggtgctgcctcatctccttttatatgttaaagtaaaactctgtccgttttgatgttctag

Basic information

species Oryza sativa
transcript LOC_Os05g45420.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaagatgtgatatatcctac-tgataaaggtgctgcctcatctccttttatatgttaaagtaaaactctgtccgttttgatgttctag
|||||| || ||||| ||||| |||||||||||||||||||||||||| || || |||||||| || ||||||||||| |||||||| |||||||||||||| ||| |  || | |   ||  ||| ||| |||| | |      || |  ||||  || |       ||| ||| |   | |  |  || |||
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctataatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatcta-attgtag

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgt-tagcaaa---gatgtgatatatcctactgataaaggtgctgcctcat--ctccttttatatgttaaagtaaaactctgtccgttttgatg---ttctag--
||| ||||| ||||| |||||||| ||| | ||||| ||||||||||| |||||||| |||||||| || |||||||| || || || |||||||||||||| | |  ||    || | || |||   | | ||  ||     | ||  |  || | || | |  |       |  |  ||  | | | |||    ||| ||  
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatc----ccaggccttggacatgtggataattttccagct

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G05700.1 (Glycine max), 5'ss of exon 5
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaagatgtgatatatcctactgataaaggtgctgcctcatctccttttatatgtt--aaag----------taaaactctgtccgttttgatgttctag-
||| ||||| ||||| |||||||| ||| | ||||||||||| ||||| || ||||| |||||||| || || |||||||| || || || |||||||||||     |  || |    ||   || | || |   |  | |||  | || ||||||  |||  ||||          ||||  ||   ||  | |  |||   |  
AGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCCAATCTCTTCAAAAAAATAAAGgt-----actatttttcttaatttaattattattatatttcctt-tttctttttatgggtttcaaaggactgatagttaaatttcctaccactgtcgtgtcaaatt

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 5
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgt-----tagcaaagatgtgatatatcctactgataaaggtgctgcctcatctccttttatatgttaaagta----aaactctgtccgttttgatgttctag
||| ||||| ||||| |||||||| ||| | ||||| ||||||||||| || ||||| |||||||| || || ||||| || || || ||||||||||||||     ||      || | || |||   | | |   ||       ||  | ||    ||||| |||||       |  |  ||  | | | | |  | |  
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCGCTTCTTTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatgttaattttatttatttaattaactgagtgatcagctgttgtctacatatatattaaaactgcccaggccttggacatatggctaattt--

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 5
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaagatgtgatatatcctactgataaaggtgctgcctcatctccttttatatgt---taaagtaa---aactctgtccgttttgatgttctag
||| ||||| |||||||| || |||||  | || |||||  | || ||||| ||||| |||||||| || || |||||||||||||| |||||||| |||||     | | | |  | |     |  | |||| |      || |  |   || ||||||   | ||||||   | |   ||   ||||     | |||
AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttgattca--gctaaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttag

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgt------tagcaaagatgtgatatatcctactgataaaggtgctg-----cctcatctccttttatatgttaaagtaaaactctgtccgttttgatgttctag------------
||| ||||| ||||| |||||||| || || || |||||||| ||||| || |||||||||||||| || || |||||||||||||||||||| ||||||||      ||  |    |    | |   ||| |   |    ||||        | || |  ||||   | | |   |   ||| |  || ||||  | |                 
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 5
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaagatgtgatatatcctactgataa-aggtgctgcctcatctccttttatatgttaaagtaaaactctgtccgttttgatgttctag-------
 || ||||| ||||| || ||||||||| | || ||||||||||||||||| |||||||||||||| || || |||||||||||||| ||||||||||||||      | || |  |  | |  |||  ||  | ||||   || | ||   | |  ||       |      || |   |||| || || | |       
GGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATAAAGgtatttctaaatttacttca-ctaacttttagcatgtgccagcttagctggatctgcattgctcttttttgtccttttactttttatttttttgtttagaa

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S28_12V6.1 (Physcomitrella patens), 5'ss of exon 4
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttag--caaagatgtgatatatcctactgataaaggtgctgcctcatctccttttata-tgttaaagtaaa--actctgtccgttttgatgttctag----------
 || ||||||||||| ||||| |||||||| ||||||||| | |||||| |  | || ||||| ||||| || ||||| || || ||||||||||| ||||||||      | |  |   | ||   ||  |        ||  || | ||   | | |  | |  |||  |  | | |||   |||   |   ||            
GGTGGATGTGTGGAGCTGTGGCGTTATTCTGTATGCTCTTTTGTGTGGTTCTTTACCCTTTGACGACGAAAACATTCCAAATCTGTTTAAGAAAATCAAGgttagattgttggttcggcgtgtctagctatt--------tgtttcgtgtctggtaacagcgctgcagtcgagtattgtgtttctttcagtccgcttagaaccgcgta

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|33676412|gb|CF304651.1|CF304651
EST:     CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAG                         GGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
genomic: CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaag ... gatgttctagGGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
EST: gi|40488690|gb|BX899031.1|BX899031
EST:     GATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAG                         GGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
genomic: GATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaag ... gatgttctagGGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
EST: gi|27576377|gb|CA999071.1|CA999071
EST:     CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAG                         GGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCCAGGGATTTG
genomic: CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaag ... gatgttctagGGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
EST: gi|27554019|gb|CA997919.1|CA997919
EST:     CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAG                         GGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
genomic: CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaag ... gatgttctagGGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
EST: gi|13420631|gb|AU174721.1|AU174721
EST:     CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAG                         GGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
genomic: CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaag ... gatgttctagGGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
EST: gi|66924039|gb|CX110887.1|CX110887
EST:     CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAG                         GGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
genomic: CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaag ... gatgttctagGGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
EST: gi|29680933|gb|CB677208.1|CB677208
EST:     CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAG                         GGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG
genomic: CCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaag ... gatgttctagGGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTG

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: 75 (upstream exon), 75 (downstream exon)
Score: 38

AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaag ... gatgttctagGGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTGATTCCCAGAATGCTTGTTGTTGATCCCATGAAGAGGATCACCATACGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaagatgtgatatatcctactgataaaggtgctgcctcatctccttttatatgttaaagtaaaactctgtccgttttgatgttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA