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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcctcatccaatttcatattttatccacttgaccatataactgcataagttgaagaggcttgtctggataattaagaaggtgtatgatcgagga...

Basic information

species Oryza sativa
transcript LOC_Os12g03470.5
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G006130_T01 (Zea mays), 5'ss of exon 11
ACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcctcatccaatttcatattttatccacttgaccatataactgcataagttgaagaggcttgtctggataattaagaaggtgtatgatcgagga---
|||||||| |||||||| ||||||||||||||||||||||| ||||  |||||| | || |||||||||||||||||||| |||||||| || ||||| |||| | |  ||| | |  ||  |||||  | |  || |  |   |  || | | ||        |  || | |  ||  || | ||    | | |   |    
ACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttatcaactacatttgtatttgcttcctttaaata---agttgaaaatgtcttctccacaagtttcgtaaaaaaaaaggggtcttcagcacagtggc

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G006130_T05 (Zea mays), 5'ss of exon 10
ACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcctcatccaatttcatattttatccacttgaccatataactgcataagttgaagaggcttgtctggataattaagaaggtgtatgatcgagga----
|||||||| |||||||| ||||||||||||||||||||||| ||||  |||||| | || |||||||||||||||||||| |||||||| || ||||| |||| | |  ||| | |  ||  |||||  | |  || |  |   |  || | | ||        |  || | | |||  || | ||| |       ||      
ACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttatcaactacatttgtatttgcttcctttaaata---agttgaaaatgtcttctccacaagtttcg-taaaaaaaagggtcttcagcacagtggcaa

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G393002_T01 (Zea mays), 5'ss of exon 20
ACATGGGGTTCTGTTAGAGCTGCAATGGGGCA-CCCTGAACCATTCCCTGTCAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcctcatccaatttcatattttatccacttgacc----atataactgcataagttgaagaggctt----gtctggataattaagaaggtgtatgatcgagga----------------------------
 ||||||| |||||||||||   ||||||||| |||| ||||||| || ||||| || ||||||||||||||||||||||||| || ||| |||||  | |||| |     |    | |||  |||   |||   || ||     || |   |||| ||  |  | || ||     || ||  ||    || |   |||   |     |                            
-CATGGGGCTCTGTTAGAGCCAAAATGGGGCATCCCTAAACCATTTCCAGTCAAGTATGTTGCAATTGGAAATGAAGATTGTGAGAGAAAGTTTTATAGAGgta-agatgacgggtacttttctatcgcatctgttttactcccaatgtttgtgcagaaaattcaaagactatgtagtttgtttagcagaggaatcgtacttttagttacaagatgttctctactgctattggacag

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G077299_T03 (Zea mays), 5'ss of exon 10
ACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcctcatccaatttcatattttatccacttgaccatataactgcataagttgaagag-gcttgtctggataattaagaaggtgtatgatcgagga
|||||||| |||||||| ||||||||||| ||||||||||||||||| || ||||| |||||||| ||||||||||||||||||||||||||||||||||||| |||   || | |  ||  | ||  ||||  || |   ||||| || | |||       |  |  |    | |  | | |||  | | |   | || |
ACATGGGGCTCTGTTAGGGCTGCAATGGGCCACCCTGAACCATTCCCAGTGAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttaccaactacattt-tgttacatcctttttagagtataagtggaaaagcacttttgcacaagggcagtttctaaggaacctctcttcactagca

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA03G00630.1 (Glycine max), 5'ss of exon 10
ACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcctcatccaatttcatattttatccacttgaccatataactgcataagttgaagaggcttgtctggataattaagaaggtgtatgatcgagga-
| |||||| ||| |||| ||| | ||||| || ||  | |||||     | | |   |||||||||||||||||||||||||  ||       |||   ||||   |  || |    ||| | || || |    | |   || | | |  || ||||        |  | |    |  ||  ||  |   |  || |||| 
AGATGGGGATCTCTTAGGGCTTCCATGGGACATCCCAAGCCATTTGACTTGAGAATTGTTGCAATTGGAAATGAAGATTGTGACAAGTTTAACTACAAAGgtacgattttccttgtttttgacatatttttttatagcatat-tgagttaattagttatcatatttcatttattgatatattaatttcgtttttccaggaa

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA03G27490.1 (Glycine max), 5'ss of exon 10
---------------------ACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcctcatccaatttcatattttatccacttgaccatataactgcataagttgaagaggcttgtctggataattaagaaggtgtatgatcgagga
                     | |||||||||  |||||||  | |||||||||||  | || ||     | ||||| ||||| ||||||||||||||||||||||| | |   ||||  || ||  ||  |       ||  | ||||  |   ||       ||| |   ||  |||| | | ||| | ||  | |  |  ||| | | |  |      
GCCAGAGGTGAGGCTACTTCAAAATGGGGTTCCCTTAGAGCATCTATGGGGCACCCAAAGCCTTTTGACCTAAAATATGTTGCTATTGGAAATGAAGATTgtgggaagacaaactaccaaggcatgctctcc-------tttttctttttccttttt-------taagtatttacattga-gtgacttttttgagtgaacacaaag-tatttacta-----

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 11
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 5'ss of exon 11
ACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcctcatccaatttcatattttatccacttgaccatataactgcataagttgaagaggcttgtctggataattaagaaggtgtatgatcgagga
|| ||||| |||||| |||||  |||||| | ||  ||||| ||     | ||||||||||| |||||||||||||||||||||||||  |  ||| | ||| |     |  || |   ||| || ||    ||||     | |   ||   |  ||  | |       ||  || |      |  | ||          
ACTTGGGGATCTGTTCGAGCTAAAATGGGACGCCAAGAACCTTTTGAACTTAAATACGTTGCTATTGGAAATGAAGATTGTGGGAAAACTTACTACAGAGgttttgcatttctctatgatcacatcttg---acttagat-ttttgttgagcatctttgaca-------ctaaatgagattacaactttacag-------

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|29667817|gb|CB664092.1|CB664092
EST:     CAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTC
genomic: CAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcct ... cgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTC
EST: gi|33381874|gb|CF197217.1|CF197217
EST:     CAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTC
genomic: CAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcct ... cgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcctcatccaatttcatattttatccacttgaccatataactgcataagttgaagaggcttgtctggataattaagaaggtgtatgatcgagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA