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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctgatttttataattttatatctgtaatattaatgatatgtgaaaaaaaccaagttgaagttcatggggatgctctgaactggaatattgtgt...

Basic information

species Oryza sativa
transcript LOC_Os09g38790.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g38790.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G081812_T02 (Zea mays), 5'ss of exon 6
GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctgatttttataattttatatctgtaatattaatgatatgtgaaaaa--aaccaagttgaagttcatggggatgctctgaactggaatattgtgt
||||||||||| |||||| | || ||||||||||||||||||||||||||||||||||||| || || |||| ||  |||   |||| | |     | |   |    |     |||  || ||||||  |  |||  |   |  |  || || | |
GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtgtttcttatgatactattattgtagtttctcaaacaaaaggtttatcgctcaatctgcagttca--gcaatgagcaatagcgatatgttattt

upper sequence: LOC_Os09g38790.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA05G34280.1 (Glycine max), 5'ss of exon 6
GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctgatttttataattttatatctgtaatattaatgatatgtgaaaaaaaccaagttgaagttcatggggatgctctgaactggaatattgtgt-----
|||||||||||| ||||  | || || ||||||||||||||||||| |||||||||||||  |  |   |     |||| ||   |    ||  |  |   |  ||  |    ||| |   ||        || | | |  |    |  | |       
GAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGgtaagtcatactacct----cttta-atagatggagttgcttttgcatctaaccagatgagtaggctttatgcttcctgttttcagattccgttgtttacacatt

upper sequence: LOC_Os09g38790.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G05390.2 (Glycine max), 5'ss of exon 6
GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctgatttttataattttatatctgtaatattaatgatatgtgaaaaaaaccaagttgaagttcatgggga-tgctctgaactggaatattgtgt---
|||||||||||| ||||  | || || ||||||||||||||||||| |||||||||||||  |  |   | |   || |||  || | |     | | || | ||  | |  |   |    || |||     || | | |  |  | |  | |     
GAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGgtaagtcatactacctct---ttaatagatggagttgctttcacatct-aaccagatgagtataggctttatgcttcctgttttcagattcagttgtttacaca

upper sequence: LOC_Os09g38790.3 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G30970.2 (Arabidopsis thaliana), 5'ss of exon 6
GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctgatttttataattttatatctgtaatattaatgatatgtgaaaaaaaccaagttgaag---ttcatggggatgctctgaactggaatattgtgt
|||||||||||| ||||  |||| || ||  | ||||| |||||||| ||||||||||||||||||||      ||| |  |    || | |     | ||  |    |||| | | |      || ||    |   |          ||  |    
GAGGAAAGAAGAATGTCCTTACCAAAATACAAAGTGCACGATGAAACCAGCCAGgtaagttctgatttaccctttttaaagttaagaagagtttgcttttgcaagtctaacccattcggtaggctttatttatacatttctgttccagatccta---

upper sequence: LOC_Os09g38790.3 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv03s0017g02160.t01 (Vitis vinifera), 5'ss of exon 6
GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctgatttttataattttatatctgtaatattaatgatatgtgaaaaaaaccaagttgaagttc-atggggatgctctgaactggaatattgtgt-
|||||||||||  ||||  |||  ||||||||||||||||||||||||||||||||||||| ||| |    |    |  |||   ||  | ||   ||| ||   |  ||  |  ||||  ||| |     |||  | ||| |    |  | |   
GAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttatgactgccttgtaatcttattcatacaactaggtatacgttgtattaa--attttgatcttctaaaaacatgtgcagaatttttgttctttcat

upper sequence: LOC_Os09g38790.3 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv01s0011g01240.t01 (Vitis vinifera), 5'ss of exon 6
GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctgatttttataattttatatctgtaatattaatgatatgtgaaaaaaaccaagttgaagttcatggggatgctctgaactg-gaatattgtgt------
|||||||||||| ||||  ||   ||||| ||||||||||||||||||||||||||||||| | | |     | || | ||  | |||| | | | |  ||   |   |      |  ||    ||||| | ||| |  | |  | || ||   |      
GAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAGgtaagttataact-----acttctgtaa-tataat-tcattcaactggatatggagttgcttccaaccagatgggtaggctttatattttgtatttttcatattcaa

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|88971854|gb|CI390446.1|CI390446
EST:     AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
genomic: AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
EST: gi|25797175|gb|CA753136.1|CA753136
EST:     AAGAAGATTGTCGCTACCCCAGGTATCAGGTGCATGATGANACTAGCCAG                         ATGAACTCAGT-GATGCAGCGAT-GATCGA
genomic: AAGAAGATTGTCGCTACCCAAG-TATCAGGTGCATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTTGATGCAGCAATTGATCGA
EST: gi|86431384|gb|CI084995.1|CI084995
EST:     AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
genomic: AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
EST: gi|86493697|gb|CI136330.1|CI136330
EST:     AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
genomic: AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
EST: gi|38475380|gb|CF959513.1|CF959513
EST:     AAGAAGATTGTCGCTACCCAAGTATCAGGTGCCATGATGAAACTAGCCAG                         ATGAACTCAGTT
genomic: AAGAAGATTGTCGCTACCCAAGTATCAGGTGC-ATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTT
EST: gi|89193768|gb|CI116401.1|CI116401
EST:     AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
genomic: AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
EST: gi|86504973|gb|CI147606.1|CI147606
EST:     AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
genomic: AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
EST: gi|86903499|gb|CI322982.1|CI322982
EST:     AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
genomic: AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
EST: gi|86498300|gb|CI140933.1|CI140933
EST:     AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
genomic: AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
EST: gi|86884774|gb|CI314350.1|CI314350
EST:     CCAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
genomic: CCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
EST: gi|33681611|gb|CF309850.1|CF309850
EST:     AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
genomic: AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
EST: gi|86538469|gb|CI178675.1|CI178675
EST:     AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT
genomic: AAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctg ... gtgtgaacagATGAACTCAGTTGATGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctgatttttataattttatatctgtaatattaatgatatgtgaaaaaaaccaagttgaagttcatggggatgctctgaactggaatattgtgt

- - AAAGAA
- -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggatg