Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgatcttctcatcagtcgtaaccagtttccagcttgcgcataactataaatttagtgctaactgatgaacctcggtataatcgtgtgactttgcattacag

Basic information

species Oryza sativa
transcript LOC_Os03g08550.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G330907_T01 (Zea mays), 5'ss of exon 14
CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgatcttctcatcagtcgtaaccagtttccagcttgcgcataactataaatttagtgctaactgatgaacctcggtataatcgtgtgactttgcattacag
|||| ||||||||||| ||||||||||| || ||||| ||||| |||||||||||||| |||||||| |||||  |||| ||||| ||||| || || |||||      ||    |||| ||  | |  || ||||   ||      |  ||||||||| ||  | | |||| |     |  || ||        ||| ||| ||||
CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTTTACAGCTTTGGAGTTGTCATGCTTGAGCTACTGACAGGACGTAGACCATTTGACAGgta---cactccaaccatctgttttta--agcttccttttt------agttataaatttggtcttga-tgatcagatatgccatcatgccactgtttttcatcacag

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G153393_T02 (Zea mays), 5'ss of exon 2
CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgatcttctcatcagtcgtaaccagtttccagcttgcgcataactataaatttagtgctaactgatgaacctcggtataatcgtgtgactttgcattacag
|||| ||||||||||| ||||||||||| || ||||| |||||||||||||||||||| |||||||| || || ||||| ||||| ||||| || || |||||         || |||||   ||      |||  ||||| |   ||  ||||||||| ||    | |||||| |   | |||     |||    || ||||||||
CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgta------cactcccatcatctgt------ttttaagctttcttttagttataaatttggt----attgatgatca--gatatgccactgt----ttccattacag

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA03G42360.1 (Glycine max), 5'ss of exon 16
CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgat---cttctcatcagtcgtaac---cagtttccagc----ttgcgcataactataaatttagtgctaactgatgaacctcggtataatcgtgtgactttgcattacag
| || || | | || |||||||||| ||  |||| || |||||||||||||||||||| |||||| | || ||| | |  ||||| | ||| || ||||||| | || ||    || |  |  |||    |   |  |||  |||    ||  ||| || |  |||||  ||    |                | || | |  || ||   | ||||
CTGAAGTTGCCTTGTCTGGTCAGTATACTTTGAAAAGTGATGTCTACAGCTTTGGAGTTGTCATGTTGGAACTTCTCAGCGGACGGAAACCATTTGATAGgtgaattaatggttttttttttggtctgctctcacgtttttgagcaatattctgcagaaattgaaattatgtagatataataatgttgtctcctgattgcgaaacattctgtaacag

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA19G45130.1 (Glycine max), 5'ss of exon 14
CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgat------cttctcatcagtcgtaaccagttt---ccagcttgcgcataactataaatttagtgctaactgatgaacctcggtataatcgtgtgactttgcattacag
| || || | | || |||||||||| ||  |||| || |||||||||||||||||||| |||||| | || ||| | |  ||||| |  ||||| ||||||| | || ||      |||    || |   | ||   |||   | |  ||  ||| |  |  |||||  |  | ||                | || |    || || ||| ||||
CTGAAGTTGCCTTGTCTGGTCAGTATACTTTGAAAAGTGATGTCTACAGCTTTGGAGTCGTCATGTTGGAACTTCTCAGTGGACGGAACCCTTTTGATAGgtgaattaatggttttctttatgtctgctctcacgtttttgagcaatattctgcagattttgaaattatgcacaaataataatgttgtctcctgattgcaaaacattccatgacag

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AT3G14350.3 (Arabidopsis thaliana), 5'ss of exon 15
CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgatcttct-catcagtcgtaaccagtttccagcttgcgcataactataaatttagtgctaactgatgaacctcggtataatcgtgtgactttgcattacag
||||       ||| | || || ||| |  ||||||||||||| ||||| ||||||||||| ||||| |||||||| || ||| | | ||| ||||| |||||  || |   ||   |||  |||    |       | |||  |  | | |  |||| |  |   || ||| | |  ||    | || ||     | ||  | ||||
CAGAAACTTCAATGTCAGGCCAATACTCTTTGAAGAGCGATGTTTACAGTTTTGGAGTAGTGATGCTCGAGCTTTTAACCGGAAGAAAACCATTCGACAGgtacttttacaatccatatccctcgccttcctaaaaaaacttaagagtga-tgcaaatgtgttcagaattgaagtaagtcctggtgattgt-----tgtgtgtgacag

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaac----ttgatcttctcatcagtcg-taaccagtttccagcttgcgcataactataaatttagtgctaactgatga--acctcggta-taatcgtgt-gactttgcattacag
| ||||| | |||| | ||||| || || |||||||| ||||| ||||| ||||| ||||||||||| |||||| |  | ||||| | ||| || |||||||||     |||  || ||   ||  |  | |     || |   ||  | | |   |   |  |    |  ||   |    || | | ||   ||  |||  || ||   | ||||
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ07060 (Selaginella moellendorffii), 5'ss of exon 4
CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgatcttctcatcagtcgtaaccagtttccagcttgcgcataactataaatttagtgctaactgatgaacctcggtataatcgtgtgactttgcattacag
| ||| | | |||| ||||   ||||||  | ||||||||||| |||||||||||||| || ||||| |||||| | || ||| | | | |  | || ||||||    |||||    |   ||    | ||  |      |  | | | ||  ||| ||    ||  | |                                     
CGGAGTTTGCCATGTCTGGCGTGTACACTGTCAAGAGCGATGTTTACAGCTTTGGAGTGGTGATGCTGGAGCTTCTAACCGGAAGAAAATCGCTAGACAGgtaa---aatcttgaagttcttccatccaagagttttatgtaagta-agctccaaacttgaaacttccag-------------------------------------

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ18843 (Selaginella moellendorffii), 5'ss of exon 4
CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgatcttctcatcagtcgtaaccagtttccagcttgcgcataactataaatttagtgctaactgatgaacctcggtataatcgtgtgactttgcattacag
| ||| | | |||| ||||   ||||||  | ||||||||||| |||||||||||||| || ||||| |||||| | || ||| | | | |  | || ||||||     |       |   ||    | ||  |      |  | | | ||  ||| ||    ||  | |                                     
CGGAGTTTGCCATGTCTGGCGTGTACACTGTCAAGAGCGATGTTTACAGCTTTGGAGTGGTGATGCTGGAGCTTCTAACCGGAAGAAAATCGCTAGACAGgtaaaagcttgaagaagttcttccatccaagagttttatgtaagta-agctccaaacttgaaacttccag-------------------------------------

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|86252666|gb|CI004002.1|CI004002
EST:     ACCTTTCGATAG                         CACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
genomic: ACCTTTCGATAGgtaacttgat ... tgcattacagCACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
EST: gi|29624949|gb|CB629960.1|CB629960
EST:     TTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAG                         CACTAGACCGAGGTCAGAGCAGTCACTCGTGCGGTGGGCGACTCCACAGCT
genomic: TTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgat ... tgcattacagCACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
EST: gi|88906724|gb|CI375796.1|CI375796
EST:     ACGCAGACCTTTCGATAG                         CACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
genomic: ACGCAGACCTTTCGATAGgtaacttgat ... tgcattacagCACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
EST: gi|29644650|gb|CB649657.1|CB649657
EST:     TTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAG                         CACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
genomic: TTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgat ... tgcattacagCACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
EST: gi|89191025|gb|CI392878.1|CI392878
EST:     ACGCAGACCTTTCGATAG                         CACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
genomic: ACGCAGACCTTTCGATAGgtaacttgat ... tgcattacagCACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
EST: gi|88253840|gb|CI352466.1|CI352466
EST:     TTGACGGGACGCAGACCTTTCGATAG                         CACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
genomic: TTGACGGGACGCAGACCTTTCGATAGgtaacttgat ... tgcattacagCACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
EST: gi|89172730|gb|CI022609.1|CI022609
EST:     TTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAG                         CACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT
genomic: TTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgat ... tgcattacagCACTAGACCGAGGTCAGAGCAGTCACTTGTGCGGTGGGCGACTCCACAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgatcttctcatcagtcgtaaccagtttccagcttgcgcataactataaatttagtgctaactgatgaacctcggtataatcgtgtgactttgcattacag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT