Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgtggttttcacaatcatttgaatgcacgtgttgaaattatgatatagtactgtcaattgaggaaaaaatgttaattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG

Basic information

species Oryza sativa
transcript LOC_Os04g51630.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G094051_T03 (Zea mays), 3'ss of exon 4
gtgggtgtggttttcacaatcatttgaatgcacgtgttgaaattatgatatagtactgtcaattgaggaaa-aaatgttaattt--tgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG
||| ||    |  |  |  |  ||  |||     || ||  ||||| || | ||    |   |||   ||   ||  ||  |||  |  ||||||| ||||| |||||| | || |||||||| || || ||||||||||| |||||||||||||||||||||||||||||
gtgtgttcactgatgtctgtttttacaattgcattgctgctattataattttgtctgattgtttgtaaaactgaacatttgtttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTACGCAGGGTTGAGCCATATGTTGCATATGG

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G094051_T06 (Zea mays), 3'ss of exon 4
gtgggtgtggttttcacaatcatttgaatgcacgtgttgaaattatgatatagtactgtcaattgaggaaa-aaatgttaattt--tgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG--------------------
||| ||    |  |  |  |  ||  |||     || ||  ||||| || | ||    |   |||   ||   ||  ||  |||  |  ||||||| ||||| |||||| | || |||||||| || || ||||||||||| |||||||||||||||||||||||||||||                    
gtgtgttcactgatgtctgtttttacaattgcattgctgctattataattttgtctgattgtttgtaaaactgaacatttgtttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTACGCAGGGTTGAGCCATATGTTGCATATGGGTAAGTTTTCTAGCTGATTT

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
gtgggtgtggttttcacaatcatttgaatgcacgtgttgaaattatgatatagtact-gtcaattgaggaaaaaatgttaattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG
      |||| |||  |||| |  |   |||   | ||||| |||||    | |  | || ||    |  |   |  |||||||| ||||| || ||||| |||||| |||| |||||||| || |||||||||||||| |||||||||||||| ||||||||||||||
------gtgggtttgccaattacgttcttgc---tattgaa-ttatggccgattgtttgtgaaactggacatttaatttaatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G344279_T02 (Zea mays), 3'ss of exon 5
--------gtgggtgtg-gttttcacaatcatttgaatgcacgtgttgaaattatgatatagtactgtcaattgaggaaaaaatgttaattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG
             |||  ||||| |||||    |   |||   | ||  |||| || |  | |  |   ||     ||| |  |||| |||||  ||||||| ||||| |||||| | || |||||||| || || ||| ||||||| ||||||||||| ||||||| |||||||||
atgtgttcactaatgtatgtttttacaattgcattgctgc---tattagaattttgtttgattgtttgtaaa-actgaacatttgtttatttt--agATCTTCAATGGCGTGTTCCTCAAAGTCAACAAGGCGACTATTGACATGCTACGCAGGGTTGATCCATATGATGCATATGG

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 4
gtgggtgtggttttcacaatcatttgaatgcacgtgttgaaattatgatatagtactgtcaattgaggaaaaaatgttaattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG
    || || |||| |||||    |   |||   | ||  |||| || |  | |  |   ||     ||| |  |||| |||||  ||||||| ||||| |||||| | || |||||||| || || ||| ||||||| ||||||||||| ||||||| |||||||||
----gtatg-tttttacaattgcattgctgc---tattagaattttgtttgattgtttgtaaa-actgaacatttgtttatttt--agATCTTCAATGGCGTGTTCCTCAAAGTCAACAAGGCGACTATTGACATGCTACGCAGGGTTGATCCATATGATGCATATGG

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 4
gtgggtgtggttttcacaatcatttgaatgca-cgtgttgaaattatgatatagtactgtca-attgaggaaaaaatgttaatt-ttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG
    ||     | | |  || |      || |   |||| ||   |||||| |  |   ||  ||     |   ||  | | || |||||||| || ||||| |||||||||||||||||||| || |||||||||||||| ||| | ||||| || |||||  | |||||
----gtaacaatcttatgatgagaactttgtaatatgtt-aaccaatgatacaaaaggatcgtatctgacacttaaaatcatttattgcagATTTTCAATGGTGTGTTCTTGAAGGTCAACAAGGCAACCATTAACATGCTTCGCCGTGTTGAACCCTATGTAACCTATGG

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S2_667V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------gtggg--tgtggttttcacaatcatttgaatgcacgt-gttgaaattatgatatagtactgtcaattgaggaaaaaatgttaattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG
                                                                     || |   | | |  || | | |        ||   || |||    || |   || |     |    ||| |  |  | ||   || |||||||||||||||| |||||| |||| || ||||||||||| || |||||| || |  | || |||||||||||  | || ||
gtacaagtattcgtcttcaatttgcttgcatgcctcttttctagctggattgggtattgaagctttaatgtagaattatagggtttagagtgccggagttgtttgttgttttctttttttcattgagtcattttctgatgtgagga-gtgctttatgcagATCTTTAATGGGGTGTTCATGAAAGTTAACAAAGCCACGATGAACATGTTGAGTCGAGTCGAGCCATATGTGACCTACGG

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|29618048|gb|CB623060.1|CB623060
EST:     CCATGCACCCAAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAG                         ATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTG
genomic: CCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAGgtgggtgtgg ... aattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTG
EST: gi|29618050|gb|CB623062.1|CB623062
EST:     CCATGCACCCAAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAG                         ATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTG
genomic: CCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAGgtgggtgtgg ... aattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTG
EST: gi|29641909|gb|CB646916.1|CB646916
EST:     CCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAG                         ATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTG
genomic: CCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAGgtgggtgtgg ... aattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTG
EST: gi|27577886|gb|CB000581.1|CB000581
EST:     CCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAG                         ATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTG
genomic: CCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAGgtgggtgtgg ... aattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttgaaattatgatatagtactgtcaattgaggaaaaaatgttaattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG
                                         tgttaat  putative branch site (score: 3)
                                   aaaaaatgttaatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgtggttttcacaatcatttgaatgcacgtgttgaaattatgatatagtactgtcaattgaggaaaaaatgttaattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC