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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttcaagctaacgtcacaaactgcctaactcctgcgcttgaaatgttgtgtatggcacattgctcacaacctgatctgtgctactgtaactgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g50480.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 1
ggttcaagctaacgtcacaa-actgcctaactcctgcgcttgaaatgttgtgtatggcacattgctcacaacctgatctgtgctactgtaactgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG
   |||       || ||   | ||  |   | |  |  | | | |||    |   | | |    |       | ||   | ||  ||| | | ||||||||||||||||||||||||||| ||||| || ||||||||||| ||||| ||||| |||||||||||||  ||  |||||| ||
tcatcagtgacttgttactttaatgtttggtttcatctgtagcattgtacaattcagtataccttttttcttataattaat-cttttgttaatattaccagGTTACTGTATTCCAGCAGCCCCATTATCTGCAGAACTTTGTCCAATCAACATTCAATGCCCTTCCTGTGGATCAAGTAAGAG

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G023289_T01 (Zea mays), 3'ss of exon 1
---ggttcaagctaacgtcacaaactgcctaactcctgcgcttgaaatgttgtgtatggcacattgctcacaacctgatctgtgctactgtaactgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG
     ||    ||   |   |   ||   ||  |   ||  | | |   || |   ||     || || | ||       | || ||   | | | || |||||||||||||||||||||||||||||| || ||||||||||| || || ||||| |||||||||||||| ||| |||||||||
atactttgttactttggatgcttgctttttatgtatagca-tagtacaattattattgttttttttcttataattaatattttgtta--attaatattgccagGTTACTGTATTCCAGCAGCCTCATTATCTGCAGAACTTTGTCCAGTCAACATTCAATGCCCTTCCTGCAGACCAAGTAAAAG
















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|33675938|gb|CF304177.1|CF304177
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|11863329|gb|AU066043.2|AU066043
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|58688355|gb|CK077042.1|CK077042
EST:     CCACGCCCTTCGACGGNCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|29612833|gb|CB617846.1|CB617846
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|29689598|gb|CB685873.1|CB685873
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|29671540|gb|CB667815.1|CB667815
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|58670502|gb|CK059188.1|CK059188
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|29682384|gb|CB678659.1|CB678659
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|33676013|gb|CF304252.1|CF304252
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|58667231|gb|CK055917.1|CK055917
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCGCGGATTACCTCCAGAACTTTGTGCAATCCAC
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGC-CTCATTACCTCCAGAACTTTGTGCAATCCAC
EST: gi|29614791|gb|CB619804.1|CB619804
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|29671584|gb|CB667859.1|CB667859
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|58668595|gb|CK057281.1|CK057281
EST:     AAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTATCTCCAGAACTTTGTGCAATCCACA
genomic: AAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
EST: gi|33675599|gb|CF303838.1|CF303838
EST:     CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAG                         GTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA
genomic: CCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACA

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: 65 (upstream exon), 72 (downstream exon)
Score: 77

GCGTGAGCCAGCAGCAGCCATGGTGCTGTTCTCGGTGACGAAGAAGGCCACCACGCCCTTCGACGGCCAGAAGCCCGGCACCTCCGGCCTCCGCAAGAAGgtttcccatc ... ctgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttcaagctaacgtcacaaactgcctaactcctgcgcttgaaatgttgtgtatggcacattgctcacaacctgatctgtgctactgtaactgttaccagGTTACTGTATTCCAGCAGCCTCATTACCTCCAGAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG

- - - - - - - - - - actgcct
- - - - - - - - - - - - - - -ctcctgc
- - - - - - - - - - - - - - - - - - gcttgaa
- - - - - - - - - - - - - - - - - - - - - - - - gtgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctact