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'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGATGATGTAGATCCGTTTGACGAGAAGCCTCCACCATCTCTTCTCTCTAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttgtttttgttactgtatctgttatatacacatatttgctaaaagagctgaaaataatgccattactttcttttatttattcaaatttgtcaactgtag

Basic information

species Oryza sativa
transcript LOC_Os01g60440.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G098042_T01 (Zea mays), 5'ss of exon 5
TGGGATGATGTAGATCCGTTTGACGAGAAGCCTCCACCATCTCTTCTCTCTAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttgtttttgttac-tgtatctgttatatacacatatttgctaaaagagctgaaaataatgccattactttcttttatttattcaaatttgtcaactgtag
|||||||||||||| |||||||| || |||||  ||||||||||||| || |||||||||||||| ||||||||||| |||||||||||||| ||| | |||| |  | | |||||| |  || ||   ||   | ||   |  |||      | ||   | ||      | ||| |     |  || |||||| ||  || |    
TGGGATGATGTAGACCCGTTTGAGGACAAGCCATCACCATCTCTTCTATCCAACATACAGGCTGCACAGAAACGTCCAGTGGCGCAACCAAAGCAAGCTGgtaag--tagcttttgtcaagtgcattatttcctttcatgcagctgcatggtcatctttcattacaattgt-actattggaaacataatcaaatgtga-aatta---

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 20
lower sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 21
TGGGATGATGTAGATCCGTTTGACGAGAAGCCTCCACCATCTCTTCTCTCTAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttgtttttgttactgtatctgttatatacacatatttgctaaaagagctgaaaataatgccattactttcttttatttattcaaatttgtcaactgtag
|||||||||||||| || ||||| || |||||  | ||||||||||| || ||||||||||||||||| |||||||| |||| ||||||||| ||||| |||| |||   |||     | |||||   ||   | ||   | | ||      | ||   | ||      | ||| |     |  || |||| | ||  || |    
TGGGATGATGTAGACCCATTTGAGGACAAGCCATCCCCATCTCTTCTATCCAACATACAGGCTGCTCAAAAACGTCCAGTGGTGCAACCAAAGCAACCGGgtaagctggctttcgtcgagtgtattgttttgtttcatgcagtcgcatggtcatctttcattacaattgt-actattgcaaacataatcaagtatga-aatt----
















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|38480058|gb|CF964147.1|CF964147
EST:     TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGGCCAAACCAGAAGAGG
genomic: TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
EST: gi|29656612|gb|CB652887.1|CB652887
EST:     TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
genomic: TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
EST: gi|58603390|gb|CK013918.1|CK013918
EST:     TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGGCCAAACCAGAAGAGG
genomic: TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
EST: gi|300215776|gb|HO088402.1|HO088402
EST:     TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
genomic: TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
EST: gi|29640582|gb|CB645591.1|CB645591
EST:     TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
genomic: TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
EST: gi|86482087|gb|CI124720.1|CI124720
EST:     CTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
genomic: CTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
EST: gi|313079997|gb|HO213317.1|HO213317
EST:     TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
genomic: TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
EST: gi|218482575|gb|FG966889.1|FG966889
EST:     TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
genomic: TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
EST: gi|218497307|gb|FG954387.1|FG954387
EST:     TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
genomic: TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
EST: gi|38477603|gb|CF961736.1|CF961736
EST:     TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
genomic: TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
EST: gi|29623604|gb|CB628615.1|CB628615
EST:     TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
genomic: TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
EST: gi|33675788|gb|CF304027.1|CF304027
EST:     TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAG                         TATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG
genomic: TAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGG

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: 75 (upstream exon), 24 (downstream exon)
Score: 4

TGGGATGATGTAGATCCGTTTGACGAGAAGCCTCCACCATCTCTTCTCTCTAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttg ... tcaactgtagTATCAAATTCGTCAAGATTAAATCAACCAAAGGTGCCCAAACCAGAAGAGGATCCTCTATGGGGTTCTATAGCTGCTCCAGCACCCAAAAATGCATCGAA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGATGATGTAGATCCGTTTGACGAGAAGCCTCCACCATCTCTTCTCTCTAACATACAGGCTGCTCAGAAACGTCCTGTGGCGCAACCAAAACAACCAGgtaggctttgtttttgttactgtatctgttatatacacatatttgctaaaagagctgaaaataatgccattactttcttttatttattcaaatttgtcaactgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT