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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatcttactaacttatggagccaactattacttgtttgaaaaacaagttggaagcattgtgtttaggttcaatgtgctgtggcttgctgaatta...

Basic information

species Oryza sativa
transcript LOC_Os02g56850.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G806449_T01 (Zea mays), 5'ss of exon 3
GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatcttactaacttatggagcca--actattacttgtttgaaaaacaagttggaag-------cattgtgtttaggttca-atgtgctgtggcttgctgaatta-------------------------------
 || |||||||||||||| || |||||||||||||| ||||||||| |||| ||||| |||||||||||||| | | || |||||  |||||   |  |  |||| |    || |  ||||    |  ||||       ||| |  | || |  || |  |||  ||  |   |  |||                                
TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATCATTCCGTGGAGAATTTGAGgttagtcatgttactgtcttattatgatagaactaatgtgggtatccaaaatggttctgaagtggctatcatggaatctaaggacacacttgccttgattg--tagattgtatgtgaactgtagttttgttacaaatgcag

upper sequence: LOC_Os02g56850.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv05s0051g00870.t01 (Vitis vinifera), 5'ss of exon 5
GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatcttactaacttatggagccaactattacttgtttgaaaaacaagttg----gaagcattgtgtttaggttcaatgtgctgtggcttgctgaatta
|||||| || ||||||||||| |||||||||||  ||||||||||  |||||||  | || ||| ||||||| |  | |  |   | ||  |  ||  |  ||| |  |   |  | || || ||      ||  | |     |   ||   ||   | ||| ||  | ||   
GTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATCTTTTAGAGGTGAAATTGAGgtgagagtttgtttgatctgtttcagaaacatatgatataaatccacaataatttatccaaaaaaaataaccatttctttcttggattttggttt--taaag--
















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|88314032|gb|CI600034.1|CI600034
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACGTG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAAC-TG
EST: gi|29670415|gb|CB666690.1|CB666690
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|88760896|gb|CI770452.1|CI770452
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTG
EST: gi|88352021|gb|CI626021.1|CI626021
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAA
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAA
EST: gi|88337120|gb|CI628206.1|CI628206
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAA
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAA
EST: gi|88430778|gb|CI596892.1|CI596892
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|2443112|gb|C74883.1|C74883
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|38469842|gb|CF953973.1|CF953973
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCA
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCA
EST: gi|88723894|gb|CI745591.1|CI745591
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTCGGGTGGGAAATCA
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCA
EST: gi|88760244|gb|CI769800.1|CI769800
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGA
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGA
EST: gi|88416046|gb|CI594158.1|CI594158
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|88396564|gb|CI601047.1|CI601047
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGG
EST: gi|29680732|gb|CB677007.1|CB677007
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|88694888|gb|CI738926.1|CI738926
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGA
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGA
EST: gi|29675048|gb|CB671323.1|CB671323
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|88726529|gb|CI750184.1|CI750184
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACA
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACA
EST: gi|88389287|gb|CI598085.1|CI598085
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAA
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAA
EST: gi|88417209|gb|CI576283.1|CI576283
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|88744812|gb|CI768172.1|CI768172
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATG

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: 70 (upstream exon), 72 (downstream exon)
Score: 78

GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatcttactaacttatggagccaactattacttgtttgaaaaacaagttggaagcattgtgtttaggttcaatgtgctgtggcttgctgaatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacaa