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

ATGGAGATTCACCTTTTCTGGGCTGGAAAAGGAACTTGTTGCATTCCTAGACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATGgtactgttcattacctaacttgatcaagagccattggttctatgtgatcatcttataattaacatctattttgtttcattttatcctactgcag

Basic information

species Oryza sativa
transcript LOC_Os08g10250.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10250.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA08G25590.1 (Glycine max), 5'ss of exon 20
---ATGGAGATTCACCTTTTCTGGGCTGGAAAAGGAACTTGTTGCATTCCTAGACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATGgtactgt---------tcattacctaa---cttgatcaagagccattggttctatgtgatcatcttataatta-acatcta----ttttgtttcattttatcctactgcag-----------------
    | |||||||| || || |||||||||||||| ||||||||||| || |  || ||  | || ||||| |||||   |||| |   ||    |||   |  |||| |         |  | |  ||     || || |  | || ||  || |   | |||   |   |  || | ||  |    || | | |  |||||   |  | ||                  
TATCTTGAGATTCATCTCTTTTGGGCTGGAAAAGGTACTTGTTGCATACCAACTCAAGGTACTTATGGGCCCTTAATTCAAGCAATCCATGCTATTCCAGgtaatactatgaaaaaaattggtaatttagatgtttaattactaacctttcattatgcataatcccttatcagctagatattcaaaatttatatatttttttaatttgatacattgttttgtgttgtacag

upper sequence: LOC_Os08g10250.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA08G25600.1 (Glycine max), 5'ss of exon 17
---ATGGAGATTCACCTTTTCTGGGCTGGAAAAGGAACTTGTTGCATTCCTAGACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATGgtactgt----------tcattacctaa---cttgatcaagagccattggttctatgtgatcatcttataatta-acatcta----ttttgtttcattttatcctactgcag-----------------
    | |||||||| || || |||||||||||||| ||||||||||| || |  || ||  | || ||||| |||||   |||| |   ||     ||   |  |||| |          |  | |  ||     || || |  | || ||  || |   | |||   |   |  || | ||  |    || | | |  |||||   |  |  |                  
TATCTTGAGATTCATCTCTTTTGGGCTGGAAAAGGTACTTGTTGCATACCAACTCAAGGTACTTATGGGCCCTTAATTCAAGCAATCCATGCTATCCCAGgtaatactatgaaaaaaatttggtaatttagatgtttaattactaacctttcattatgcataatcccttatcagctagatattcaaaatttatatatatttttaatttgataaattgttttgtgttgtacag

upper sequence: LOC_Os08g10250.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT1G56120.1 (Arabidopsis thaliana), 5'ss of exon 17
---ATGGAGATTCACCTTTTCTGGGCTGGAAAAGGAACTTGTTGCATTCCTAGACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATGgtactgttcattacctaacttgatcaagagccattggttctatgtgatcatcttataattaacatctattttgtttcattttatcctactgcag
    | ||  | || ||||||||||||||||||||||| ||||| |||||||  || ||  | || |||||||||||  | ||  | ||||   | ||   |   ||      ||     | ||  |      ||  || || |     |||  |  |||  ||     |    |||  ||| || |  | | |   
CATCTCGAAGTCCATCTTTTCTGGGCTGGAAAAGGAACATGTTGTATTCCTATCCAAGGGGCTTATGGGCCATTAATAGCGGCCGTCAGTGCGACACCAGgtaacacaaacggttgatatatttttttt----cctctgatttt-cactatctcccgata-ctagttagtgccgtgtcacatattcttgttcag---

upper sequence: LOC_Os08g10250.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT1G56140.1 (Arabidopsis thaliana), 5'ss of exon 18
---ATGGAGATTCACCTTTTCTGGGCTGGAAAAGGAACTTGTTGCATTCCTAGACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATGgtactgttcattacctaacttgatcaagagccattggttctatgtgatcatcttataattaacatctattttgtttcattttatcctactgcag
    | || ||||| ||||||||||||||||||||||| || || |||||||  || ||  | || ||||||||||| || ||  |  ||| | | ||   |   |    |  | |  |    |  |      ||||    |     |  | |     ||| |   |  |||||   ||||                
CATCTCGAAATTCATCTTTTCTGGGCTGGAAAAGGAACATGCTGTATTCCTATCCAAGGGGCTTATGGGCCATTAATATCGGCCGTCGGTGCAACACCAGgtaa-ataaatggtgaattcttcttgttttacaccatctcctgatgctagttagtgcttaagtgttacatatttctgttcag---------------

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|29669416|gb|CB665691.1|CB665691
EST:     ACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATG                         GTGGCAACAATAAGGTTGATCCTGGTCCTATTAAAAACAGTGCTGGTAAAA
genomic: ACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATGgtactgttca ... cctactgcagGTGGCAACAATAAGGTTGATCCTGGTCCTATTAAAAACAGTGCTGGTAAAA
EST: gi|29674676|gb|CB670951.1|CB670951
EST:     ACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATG                         GTGGCAACAATAAGGNTGAT
genomic: ACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATGgtactgttca ... cctactgcagGTGGCAACAATAAGGTTGAT
EST: gi|29669536|gb|CB665811.1|CB665811
EST:     ACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATG                         GCGGCAACAATAAGGTTGATCCTGGTCCTATTAAAAACAGTGCTGGTAAAA
genomic: ACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATGgtactgttca ... cctactgcagGTGGCAACAATAAGGTTGATCCTGGTCCTATTAAAAACAGTGCTGGTAAAA
EST: gi|86493648|gb|CI136281.1|CI136281
EST:     ACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATG                         GTGGCAACAATAAGGTTGATCCTGGTCCTATTAAAAACAGTGCTGGTAAAA
genomic: ACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATGgtactgttca ... cctactgcagGTGGCAACAATAAGGTTGATCCTGGTCCTATTAAAAACAGTGCTGGTAAAA

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: 38 (upstream exon), 46 (downstream exon)
Score: 8

ATGGAGATTCACCTTTTCTGGGCTGGAAAAGGAACTTGTTGCATTCCTAGACAGGGATCCTACGGGCCATTAATCTCAGCATTAAGTGTATCTCCTTATGgtactgttca ... cctactgcagGTGGCAACAATAAGGTTGATCCTGGTCCTATTAAAAACAGTGCTGGTAAAAGTAAAATAGCTTTGGTAGCTGGAGTTGTTGTCTGTACTATAGTTTTAGG




<











<


<