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'   
21  
 5'  3'   
22  
 5'  3'   
23  
 5'  3'   
24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttcttcaaaatcaactgtaattatttcaaacatcatttgtttgtgagaatgacttgtcttgctgcctcatcagGCCAACAACAAAAGAGTATTTGGAAACCGTTCTTTTCGCCCAAATCAACGAGAAATAATCAACGCCACAATGAGTGGGAATGATGTTTTTGTTTTGATGC

Basic information

species Oryza sativa
transcript LOC_Os04g35420.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g35420.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G319573_T03 (Zea mays), 3'ss of exon 6
gttattttcttcaaaatcaactgt-aattatttcaaacatcatttgtttgtgagaatgacttgtctt-gctgcctcatcagGCCAACAACAAAAGAGTATTTGGAAACCGTTCTTTTCGCCCAAATCAACGAGAAATAATCAACGCCACAATGAGTGGGAATGATGTTTTTGTTTTGATGC
||||||||||||| |||| | | |||||||| ||||| | ||| ||| | | | ||| ||| | |||||||| |||| || |||||||||| |||||| ||||| || ||||||||||||||||| ||||||||||||||| |||||||||||||||||||||
gttattttcttcagcatcattttttaattatttacgccatcactgatttttgaatactattaacctttagtgcatatccagGCCAAGAACAGAAATAAGTTTGGAAACCATTCTTTCCGCCCCAACCAACGAGAAATAATCAATGCCACAATGAGTGGGCATGATGTTTTTGTTTTGATGC

upper sequence: LOC_Os04g35420.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 10
gttattttcttcaaaatcaactgtaattattt-caaacatcatttgtttgtgagaatgacttgtcttgctgcctcatcagGCCAACAACAAAAGAGTATTTGGAAACCGTTCTTTTCGCCCAAATCAACGAGAAATAATCAACGCCACAATGAGTGGGAATGATGTTTTTGTTTTGATGC
| || | ||| | | || || | | | | | | || |||| | | | | | | ||| || || |||| |||||||||||| | || |||||||| |||||| |||| || || || ||| |||||||||| ||||||||||||| ||||||
---gtatttaactgaattattgtcagtttccagtgaatgtaactcatcttt----ataactt-tttccttactt--ttagGTTAATAATAAAAAAGTATTTGGAAATCACTCATTTCGCCCCAATCAAAGAGAGATCATTAATGCCTCAATGAGTGGATGTGATGTTTTTGTTCTGATGC

upper sequence: LOC_Os04g35420.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G10930.1 (Arabidopsis thaliana), 3'ss of exon 8
gttattttcttcaaaatcaactgtaattatttcaaacatcatttgtttgtgagaatgacttgtcttgctgcctcatcagGCCAACAACAAAAGAGTATTTGGAAACCGTTCTTTTCGCCCAAATCAACGAGAAATAATCAACGCCACAATGAGTGGGAATGATGTTTTTGTTTTGATGC
|| |||| || | | || | || |||| | | || | ||| ||| || ||||| | ||||| || ||||||| ||| |||||||| | ||| ||||| || || || ||||||| ||||| || ||||||||||| ||||||||||||||||||||
gtgatttgct--gagtttctcttttctttgttcactta-cgttcaat-gtgctcatgtgtttccttgcaaagt--tcagGTTAATAACAAAAAAGTGTTTGGAAATCATTCGTTTCGACCTAACCAGAGAGAAATTATCAATGCAACAATGAGTGGCTCTGATGTTTTTGTTTTGATGC

upper sequence: LOC_Os04g35420.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv12s0035g00400.t01 (Vitis vinifera), 3'ss of exon 4
gttattttcttcaaaatcaactgtaattat-ttcaaacatcatttgtttgtgagaatgacttgtcttgctgcc-tcatcagGCCAACAACAAAAGAGTATTTGGAAACCGTTCTTTTCGCCCAAATCAACGAGAAATAATCAACGCCACAATGAGTGGGAATGATGTTTTTGTTTTGATGC
|| | ||| || || || | | || | | ||| | || ||| | || || | || | ||||||||||||||| | ||| |||||||||| || || ||||| |||||| | || | ||||| || ||||||||||| |||||||||||||| | ||||
gtgctcatctgcattgatgtttgaaaatctatttacattgcatgtacttctgattgttacactcactggtcccgttttcagGCCAACAACAAGAAAGTTTTTGGAAACCACTCATTCCGCCCCAATCAAAGGGAGGTCATCAATGCTACAATGAGTGGATATGATGTTTTTGTTCTAATGC

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|218480652|gb|FG970533.1|FG970533
EST:     GTGATAAACAGTGGAGTAGTACACACTTTGCATGGACTAAGGAACTCGAG                         GCCAACAACAAAAGAGTATTTGGAAACCGTTCTTTT
genomic: GTGATAAACAGTGGAGTAGTACACACTTTGCATGGACTAAGGAACTCGAGgttattttct ... gcctcatcagGCCAACAACAAAAGAGTATTTGGAAACCGTTCTTTT




















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: 54 (upstream exon), 52 (downstream exon)
Score: 3

GAGAGATTACACTCCAAGGGCTATTGATATCAGTTACACTGAAGGTTCTGGTGATAAACAGTGGAGTAGTACACACTTTGCATGGACTAAGGAACTCGAGgttattttct ... gcctcatcagGCCAACAACAAAAGAGTATTTGGAAACCGTTCTTTTCGCCCAAATCAACGAGAAATAATCAACGCCACAATGAGTGGGAATGATGTTTTTGTTTTGATGC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattatttcaaacatcatttgtttgtgagaatgacttgtcttgctgcctcatcagGCCAACAACAAAAGAGTATTTGGAAACCGTTCTTTTCGCCCAAATCAACGAGAAATAATCAACGCCACAATGAGTGGGAATGATGTTTTTGTTTTGATGC
                                           ctgcctc  CT-rich tract
 atttgttt  TA-rich tract