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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttttattaaatgccttgtctcttgaaaaaaaatacttgattgataatttttctttgtattttcaagattgtatgctaactctaattccactttatttttctcgttttcgctcatcattttgaattttcagGGCTCTGGTGGGGGTCATTGATGAGTATTTTGATGGTTATTACACTGAGGAAATGATTGAATCTCAG

Basic information

species Oryza sativa
transcript LOC_Os03g17540.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17540.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G095868_T03 (Zea mays), 3'ss of exon 6
gtatgcttttattaaatgccttgtctcttgaaaaaaaatacttgattgataatttttctttgtattttcaagattgtatgctaactctaattccactttatttttctcgttttcgctcatcattttgaattttcagGGCTCTGGTGGGGGTCATTGATGAGTATTTTGATGGTTATTACACTGAGGAAATGATTGAATCTCAG
|||||  ||| ||  ||        |      |||||| | |  || |  |||||||  |        || || ||||||                      ||   | ||||| ||     |||||||||| ||||||| | || ||||| |||||||| ||||||||||| || |||||||| |||||||||||||| |||
gtatgtctttcttgtata-------tggaaggaaaaaagattcaatggccaatttttagtg-------catgactgtatgg--------------------cttctccattttcacttgc--ttttgaattt-cagGGCTTTAGTAGGGGTTATTGATGATTATTTTGATGGATACTACACTGAAGAAATGATTGAATCACAG

upper sequence: LOC_Os03g17540.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G154883_T01 (Zea mays), 3'ss of exon 6
gtatgcttttattaaatg--ccttgtctcttgaaaaaaaatacttgattgataatttttctttgtattttcaagattgtatgctaactctaattccactttatttttctcgttttcgctcatcattttgaattttcagGGCTCTGGTGGGGGTCATTGATGAGTATTTTGATGGTTATTACACTGAGGAAATGATTGAATCTCAG
|||||  || || |||||  |||||| | | |||   ||| |  |  |  ||     || |||     | ||||  ||||||    ||| | ||  ||||          | ||| ||              |||||||||  | || ||||| |||||||| ||||||||||| || |||||||| ||||||||||||||||||
gtatgtcttcatgaaatggaccttgtatatggaagggaaaaaaatattcaatggccctttttta---gtgcaaggctgtatggcttctccattttgactt----------gcttttgca-------------tttcagGGCCTTAGTAGGGGTTATTGATGATTATTTTGATGGATACTACACTGAAGAAATGATTGAATCTCAG

upper sequence: LOC_Os03g17540.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G05490.1 (Glycine max), 3'ss of exon 7
gtatgcttttattaaatgccttgtctcttgaaaaaaaatacttgattgataatttttctttgtatt-ttcaagattgtatgctaactctaattccactttatttttctcgttttcgctcatcattttgaattttcagGGCTCTGGTGGGGGTCATTGATGAGTATTTTGATGGTTATTACACTGAGGAAATGATTGAATCTCAG
                     ||||| || ||| | |         |||||||   |||||||||| || || |    |  ||   | |   | |  ||||| ||      |   | | |     |||   | |||||||  | |  ||  | |||||||| |||||||  || ||||| |||||||| |||||||||||||| 
-------------------gctgtctatttaaagaca---------tgataata--tctttgtattgtttaacaaaaaacacttggtttgtcttctgtttatattatctaat---gtttaa----ttgggatctcagGGCATTTGCTGGCATTATTGATGAATATTTTGCAGGCTATTATACTGAGGATATGATTGAATCTCAA

upper sequence: LOC_Os03g17540.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G37290.2 (Arabidopsis thaliana), 3'ss of exon 6
gtatgcttttattaaatgccttgtctcttgaaaaaaaatacttgattgataatttttctttgtattttcaagattgtatgctaactctaattccactttatttttctcgttttcgctcatcattttgaattttcagGGCTCTGGTGGGGGTCATTGATGAGTATTTTGATGGTTATTACACTGAGGAAATGATTGAATCTCAG
                                         | || ||||||   |  ||| | | |      ||| |  |||||      | || |    |   ||  ||||      | | |   |  | ||||| || |||| ||| | |||||||| ||||||||||| || || ||||| |||||||| |||||||||
----------------------------------------gtagagtgataaagctgttttctctgtct----ttgaaccctaaca-----tgcattggtatgagctgatttttttgtgtaactgaaatgtctcagGACTTTGGTTGGGATAATTGATGATTATTTTGATGGCTACTATACTGAAGAAATGATAGAATCTCAG

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|29626820|gb|CB631831.1|CB631831
EST:     TTTTTTGCTGGCCTATTTTTATTATTCATGCCTGAAGAGCATGCATTCTG                         GGCTCTGGTGGGGGTCATTGATGAGTATTTTGATGGTTATTACACTGAGGA
genomic: TTTTTTGCTGGCCTATTTTTATTATTCATGCCTGAAGAGCATGCATTCTGgtatgctttt ... gaattttcagGGCTCTGGTGGGGGTCATTGATGAGTATTTTGATGGTTATTACACTGAGGA
EST: gi|29626861|gb|CB631872.1|CB631872
EST:     TTTTTTGCTGGCCTATTTTTATTATTCATGCCTGAAGAGCATGCATTCTG                         GGCTCTGGTGGGGGTCATTGATGAGTATTTTGATGGTTATTACACTGAGGA
genomic: TTTTTTGCTGGCCTATTTTTATTATTCATGCCTGAAGAGCATGCATTCTGgtatgctttt ... gaattttcagGGCTCTGGTGGGGGTCATTGATGAGTATTTTGATGGTTATTACACTGAGGA

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: 50 (upstream exon), 65 (downstream exon)
Score: 5

GCCATGAACTTTTTTGCTGGCCTATTTTTATTATTCATGCCTGAAGAGCATGCATTCTGgtatgctttt ... gaattttcagGGCTCTGGTGGGGGTCATTGATGAGTATTTTGATGGTTATTACACTGAGGAAATGATTGAATCTCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactctaattccactttatttttctcgttttcgctcatcattttgaattttcagGGCTCTGGTGGGGGTCATTGATGAGTATTTTGATGGTTATTACACTGAGGAAATGATTGAATCTCAG
                                                ttttc  CT-rich tract
                                     atcattttgaatttt  TA-rich tract