Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgatataccatactgccttctctaaacaatgagctgatgcaaatactgccttccctaaaacccagtgctatagctgatgcttttttaccactgcaaactgtttgatttcagCTCGAGATGGAAGACGGCGACGAGATTGACGCCATGCTTCACCAGACTGGGGGCTCTCTGCCTGCCTAG

Basic information

species Oryza sativa
transcript LOC_Os01g68940.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68940.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G053898_T02 (Zea mays), 3'ss of exon 2
gtgcgtgatataccatactgccttctctaaacaatgagctgatgcaaatactgccttccctaaaacccagtgctatagctgatgcttttttaccactgcaaactgtttgatttcagCTCGAGATGGAAGACGGCGACGAGATTGACGCCATGCTTCACCAGACTGGGGGC-----TCTCTGC-CTGCCTAG-------------------------
                                  ||| |  || |     ||      || |  |   ||||  ||   ||||   | ||||  |  ||            | ||||| |||||||| |||||||||||||| |||||||||||||||||||| || |||     ||   || |  ||||                          
---------------------------------gtgacccaattcgg---ctttagatcccagcattgagtggaatcattgatcgatatttattatggctg----------tgcagCTGGAGATGGAGGACGGCGACGAGATCGACGCCATGCTTCACCAGACCGGAGGCAGCGTTCCTAGCACCACCTAAAAGCAGCAGCTGCGGAGCCTCGTTT

upper sequence: LOC_Os01g68940.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G082390_T01 (Zea mays), 3'ss of exon 2
gtgcgtgatataccatactgccttctctaaacaatgagctgatgcaaatactgccttccctaaaacccagtgctatagctgatgcttttttaccactgcaaactgtttgatttcagCTCGAGATGGAAGACGGCGACGAGATTGACGCCATGCTTCACCAGACTGGGGGC-----TCTCTGC-CTGCCTAG-------------------------
                                       |||  ||| |     |  |  || | |||||   |       || ||   | | |  |  |   | |     | ||||| |||||||| |||||||||||||| |||||||||||||||||||| || |||     ||   || |  ||||                          
--------------------------------------gtgacccaatt-----cggctttagatcccagcattgagtggaatact---tgatcgatagatcttttgcctgtgcagCTGGAGATGGAGGACGGCGACGAGATCGACGCCATGCTTCACCAGACCGGAGGCAGCGTTCCTAGCACCACCTAAAAGCCTCGTTTTGCTCTCCGTCCTG

upper sequence: LOC_Os01g68940.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S61_57V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgcgtgatataccatactgccttctctaaacaatg-agctgatgcaaatactgccttccctaaaacccagtgctatagctg-atgcttttttaccac-tgcaaactg--tttgattt-cagCTCGAGATGGAAGACGGCGACGAGATTGACGCCATGCTTCACCAGACTGG-GGGCTCTCTGCCTGCCTAG------------------------------
                   |    | ||  |||||  ||||  || |     ||   ||  | |   |  ||    |   || ||  ||  |||  |   |  | | |  | |    | |||||||| |||||||| || ||||||||||| |||||||| || || || || ||   |||| ||||    |                              
------------------cgataacactcgacaatacagcttttgtag----tgtgctcagtgattactcgtatatttattgtatatttccttatgaaacgtgacccggctctaccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGCGGAGCCTCTTCCTGATATGAATATGCCGTCTCAGGCAGTGTGGTCCTGA

upper sequence: LOC_Os01g68940.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ27988 (Selaginella moellendorffii), 3'ss of exon 2
gtgcgtgatataccatactgccttctctaaacaatgagctgatgcaaatactgccttccctaaaacccagtgctatagctgatgcttttttaccactgcaaactgtttgatttcagCTCGAGATGGAAGACGGCGACGAGATTGACGCCATGCTTCACCAGACTGGGGGCTCTCTGCCTGCCTAG-------------------------------
                                                              | |   |   ||   ||  |         ||         |||| |  | |||||| || ||||||||||||||||| || ||||||||||| || ||||| |||||| |   |   ||                                   
------------------------------------------------------------gtagagtaatccctcgcgcccacatgcaccgactgacttggcctgtctc-tctcagCTGGAAATGGAAGACGGCGACGAAATCGACGCCATGCTCCATCAGACCGGGGGCGCCTCGTAAGCTCCTCTCGCACATTTGTTGTCAAGCCTCTGGTTTC

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: 73 (upstream exon), 75 (downstream exon)
Score: 75

GCTGATGAACGCCTACTGTGATCGCCAGTCCGTGGATATCAAATCTATTGCCTTCCTGTTTGATGGTCGTAGGCTCAATGCTGAGCAGACCCCTGACCAGgtgcgtgata ... ttgatttcagCTCGAGATGGAAGACGGCGACGAGATTGACGCCATGCTTCACCAGACTGGGGGCTCTCTGCCTGCCTAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaacccagtgctatagctgatgcttttttaccactgcaaactgtttgatttcagCTCGAGATGGAAGACGGCGACGAGATTGACGCCATGCTTCACCAGACTGGGGGCTCTCTGCCTGCCTAG
                        tttttta  TA-rich tract