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'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttggttgccacattctttcaaccatagttttattggatagtttttttgctggttttttaatgcttctattcacgtcaccttttgcagAGCGATGAATCTTTATATGAGCGTGAATGTGGAAATAAGCCAGGTTTCGCTGTGTACATCAGATATCCAAATAGCCAGCGTGTATCTTATAGCCAGTTTG

Basic information

species Oryza sativa
transcript LOC_Os01g68810.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68810.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G461356_T01 (Zea mays), 3'ss of exon 2
----------------------------gtatttggttgccacattctt--tcaaccatagttttattggatagtttttttgctggttttttaatgcttctattcacgtcaccttttgcagAGCGATGAATCTTTATATGAGCGTGAATGTGGAAATAAGCCAGGTTTCGCTGTGTACATCAGATATCCAAATAGCCAGCGTGTATCTTATAGCCAGTTTG
                             | | |  ||||   |||| |  | ||  || |   | | || || || ||||  || || || | || || | | ||    || |  ||||||| ||||||||| | ||||||||||||||||  || || || ||||| || |||||| ||||||| ||||| ||||||||||| || || || |||||||
gtattttccctctcaactgttaccacacatttatcattgctgtattcatggtaaagaatgggagtgtcggtta-ttgttttagtgcttcttaattgtttatctcca----acatactgcagAGTGATGAATCTGTCTATGAGCGTGAATGTGCGAACAAACCTGGTTTTGCAGTGTACTTCAGATACCCAAACAGCCAGCGTGTGTCCTACAGTCAGTTTG

upper sequence: LOC_Os01g68810.1 (Oryza sativa), 3'ss of exon 26
lower sequence: EFJ25405 (Selaginella moellendorffii), 3'ss of exon 24
gtatttggttgccacattctttcaaccatagttttattggatagtttttttgctggttttttaatgcttctattcacgtcaccttttgcagAGCGATGAATCTTTATATGAGCGTGAATGTGGAAATAAGCCAGGTTTCGCTGTGTACATCAGATATCCAAATAGCCAGCGTGTATCTTATAGCCAGTTTG
                              ||     |   |||    ||||      ||||||         | | ||    || ||||||||||||||||  | ||||| || ||||||||||||| ||| ||||| |||||      |||| |||| || || || || ||| |||     |||||||
------------------------------gtacacatcattagcaactttgacaacgttttaacaacctc--tgatgt----ttctgcagAGCGATGAATCGGTTTATGATCGAGAATGTGGAAATATGCCTGGTTTTGCTGTTCTGTACAGAGATCCGAACAGTCAACGGGTAACTTTCGCACAGTTTG

upper sequence: LOC_Os01g68810.1 (Oryza sativa), 3'ss of exon 26
lower sequence: EFJ23423 (Selaginella moellendorffii), 3'ss of exon 24
gtatttggttgccacattctttcaaccatagttttattggatagtttttttgctggttttttaatgcttctattcacgtcaccttttgcagAGCGATGAATCTTTATATGAGCGTGAATGTGGAAATAAGCCAGGTTTCGCTGTGTACATCAGATATCCAAATAGCCAGCGTGTATCTTATAGCCAGTTTG
                                      | | |  |  ||  |   |||   ||     | |     |     || ||||||||||||||||  | ||||| || ||||||||||||| ||| ||||| |||||      |||| |||| || || || || ||| |||     |||||||
--------------------------------------gtacacatcattatcaactttgacaacataacaacctctgatgt-ttctgcagAGCGATGAATCAGTTTATGATCGAGAATGTGGAAATATGCCTGGTTTTGCTGTTCTGTACAGAGATCCGAACAGTCAACGGGTAACTTTCGCACAGTTTG

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|29677496|gb|CB673771.1|CB673771
EST:     GGCTGGGAAGGTTTCTTCATGAGACACTGAAGATGGCCTACCGTTGGAAG                         AGCGATGAATCTTTATATGAGCGTGAATGTGGAAATAAGCCAGGTTTCGCT
genomic: GGCTGGGAAGGTTTCTTCATGAGACACTGAAGATGGCCTACCGTTGGAAGgtatttggtt ... ccttttgcagAGCGATGAATCTTTATATGAGCGTGAATGTGGAAATAAGCCAGGTTTCGCT




















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: 59 (upstream exon), 66 (downstream exon)
Score: 16

CAAAACTCTACAGCCAATGATTTGTTGCTGCACAGAGTATGAGGCTGGCAGGCTGGGAAGGTTTCTTCATGAGACACTGAAGATGGCCTACCGTTGGAAGgtatttggtt ... ccttttgcagAGCGATGAATCTTTATATGAGCGTGAATGTGGAAATAAGCCAGGTTTCGCTGTGTACATCAGATATCCAAATAGCCAGCGTGTATCTTATAGCCAGTTTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggatagtttttttgctggttttttaatgcttctattcacgtcaccttttgcagAGCGATGAATCTTTATATGAGCGTGAATGTGGAAATAAGCCAGGTTTCGCTGTGTACATCAGATATCCAAATAGCCAGCGTGTATCTTATAGCCAGTTTG
                      ttttaat  putative branch site (score: 16)
                                          tcacctttt  putative PPT
                    ttttttaat  TA-rich tract