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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcaacagtttgtgcacaatggcctttttttaacccctttttttcactaaacagcggtttacttttgcagTCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG

Basic information

species Oryza sativa
transcript LOC_Os01g56630.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 12
----------------gtactcaacagtttgtgcacaatggcctttttttaacccctttttttcactaaacagcggtttacttttgcagTCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG
                 || || |   | |   |   |       || |    | ||| ||||  ||||| |   ||||| |||||||||| ||||| |||||||| ||||| || ||||| ||||||||||| ||||| ||||||||||| ||||||||||||||||| |||||||| |||
gtagtcttcctttattttattccatgatgtcatcttcaccattgcttatctttctcttcttttt-ctaaataattgtttatttttgcagTCTACAGAGCTTCACATATATACAGATTTCTTGAGAATTGTTCTGGAAATAATCAATGCAATCCTTACATATGCATTGCCCAGAAATCCCGAG

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G079389_T01 (Zea mays), 3'ss of exon 12
gtactcaacagtt--tgtgcacaatggcctttttttaacc-------------cctttttttcactaaacagcggtttacttttgcagTCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG
||| || | | ||  | ||  | |||     || || | |             |  || |||  ||||| |    |||| |||||||||| | ||| |||||||| ||||| || ||||||||||||||||| || || || | ||| || ||||||||||||||||| ||||||||||||
gtagtctagatttattttgttccatgatgccttcttcatcattgcatgtgtttctcttctttttctaaataattatttatttttgcagTCTATAGAGCTTCACATATATACAGATTTCTTAAGAATTGTTCTGGAGATAATTATTGCCATCCTTACATATGCATTGCCCAGAAATCCTGAG
















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|58684083|gb|CK072770.1|CK072770
EST:     TCAAAGTTATATCTGATCAGATTGAAGCAGACAACATCTCAGATGATACG                         TCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATC
genomic: TCAAAGTTATATCTGATCAGATTGAAGCAGACAACATCTCAGATGATACGgtactcaaca ... acttttgcagTCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATC
EST: gi|426809|gb|D22882.1|D22882
EST:     TCAAAGTTATATCTGATCAGATTGAAGCAGACAACATCTCAGATGATACG                         TCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATC
genomic: TCAAAGTTATATCTGATCAGATTGAAGCAGACAACATCTCAGATGATACGgtactcaaca ... acttttgcagTCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATC
EST: gi|58678344|gb|CK067031.1|CK067031
EST:     TCAAAGTTATATCTGATCAGATTGAAGCAGACAACATCTCAGATGATACG                         TCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATC
genomic: TCAAAGTTATATCTGATCAGATTGAAGCAGACAACATCTCAGATGATACGgtactcaaca ... acttttgcagTCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATC
EST: gi|29639051|gb|CB644060.1|CB644060
EST:     TCAAAGTTATATCTGATCAGATTGAAGCAGACAACATCTCAGATGATACG                         TCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATC
genomic: TCAAAGTTATATCTGATCAGATTGAAGCAGACAACATCTCAGATGATACGgtactcaaca ... acttttgcagTCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATC

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: 74 (upstream exon), 57 (downstream exon)
Score: 9

GTATACCAAATTAGCCGAGTTAAAAAATGACAAAGCTATCAAAGTTATATCTGATCAGATTGAAGCAGACAACATCTCAGATGATACGgtactcaaca ... acttttgcagTCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatggcctttttttaacccctttttttcactaaacagcggtttacttttgcagTCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG
                             cactaaa  putative branch site (score: 9)
                                          tttactttt  putative PPT
                      tttttttcactaaa  TA-rich tract