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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattgccctgtagagttgttctgttttactacttacaatgctatatcgtactaattattgacaagtaagtattgctttaccatttgtctggcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG

Basic information

species Oryza sativa
transcript LOC_Os01g60440.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 15
gtacattgccctgtagagttgttctgttttactacttacaatgctatatcgtactaattattga-caagtaagtattgctt-taccat---------ttgtctg-------------gcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG
||||||  |  || | |   || |||||||| |||    |   |||    ||| |  | | ||| |||||  | ||   || ||||||         || | |              ||||| |||||||| || |||||||||||||||||||||||||||||||||||||||||||| || ||||||||| ||||||| ||||||||||| ||| ||||
gtacatacctttgcaaa--cgtgctgttttagtaccgttagatctacga-gtatttttcagtgagcaagtgtgaatgctttgtaccatgcctaacaattatttactcttgcttcattgcagGAATCATGGCACTGAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGCATCCTGCCTAACATTGTTGTGCTCACATTTGACCCAAATAG

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 15
gtacattgccctgtagagttgttctgttttactacttacaatgctatatcgtactaattattgacaagtaagtat------tgctttacc----atttgtct-------------ggcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG
||||||  |  || | |   || |||||||| || |   |   ||||       |  || |   ||| |  | ||      | |  ||||    |||| | |             || ||| |||||||| || ||||||||| |||||||||| ||||||||||||||||||||||| || ||||||||| ||||||||||||||||||| ||||||||
gtacatacctttgcaaa--cgtgctgttttagtattgttaggtctatgagtatttttttgtgagcaaatgtgaatgctttgtaccatacctgacatttatttactcttgcttcatggtagGAATCATGGCACTGAGTGTCACTGGTTCATACTACGAAATGACAGAGATTGCAACTCGCATCCTGCCTAACATTGTTGTCCTCACATTTGACCCAGATAG

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 15
------gtacattgccctgtagagttgttctgttttactacttacaatgctatatcgtactaattattgacaagtaagtattgctttaccatt--tgtctggcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG
      | | |    |  | | |    ||    ||||    || ||||   ||     | | | | | ||   ||    |    ||||  |||  | | |||||||  | |||||  || |||  || ||||| || ||||| || ||||||||||||||||| |||||||| || |||||||| || ||  ||||||| || ||
cagaaggaaaaagaacaagaaaaaaaatta---ttta--ggttgcaatttaattcgtcagttaatgtggatgggttttgacaaatttaaaattgttttgtggcagGAGTTATGGCTTTATGTGCGACCAGTTCTTATTATGACATCACAGAGATTGCAACTCGGATTCTGCCAAATGTTGTTGTACTTACCATTGATCCTGACAG

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|29656612|gb|CB652887.1|CB652887
EST:     ATCTACTGTCCGTGCATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTG                         GCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG
genomic: ATTTACTGTCCGTGCATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTGgtacattgcc ... tgtctggcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG
EST: gi|701421|gb|D47712.1|D47712
EST:     ATTTACTGTCCGTGCATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTG                         GCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG
genomic: ATTTACTGTCCGTGCATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTGgtacattgcc ... tgtctggcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG
EST: gi|109974420|gb|DT806899.1|DT806899
EST:     TTTACTGTCCG-GACATGACGTGATACCTTCCCCCCTGCTAGAGCAGCTG                         GCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG
genomic: TTTACTGTCCGTG-CATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTGgtacattgcc ... tgtctggcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG
EST: gi|701323|gb|D47614.1|D47614
EST:     ATTTACTGTCCGTGCATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTG                         GCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG
genomic: ATTTACTGTCCGTGCATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTGgtacattgcc ... tgtctggcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG
EST: gi|426538|gb|D22359.1|D22359
EST:     ATTTACTGTCCGTGCATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTG                         GCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG
genomic: ATTTACTGTCCGTGCATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTGgtacattgcc ... tgtctggcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG
EST: gi|58607870|gb|CK035903.1|CK035903
EST:     ATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTG                         GCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG
genomic: ATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTGgtacattgcc ... tgtctggcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTG

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), 75 (downstream exon)
Score: 22

ACTAGGAAAAGGGTATTGATCAACGCATTTACTGTCCGTGCATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTGgtacattgcc ... tgtctggcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctatatcgtactaattattgacaagtaagtattgctttaccatttgtctggcagGCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG
                                           tttgtct  CT-rich tract
         tactaattatt  TA-rich tract