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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtattttaagagttagtggacatcaattttataataagataggatatgtcttttcacagtaaagttaccttcccttcattacttcattacttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG

Basic information

species Oryza sativa
transcript LOC_Os12g01140.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 7
ttgtattttaagagttagtggacatcaattttataataagataggatatgtcttttcacagtaaagttaccttcccttcattacttcattacttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
 |   |  |   || ||| ||  |  ||| |    |||   |    | | |  |       |||| | |  || | |    |  |  || |||||   |||||| || || |||||||||||||||||||| || ||||||||||| |||
ctagttgcttgtagatagaggctactaatgtgcagatatctttatttctatggtaatgagttaaactgaaatttcttgtggttgtgtatcacttgagtagGTAAGAAATTCTGGAACCTCTTTCACTTGCAGCCTATGCGTGATCAGAAG

upper sequence: LOC_Os12g01140.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 9
--ttgtattttaagagttagtggacatcaattttataataagatagg-atatgtcttttcacagtaaagttaccttcccttcattacttcattacttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
  ||  || | | || |   |   |||   ||| | |  || ||    || |  |   |   ||  || |    || |    |||| |      |     ||||||||||||| |||||| | ||||| ||||| || ||||||||||| |||
gttttcatatcatgaatcc-ttttcatagttttcaaaggaaaatgactatttaacaacttgaagctaaatatggttgctaatattattctgc--ccaattcagGTAAAAAGTTCTGGAACTTGTTTCATTTGCAGCCTATGCGTGATCAGAAG

upper sequence: LOC_Os12g01140.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G40550.1 (Glycine max), 3'ss of exon 7
ttgtattttaagagttagtggacat-caattttataataagataggatatgtcttttc-acagtaaagttaccttcccttcattacttcattacttggac-agGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
   | | |||      |  ||| ||  |  | | |||   ||      ||    || | |   | |    || | |  || |  | |||  |  |    | ||| || ||||| |||||||| ||||| |||||||| ||||||||||| |||
---tttcttagcgtacaaaggatatatagctatttaacgtgaagatcaataatgttgcgattattattccacttgctattgaagatttctctgttcaatccagGAAAGAAGTTCTGGAACCTGTTTCATTTGCAACCTATGCGTGATCAGAAG

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|29624477|gb|CB629488.1|CB629488
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29681859|gb|CB678134.1|CB678134
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29624448|gb|CB629459.1|CB629459
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29641853|gb|CB646860.1|CB646860
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|2317379|gb|C22433.1|C22433
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29672018|gb|CB668293.1|CB668293
EST:     AGATCCCCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29628293|gb|CB633304.1|CB633304
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29613611|gb|CB618624.1|CB618624
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29678744|gb|CB675019.1|CB675019
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29627346|gb|CB632357.1|CB632357
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29630466|gb|CB635475.1|CB635475
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|2317377|gb|C22431.1|C22431
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29624450|gb|CB629461.1|CB629461
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29630119|gb|CB635128.1|CB635128
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29646710|gb|CB651717.1|CB651717
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG

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: 52 (upstream exon), 50 (downstream exon)
Score: 27

CAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGATGCCATAGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtcttttcacagtaaagttaccttcccttcattacttcattacttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
                taaagtta  TA-rich tract