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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcctgaattattctttgcctagtacaggtccacgagagttacttgggtaatctggtgtttgaatgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATACGGTGCCCTAGCCCGAGGTGACGGTGCCATTTACTTGCGTTTTCCACACA

Basic information

species Oryza sativa
transcript LOC_Os12g08280.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g08280.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G152757_T04 (Zea mays), 3'ss of exon 6
gtttgtcctgaattattctttgcctagtacaggtccacgagagttacttgggtaatctggtgtttgaatgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATACGGTGCCCTAGCCCGAGGTGACGGTGCCATTTACTTGCGTTTTCCACACA
||   | |  || |||||||||| || |  |  |||||  |||| || |  |||||||||| ||| ||||||  ||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||| || ||||||||||| || |||||||||||||| ||||||||||
gtagcttccaaactattctttgcttactcgatatccacaggagt-acataagtaatctggttttttaatgctatcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATCGACAGCCAAGCAAAATATGGTGCTCTGGCCCGAGGTGATGGCGCCATTTACTTGCGCTTTCCACACA

upper sequence: LOC_Os12g08280.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G26250.1 (Glycine max), 3'ss of exon 6
-----------------------------------------gtttgtcctgaattattc-tttgcctagtacaggtccacgagagttacttgggtaatctggtgtttgaatgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATACGGTGCCCTAGCCCGAGGTGACGGTGCCATTTACTTGCGTTTTCCACACA
                                          | | |  | | || ||| |||  ||  |  || |  |        || |   |   |   | ||          ||||||||||||||| |||| || ||||| ||||||||||||||||||||||| || ||  |  |  |||| || || || || || |||||||| || ||||
gtagtactgtttctatagttaacacatttttccttattcatatatttttttagtttttcatttagctcttttagatttaatctgcagacatttcttgaccattattacttcatgaacagAAACTTGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA

upper sequence: LOC_Os12g08280.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 6
---------------------------------------------gtttgtcctgaattattctttgcctagtacaggtccacgagagttacttgggtaatctggtgtttgaatgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATACGGTGCCCTAGCCCGAGGTGACGGTGCCATTTACTTGCGTTTTCCACACA
                                              ||| |  |   || |  |||  ||  |  || |  |        || |   |   |   | ||          |||||||| |||||| |||| || ||||| ||||||||||||||||||||||| || ||  |  |  |||| || || || || || |||||||| || ||||
gtaatactgttagaactagaagttaacatatttgtcctttttcatattttttttagtttttcttttagctcttttagatttattctgcagacatttcttgaccattattacttcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA

upper sequence: LOC_Os12g08280.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G63980.1 (Arabidopsis thaliana), 3'ss of exon 5
-------gtttgtcctgaattattctttgcctagtacaggtccacgagagttacttgggtaatctggtgt-ttgaatgctg------gcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATACGGTGCCCTAGCCCGAGGTGACGGTGCCATTTACTTGCGTTTTCCACACA
       | || |        ||    | ||   ||   |   || |   || ||     | |      | ||  ||| ||       |||||||| |||||| ||||||| |||||  | ||||||||||||||||| || || ||  || |  |||| || || || || ||||| || ||||| || |
gtaaattgcttctttccttccatgtgattccagctaatagctaactaattttcctcatccatttgatcatgttctatgttgtaatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAGCAAAGTATGGAGCTTTATCAAGAGGAGATGGAGCTATATACTTACGGTTTCCTCATA

upper sequence: LOC_Os12g08280.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 6
gtttgtcctgaattattcttt---gcctagtacaggtccacgagagttacttgggtaatctggtgtttgaatgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATACGGTGCCCTAGCCCGAGGTGACGGTGCCATTTACTTGCGTTTTCCACACA
    || ||| ||| |  ||     | |  ||  | ||     |  |||  ||  |||| |  | | ||||      ||||||||||| ||| |||| || |||||||||||||||||||| || || || || || ||| || |||| || || ||||||||  | || || || || |
----gtactgtattgtctttgcagacgtcttattgttctctctgtcttatatgcctaat-tattttctgaa------cagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTATGGGGCTCTATCCAGAGGAGATGGGGCCATTTATCTTCGCTTCCCTCATA

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|14981612|gb|BI306290.1|BI306290
EST:     CCTACGAAGGGGCACACTCCTTGGGTGATTTAACAGGCTCCATTGCGGAG                         AAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
genomic: CCTACGAAGGGGCACACTCCTTGCGTGATTTAACAGGCTCCATTGCGGAGgtttgtcctg ... atgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
EST: gi|86428929|gb|CI075610.1|CI075610
EST:     GTGATTTAACAGGCTCCATTGCGGAG                         AAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
genomic: GTGATTTAACAGGCTCCATTGCGGAGgtttgtcctg ... atgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
EST: gi|86254983|gb|CI017103.1|CI017103
EST:     CAGGCTCCATTGCGGAG                         AAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
genomic: CAGGCTCCATTGCGGAGgtttgtcctg ... atgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
EST: gi|117227330|gb|CT846542.1|CT846542
EST:     CCTACGAAGGGGCACACTCCTTGCGTGATTTAACAGGCTCCATTGCGGAG                         AAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAG
genomic: CCTACGAAGGGGCACACTCCTTGCGTGATTTAACAGGCTCCATTGCGGAGgtttgtcctg ... atgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAG
EST: gi|89175133|gb|CI111652.1|CI111652
EST:     CCTACGAAGGGGCACACTCCTTGCGTGATTTAACAGGCTCCATTGCGGAG                         AAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
genomic: CCTACGAAGGGGCACACTCCTTGCGTGATTTAACAGGCTCCATTGCGGAGgtttgtcctg ... atgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
EST: gi|25803591|gb|CA759552.1|CA759552
EST:     AAGGGGCCCACTCCTTGCGTGATTTAACAGGCTCCATTGCGGAG                         AAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
genomic: AAGGGGCACACTCCTTGCGTGATTTAACAGGCTCCATTGCGGAGgtttgtcctg ... atgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
EST: gi|88904072|gb|CI006305.1|CI006305
EST:     GTGATTTAACAGGCTCCATTGCGGAG                         AAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
genomic: GTGATTTAACAGGCTCCATTGCGGAGgtttgtcctg ... atgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC
EST: gi|88832353|gb|CI019294.1|CI019294
EST:     CCTACGAAGGGGCACACTCCTTGCGTGATTTAACAGGCTCCATTGCGGAG                         AAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAGTAC
genomic: CCTACGAAGGGGCACACTCCTTGCGTGATTTAACAGGCTCCATTGCGGAGgtttgtcctg ... atgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATAC

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: 69 (upstream exon), 70 (downstream exon)
Score: 20

ATTAGTGTCTGTTCCATCGACAATCCAGTCGAAGCTTCATTCTTTGAGTCCTACGAAGGGGCACACTCCTTGCGTGATTTAACAGGCTCCATTGCGGAGgtttgtcctg ... atgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATACGGTGCCCTAGCCCGAGGTGACGGTGCCATTTACTTGCGTTTTCCACACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctagtacaggtccacgagagttacttgggtaatctggtgtttgaatgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATACGGTGCCCTAGCCCGAGGTGACGGTGCCATTTACTTGCGTTTTCCACACA
                                        tttgaat  TA-rich tract