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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatcaaaagaatcacatctatagagaacgagatgcccggaaaagtttgtgcttaatgtctttgtcttttgttgaaaattcacag

Basic information

species Oryza sativa
transcript LOC_Os01g73970.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73970.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA12G29800.1 (Glycine max), 5'ss of exon 13
CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatcaaaagaatcaca-tctatagagaacgagatg----cccggaaaagtttgtgcttaat-------gtctttgtct-tttgttgaaaattcacag
|| |||||||| ||||| |||||  ||||||| ||||||||||| ||||||||  |||||||||||||||||||||| ||     |     | ||| | ||   ||  | |  |     |   ||  |  |  |  | |||       || ||| | | |||||||  | |  |   
CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgttagacctcactagcttacaatatagttagggccacttattttctttgatgatatcattttaaattgagtgtgtttttatatatttgttgggagtatat--

upper sequence: LOC_Os01g73970.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA13G39990.1 (Glycine max), 5'ss of exon 13
CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaagg-atcaaaagaatcacatctatagagaacgagatg----cccggaaaagtttgtgcttaat-------gtctttgtct-tttgttgaaaattcacag
|| |||||||| ||||| |||||  ||||||| ||||||||||| ||||||||  |||||||||||||||||||||| ||  ||||  ||  |   || ||   ||| | |  |     |   ||  |  |  |  | |||       || ||| | | ||| |||  | |  |   
CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgttagacatcactagcttacaatatagttagagccacttattttctttgatgatatcattttaaattgagcatgtttttatatatttattgggagtatat--

upper sequence: LOC_Os01g73970.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 5'ss of exon 13
CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatcaaaagaatcacatctatagagaacgagatgcccggaa------aagtttgtgcttaatgtctt-tgtcttttgttgaaaattcacag----
||||||||||||||||||||||| |||||||| || |||||| | ||| |||| || ||||||||||||| ||| |||||    |         ||| |   || ||     ||    |||       | | |||||      | |  ||   |||||||   | |  |      
CCTGCACATGAGAAAATCGGTGTGGTTGATTCACAGTGGATTATTCATAAAGTAGTACCTTCTCTTGGGAGCCAAgtaagtcatatttttgaggcatattgtgataaaattttgttgtgaatttcatgaatctgtgccatgcatttgatgcactttgttgttgactggcttgttt

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|86841951|gb|CI338360.1|CI338360
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|86424012|gb|CI062773.1|CI062773
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88470908|gb|CI408179.1|CI408179
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|58595145|gb|CF993453.1|CF993453
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|86536269|gb|CI176475.1|CI176475
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88479440|gb|CI416711.1|CI416711
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|12404721|gb|AU166322.1|AU166322
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|86893421|gb|CI313341.1|CI313341
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88522872|gb|CI450665.1|CI450665
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|1854181|gb|AA231809.1|AA231809
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|29663566|gb|CB659841.1|CB659841
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88279267|gb|CI400267.1|CI400267
EST:     TGATTCCCAATGGATTGTACATCAAGT-GTNTCCTTCTCTTGGGAACCAG                         GGGCANTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TGATTCCCAATGGATTGTACATCAAGTGGT-TCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88523350|gb|CI451164.1|CI451164
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88489023|gb|CI426294.1|CI426294
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88902346|gb|CI374954.1|CI374954
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|3760914|gb|C98168.1|C98168
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|29641985|gb|CB646992.1|CB646992
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|86526488|gb|CI166694.1|CI166694
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCGG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|5803529|gb|AI978499.1|AI978499
EST:     TTGATTCCCAATGGNNNGTACATCAAGTGGTTCCNNCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|86888761|gb|CI307819.1|CI307819
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         CGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88663212|gb|CI479204.1|CI479204
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG

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), 73 (downstream exon)
Score: 26

CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG




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