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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatgctttgccccatagctcacaatgatgttagtatttttagagcattgacacatccaccattttgttgcaagtatctcaggcatcagcttaagtaatctaaagatttcagttaaatctttgtttgttcttagATCCTCCCAGTTAGCATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCA

Basic information

species Oryza sativa
transcript LOC_Os05g49260.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G160504_T02 (Zea mays), 3'ss of exon 15
-----------------------------------gtataatgctttgccccatagctcacaatgatgttagtatttttagagc-attgacacatccaccattttgttgcaagtatctcaggcatcagct-taagtaatctaaagattt-cagttaaatctttgtttgttctt-agATCCTCCCAGTTAGCATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCA
                                   ||||||||| |     | |  ||     |||  |    |      || | ||   ||||  || |  | ||  || |  | |||||| |    || |||| ||| |    || |  |||| || ||||||  ||| || |||||||||| |||||||||||||| ||||| |||||| | || ||||| ||||||  ||| |||||||  || |||||||||||  | || ||| | ||||
gtacgctacttctttgcacacctgatataaagcttgtataatgcctcattgcctc-ctagttttgacatcccaacgaagggaactatctgcacaatcaactgtctgaagcta-cagctcaggaacgtactgtaagaaatatctgaatgtatagttcaaactttgtgcgtttttcagATCCTCCCGGTTAGCATCAAGAGCCTTGGCGGAAGCATCGCAACACTGGCCAACTGGCTGACATCCTTCGCCATAACAATGACGACGAACTTGATGCTCA

upper sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G028570_T01 (Zea mays), 3'ss of exon 8
gtataatgctttgccccatagctcacaatgatgttagtatttttagagcattgacacatccaccattttgttgcaagtatctcaggcatcagcttaagtaatctaaagatttcagttaaatctttgtttgttcttagATCCTCCCAGTTAGCATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCA
||||| | | ||  | ||||              |||    |||||  ||| |  |    ||      ||||| ||| ||          |||| |              |||  | ||| |||||  | ||   ||||||| || ||||||||||| ||  | |  ||||||||||| || |||||||||  ||| |||||||  | |||||||||||||||||||||| | || |
gtatagtaccttatcacata--------------tagctaatttagctcatagtaagcctcatgcacatgttgaaaggatgctgaatgaaagctca--------------ttc--tcaaaactttgcatattgacagATCCTTCCTGTTAGCATCAATAGCGTGGCAGGAAGCTTTGCCACCCTTGCCAACTGGCTGACATCCTTTGGAATAACAATGACAGCAAATTTGCTTCTAA

upper sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G098679_T01 (Zea mays), 3'ss of exon 15
gtataatgctttgccccatagctcacaatgatgttagtatttttagagcattgacacatccaccattttgttgcaagtatctcaggcatcagcttaagtaatctaaagatttcagttaaatctttgtttgttcttagATCCTCCCAGTTAGCATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCA
                                     || |   | |  | | |   | |    |   || |  | | |  | | | |     |    |||   || | ||    |  || |||||  | ||   ||||||| |||||||||||||||||| | |  |||||||||||||| || ||||||  | | |||||||  | |||||||||||||||||||||| | ||  
----------------------------------gtatagtcacatataactaatttagctcataagatgcttgaggcacatgatgaaaggattc---taaatgaaggcttaatctcgaaactttgcatattggcagATCCTTCCAGTTAGCATCAAGAGTGTGGCAGGAAGCTTTGCGACCCTAGCCAACTGGTTGACATCCTTTGGAATAACAATGACAGCAAATTTGCTTCTGT

upper sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G077546_T01 (Zea mays), 3'ss of exon 15
gtataatgctttgccccatagctcacaatgatgttagtatttttagagcattgacacatccaccattttgttgcaagtatctcaggcatcagcttaagtaatctaaagatttcagttaaatctttgtttgttcttagATCCTCCCAGTTAGCATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCA
                                         | |||  | |  ||||||       || |   ||  |     | ||       | |   |   |  ||||    |  || |||||  | |    ||||||| || ||||||||||||||| | |  |||||||||||||| || ||||||  | | |||||||  |  ||||||||||||||||||||| |  | |
----------------------------------------gtatagtacctcaacacatgagatgctt-gagacacatgctgaaagctct---ctgaacga---agggattattctcgaaactttgcatatcgacagATCCTTCCGGTTAGCATCAAGAGTGTGGCAGGAAGCTTTGCGACCCTAGCCAACTGGTTGACATCCTTTGGGATAACAATGACAGCAAATTTGCTCTTGA

upper sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G160430_T04 (Zea mays), 3'ss of exon 14
gtataatgctttgccccatagctcacaatgatgt-tagtatttttagagcattgacacatccaccattttgttgcaagtatctcaggcatcagcttaagtaatctaaagatttcagttaaatctttgtttgttcttagATCCTCCCAGTTAGCATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCA
                                || || ||   |||   |||    | ||   | | | |    ||       | |  | ||   | | | |      ||||   |    | |||||  | ||   ||||||| || |||||||||||| || | |  |||||||| ||||| |||||||||  | | || ||||  | |||||||||||||||||||||| | || |
--------------------------------gtataatacccttatcacat----atataagctaatataactcataagatgctgaaagcattctgaatgaaaggctgattctgg---gaactttgcctattgacagATCCTTCCGGTTAGCATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACGTCCTTTGGAATAACAATGACAGCAAATTTGCTTCTGA

upper sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 15
gtataatgctttgccccatagctcaca-atgatgtta-gtatttttagagcattgacacatccaccattttgttgcaagta-tctcaggcat-cagcttaagtaatctaaagatttcagttaaatctttgtttgttcttagATCCTCCCAGTTAGCATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCA
||||| | | ||    || |||  | | ||     ||  |   | |    || |   |  |   ||| |     ||||||  ||| ||||||  ||  |    | | | |||  || | || || |||||  | ||  |||||||||||||||||||||||||||||||  |||||||| ||||| |||||||||  | | |||||||  | |||||||||||| ||||||||| |  |||
gtatagtaccttaatgcacagcgaagatatatcaatacatgcctctctcccagttttaggttt-ccactgaagagcaagtgctcttaggcatataggctttaaagtttgaaggctt-acttcaaactttgcatttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACATCCTTTGGAATAACAATGACGGCAAATTTGCTGATCA

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: 53 (upstream exon), 71 (downstream exon)
Score: 15

GCTTATATCATCACCTTTTCCTTCGGCATGGGTGCCATTCCATGGGTCATGATGTCTGAGgtataatgct ... ttgttcttagATCCTCCCAGTTAGCATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggcatcagcttaagtaatctaaagatttcagttaaatctttgtttgttcttagATCCTCCCAGTTAGCATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCA
                  atctaaa  putative branch site (score: 15)
                                      tctttgtttgttctt  putative PPT
           ttaagtaatctaaa  TA-rich tract