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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcatttcatggtttggttaaattggataaacattgaattgttgccttttattgctaatacatttgactcattttacaattgttgtttcaacaatgtgtattatgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG

Basic information

species Oryza sativa
transcript LOC_Os11g01140.3
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 12
gtaaatcatttcatggtttggtt--aaattggataaacattgaattgttgcct-tttattgctaatacatttgactcatttta-----caattgttgtttcaaca------atgtgtattatgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG
|||| |  ||  ||  | | |||  || |  |  ||  | | | ||        |  |||    | ||   |  || |||||      | |||   |||| ||||      ||||| ||| |  ||| ||||| ||||| |||||||| |||||| |    ||||| ||||||||||||||||||||||||||||||||  ||||||||||||| || |||
gtaagtacttctatattatagtttcaactatggcaatgactcagtttgcatgaatccattagacacactcctttctaattttcactccctatttacgtttaaacagtaaacatgtgaattgttgttg-aattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG

upper sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 13
gtaaatcatttcatggtttggttaaattggataaacattgaattgttgccttttattgctaatacatttgactcattttacaattgttgtttcaacaatgtgtatta--tgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG
                            ||   |  ||  | |  ||    | |     |  |    ||  ||||   |     |||   ||  | ||| |  | |   |||||||  | | ||||| ||  |||| || || |     || || |||||||||||||||||||||||||||||||   ||||||| |||||||| |||
------------------------ctcaggggtatgatcaagtccttattctctccattttgttttcttagctcaaacttttgctgtgtcttggaaaatttagactcattgattggtttggcagTGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG
















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), 74 (downstream exon)
Score: 27

GTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAGgtaaatcatt ... ggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactcattttacaattgttgtttcaacaatgtgtattatgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG
 atttgac  putative branch site (score: 27)
       attttacaattgtt  TA-rich tract