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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGAGGATGTCATGCAGCCTGTACCTGGTGTTCGAGTATATGGAGCATGACCTTGCTGGCCTGGCAGCGAGCCCGGACGTCAAGTTTACTCTGCCGCAGgtgtttaaggatcccgtgctatctcgttttataggcgaatacttgctgggaatatgttaaatttgatgatgatgtacttctcgcag

Basic information

species Oryza sativa
transcript 13113.m00244
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g27020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G156251_T01 (Zea mays), 5'ss of exon 2
GTCGAGGATGTCATGCAGCCTGTACCTGGTGTTCGAGTATATGGAGCATGACCTTGCTGGCCTGGCAGCGAGCCCGGACGTCAAGTTTACTCTGCCGCAGgtgtttaaggatcccgtgctatctcgttttataggcgaatacttgctgggaatatgttaaatttgatgatgatgtact-tctcgcag
 || ||||||||||||||||| ||||| || |||||||| ||||||||||| |||||||| || || || ||    || |||||||| ||  |||| ||||||| | |   |    |||| | ||   | |  | ||| ||| || ||| |  ||||    |||||||    | |  | ||| ||||
CTCCAGGATGTCATGCAGCCTTTACCTTGTCTTCGAGTACATGGAGCATGATCTTGCTGGTCTTGCGGCAAGTTGTGATGTCAAGTTCACGTTGCCTCAGgtgtgtgaaactgggttgctgtttcagat-acggtcgattacatggtggaataatgt-gggtttgatgtcactatgttatcttgcag

upper sequence: LOC_Os01g27020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S271_84V6.1 (Physcomitrella patens), 5'ss of exon 2
GTCGAGGATGTCATGCAGCCTGTACCTGGTGTTCGAGTATATGGAGCATGACCTTGCTGGCCTGGCAGCGAGCCCGGACGTCAAGTTTACTCTGCCGCAGgtgtttaaggat--cccgtgctatctcgttttataggcgaatacttgctgggaatatgttaaatttgatgatgatgtacttctcgcag------------
|||  | ||||| ||||||||||| |||||||||||||| |||||||| ||||| || || ||||| ||| |||||| | | | ||| ||     | |||||    | | ||  ||||   ||           ||| |||   | |   |  || ||||   |   |   || || |   || |               
GTCTCGAATGTCGTGCAGCCTGTATCTGGTGTTCGAGTACATGGAGCACGACCTGGCGGGGCTGGCGGCGTGCCCGGGCATAATGTTCACGGAAGCTCAGgttcggatgcatgccccgcagtaggggaaggggaaggggaagggtagggagtgatctgtttggtgacagcgtggtggagagctggggtcgatggtggtcg

upper sequence: LOC_Os01g27020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S428_20V6.1 (Physcomitrella patens), 5'ss of exon 2
GTCGAGGATGTCATGCAGCCTGTACCTGGTGTTCGAGTATATGGAGCATGACCTTGCTGGCCTGGCAGCGAGCCCGGACGTCAAGTTTACTCTGCCGCAGgtgtttaaggatcccgtgctatctcgttttataggcgaatacttgctgggaatatgttaaatttgatga-tgatgtacttctcgcag-------------
|||  | ||||| |||||| |||| |||||||||||||| |||||||| ||||| || || ||||| ||  |||| |   | | ||| ||     | |||||     |  || |    ||   |||| |  |   |   |   |   || ||  || |  ||      | |     |   |   ||              
GTCTCGAATGTCGTGCAGCTTGTATCTGGTGTTCGAGTACATGGAGCACGACCTGGCCGGGCTGGCCGCATGCCCTGGTATAATGTTCACAGAATCTCAGgttcgggaatatactccactccatcgtatcctctccccttctctctaggaaaactgctgcatgcagccagtcccagatggcagccaatcaagattgaaca

upper sequence: LOC_Os01g27020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ30402 (Selaginella moellendorffii), 5'ss of exon 2
GTCGAGGATGTCATGCAGCCTGTACCTGGTGTTCGAGTATATGGAGCATGACCTTGCTGGCCTGGCAGCGAGCCCGGACGTCAAGTTTACTCTGCCGCAGgtgtttaaggatcccgtgctatctcgttttataggcgaatacttgctgggaatatgttaaatttgatgatgatgtacttctcgcag
||| |||||||| | |||||| || || ||||||||||| |||||||| |||||||| || || || ||| | || | | ||| ||||||   ||||||||||      ||   ||||    ||   || ||    || ||||   || |||       |                          
GTCCAGGATGTCCTTCAGCCTCTATCTCGTGTTCGAGTACATGGAGCACGACCTTGCCGGGCTTGCTGCGTGTCCAGGCATCACGTTTACAGAGCCGCAGgtgagacgaga---cgtgaatgcttccttgatttctgattactgaatgcgaaagccgacag-------------------------

upper sequence: LOC_Os01g27020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ28510 (Selaginella moellendorffii), 5'ss of exon 2
GTCGAGGATGTCATGCAGCCTGTACCTGGTGTTCGAGTATATGGAGCATGACCTTGCTGGCCTGGCAGCGAGCCCGGACGTCAAGTTTACTCTGCCGCAGgtgtttaaggatcccgtgctatctcgttttataggcgaatacttgctgggaatatgttaaatttgatgatgatgtacttctcgcag
||| |||||||| | |||||| || || ||||||||||| |||||||| |||||||| || || || ||| | || | | ||| ||||||   ||||||||||      ||   ||||    ||   || ||    || ||||   || |||       |                          
GTCCAGGATGTCCTTCAGCCTCTATCTCGTGTTCGAGTACATGGAGCACGACCTTGCCGGGCTTGCTGCGTGTCCAGGCATCACGTTTACAGAGCCGCAGgtgagacgaga---cgtgaatacttccttgatttctgattactgaatgcgaaagccgacag-------------------------

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: 65 (upstream exon), 72 (downstream exon)
Score: 14

GTCGAGGATGTCATGCAGCCTGTACCTGGTGTTCGAGTATATGGAGCATGACCTTGCTGGCCTGGCAGCGAGCCCGGACGTCAAGTTTACTCTGCCGCAGgtgtttaagg ... cttctcgcagATAAAATGCTATGTGCAGCAGCTATTGTCAGGGCTTGAGCATTGCCACAATAATAATGTATTGCATCGGGATATCAAGGGATCAAACTTATTGTTGGATA




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