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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGATGGTGTTTGGGgtatcttctgaattctcatcttccagtcttgtcaacttatggtgctgatgagaacaatccaattaatcttctaatttgtgtaccag

Basic information

species Zea mays
transcript GRMZM5G871262_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g03760.3 (Oryza sativa), 5'ss of exon 7
TCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGATGGTGTTTGGGgtatcttctgaattctcatcttccagtcttgtcaacttatggtgctgatgagaacaatccaattaatcttctaatttgtgtaccag
|| || |||||||||||||||||||||||||||||||||||||| |||||| | || || |||||||||||| ||||| |||| |||||||||||||||||||| ||     |  ||||  | || | || | ||||  |  |  |||||| |  |     |  ||| ||||  ||| ||||  ||
TCGATTGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGACCCTCCTTTGTCCTCCTTCCTGAATGAAATCTTCGTAAAATTGGATGGTGTTTGGGgtatatttc---tgttcat--tacattgttctgaactcgtcctattgatgacagtagcttgaccaatattctgttttctgtattag

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA16G19230.1 (Glycine max), 5'ss of exon 8
TCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGATGGTGTTTGGGgtatcttctgaattctca---tcttccagtcttgtcaacttatg-gtgctgatgagaacaatccaattaatcttc---taatttgtgtaccag--------------------------
||| | || |||||  | |||||  | || ||| | || ||||||||||| || ||| ||||| |||||||||| ||||| ||| | |||| ||| |||||||| ||  |||  ||||   | ||    | |  |  | |||||  |  | ||    ||| |  |  |||| |||    | ||  | ||   |                          
TCAGTGGCGTGGGTCACTCATATAATTATCTACCTATTAATTGATCCTCCACTTTCTCCTTTCTTGAATGAAGTTTTCATCAAGCTAGATGATGTCTGGGgtatgttg-gaaagctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgtaatttgttctttcatcag

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA01G30400.1 (Glycine max), 5'ss of exon 9
TCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGATGGTGTTTGGGgtatcttctga-attctcatcttccagtcttgtcaacttatggt--gctgatgagaacaatccaatta-atcttctaattt-gtgtaccag---------------------------------
||  | || |||||||| |||||| | || ||  | || |||||||||||||| ||| ||||| |||||||||| ||||| ||| |||||| | | |||||||| ||   | | ||| | |||      || |    |||   |  |||   ||| | |     |||| || || || |||  |  |  |                                  
TCTGTGGCATGGGTTGCTCATATCATTATCTATCTATTAATTGATCCTCCTCTTTCTCCTTTCTTGAATGAAGTTTTCATCAAGCTGGATGATATCTGGGgtatgttggaatactcttacctttagtgattattccattaccataagctatagagtatagagacattatatattttattttcattcagtaattcttcatgatgtatgcattcttctttcatcag

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA18G43020.1 (Glycine max), 5'ss of exon 9
TCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGATGGTGTTTGGGgtatcttctgaattctca---tcttccagtcttgtcaacttatg-gtgctgatgagaacaatccaattaatcttctaatttgtgtaccag----------------------------------
||| | || ||||| || |||||  | || ||| | || ||||||||||| || ||| ||||| |||||||||| ||||| ||| | |||| ||| |||||||| ||  |||  ||||   | ||    | |  |  | |||||  |  | ||    ||| |  | |  || |  || | | |  |  |                                   
TCAGTGGCATGGGTCGCTCATATTATTATCTACCTATTAATTGATCCTCCACTTTCTCCTTTCTTGAATGAAGTTTTCATTAAGCTAGATGATGTCTGGGgtatgttg-gaaaactcaggctatttttctttccttcagttatgtataataattgatacattatattatatgtaatattctttcaattaatctagatgatatatgtaatttgttctttcatcag

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G18160.1 (Glycine max), 5'ss of exon 9
TCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGATGGTGTTTGGGgtatcttctgaattctca---tcttccagtcttgtcaacttatg-gtgctgatgagaacaatccaattaatcttc---taatttgtgtaccag--------------------------
||| | || |||||  | |||||  | || ||| | || ||||||||||| || ||| ||||| |||||||||| ||||| ||| | |||| ||| |||||||| ||  |||  ||||   | ||    | |  |  | |||||  |  | ||    ||| |  |  |||| |||    | ||  | ||   |                          
TCAGTGGCGTGGGTCACTCATATAATTATCTACCTATTAATTGATCCTCCACTTTCTCCTTTCTTGAATGAAGTTTTCATTAAGCTAGATGATGTCTGGGgtatgttg-gaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgcaatttgttctttcatcag

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 9
TCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGATGGTGTTTGGGgtat--cttctgaattctcatcttccagtcttgtcaacttatggtgct-gatgagaacaatccaattaatcttcta-atttgtgtaccag
||| | |||||| |||| |||||||||||||| ||| |||||||||||||||| ||| ||||| | ||||| || ||||| ||| | |||| ||| |||||||   ||   || || |  | |  | ||  | | |  |  |    || |||||    | ||  |    | |  |  | || |    |||
TCAGTGGCTTGGATTGCTCATATCGTCATATATTTGCTGATTGATCCTCCTCTGTCTCCTTTCTTAAATGAGGTTTTCATCAAGCTAGATGATGTCTGGGgtactgctatagatttttgctgtctctgttattttatttcctttcactagatgatcttattctgagatgtatcttgtacttcttcgtcag

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 124

TCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGATGGTGTTTGGGgtatcttctg ... tgtgtaccagGTCTCCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTCCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGTTTGAAACTTGTTTTCATCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

TCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGATGGTGTTTGGGgtatcttctg ... tgtgtaccagGTCTCCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTCCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGTTTGAAACTTGTTTTCATCAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 155

TCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGATGGTGTTTGGGgtatcttctg ... tgtgtaccagGTCTCCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTCCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGTTTGAAACTTGTTTTCATCAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 125

TCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGATGGTGTTTGGGgtatcttctg ... tgtgtaccagGTCTCCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTCCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGTTTGAAACTTGTTTTCATCAC