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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGAATATTTCCTTATGTACTCAAACTGCTTCAAACAAGTGCAATGGAGTTGCGTCAAATTCTTGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactcttcattgtaatattttaagagttcttttattgtcttagattcaggtgtttaacgtttagttttttctcaaatgacag

Basic information

species Zea mays
transcript GRMZM2G048067_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 5'ss of exon 12
CGGAATATTTCCTTATGTACTCAAACTGCTTCAAACAAGTGCAATGGAGTTGCGTCAAATTCTTGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactcttcattgtaatatt-------ttaagagttc-ttttattgtcttagattcaggtgtttaac--gtttagttttttctcaaatgacag
 || || || ||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||| |   |||   ||| ||  ||        | | ||||| |||||||     |||||||||| ||||    ||| |  | ||| |||||||||||
TGGCATCTTCCCTTATGTACTTAAACTGCTTCAAACAAGTGCAATGGAGTTGCGCCAAATTCTTGTGTTCATATGGACAAAAATTCTCTCTCTTGATAAGgta-gtgttctatgttgaaaacttgaaatctctgacagttcattttatttctcaagattcaggtatttacttagttgatctgtttttcaaatgacag

upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 5'ss of exon 11
CGGAATATTTCCTTATGTACTCAAACTGCTTCAAACAAGTGCAATGGAGTTGCGTCAAATTCTTGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactcttcattgtaatatt-------ttaagagttc-ttttattgtcttagattcaggtgtttaac--gtttagttttttctcaaatgacag
 || || || ||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||  |   |||   ||| ||  ||        | | ||||| |||||||     |||||||||| ||||    |||    | ||| |||||||||||
TGGCATCTTCCCTTATGTACTTAAACTGCTTCAAACAAGTGCAATGGAGTTGCGCCAAATTCTTGTGTTCATATGGACAAAAATTCTCTCTCTTGATAAGgtg-gtgttctatgttgaaaacttgaaatctctgacagttcattttatttctcaagattcaggtatttacttagttgctctgtttttcaaatgacag

upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 5'ss of exon 12
CGGAATATTTCCTTATGTACTCAAACTGCTTCAAACAAGTGCAATGGAGTTGCGTCAAATTCTTGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgc------actcttcattgtaatattttaagagttcttttattgtcttagattca---ggtgtttaacgttt--agttttttctcaaatgacag---
 ||||||||||| ||||| || || ||| | |||||||   |    || ||  | ||||||||||| |||||||||||||| || ||  | ||||||||||||| |         || |||| |  | ||| |  |  | ||| | | | | ||  | |    ||   ||   ||   ||   |    || |||       
TGGAATATTTCCATATGTTCTGAAGCTGTTGCAAACAACAACTCCAGAATTAAGACAAATTCTTGTATTTATATGGACAAAGATCCTTGCACTTGATAAGgtatacttagaagtcctccattatt-tttttcacaatatatttgagtatttgaggatgacaaagttgctactattagaagacatgctccatatgttcttga

upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 12
lower sequence: PP1S26_271V6.1 (Physcomitrella patens), 5'ss of exon 12
CGGAATATTTCCTTATGTACTCAAACTGCTTCAAACAAGTGCAATGGAGTTGCGTCAAATTCTTGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactcttcattgtaatattttaagagttcttttatt-gtcttagattcaggtgtttaacgtttagttttttctcaaatgacag-------------
 |||||||| || ||||| || || ||||| ||| |||  || |  || ||||| ||||||||||| |||||||||||||| |||||  ||||||| ||||| |    |||   |    ||| ||||    || |||| ||     ||| |  |  |||      | |   |   | | || ||                 
AGGAATATTCCCCTATGTCCTTAAGCTGCTGCAAGCAACGGCTACTGATTTGCGGCAAATTCTTGTATTTATATGGACAAAGATTCTAGCTCTTGACAAGgtgt-tgttctcattctgtatagtttatctcttattttgttcagaatagttctatatgtaagggctctttgtgggtatgaagtgctgtttagcttgcgcca

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: 46 (upstream exon), 48 (downstream exon)
Score: 117

CGGAATATTTCCTTATGTACTCAAACTGCTTCAAACAAGTGCAATGGAGTTGCGTCAAATTCTTGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactc ... caaatgacagTCGTGCCAGGTTGATTTGGTTAAAGATGGAGGACACACATATTTTGTTAGGTTTCTTGACAGTTTGGATGCTTACCCAGAACAGCGTGCAATGGCTGCTT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 55

CGGAATATTTCCTTATGTACTCAAACTGCTTCAAACAAGTGCAATGGAGTTGCGTCAAATTCTTGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactc ... caaatgacagTCGTGCCAGGTTGATTTGGTTAAAGATGGAGGACACACATATTTTGTTAGGTTTCTTGACAGTTTGGATGCTTACCCAGAACAGCGTGCAATGGCTGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

CGGAATATTTCCTTATGTACTCAAACTGCTTCAAACAAGTGCAATGGAGTTGCGTCAAATTCTTGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactc ... caaatgacagTCGTGCCAGGTTGATTTGGTTAAAGATGGAGGACACACATATTTTGTTAGGTTTCTTGACAGTTTGGATGCTTACCCAGAACAGCGTGCAATGGCTGCTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 79

CGGAATATTTCCTTATGTACTCAAACTGCTTCAAACAAGTGCAATGGAGTTGCGTCAAATTCTTGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactc ... caaatgacagTCGTGCCAGGTTGATTTGGTTAAAGATGGAGGACACACATATTTTGTTAGGTTTCTTGACAGTTTGGATGCTTACCCAGAACAGCGTGCAATGGCTGCTT