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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAAGATGACTGAAGAAGAGGAAGACGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGTACACGTTTAGTTTCACAGCCTTCATgtgagtactttgctgactacttgttactaccttgacatgtaatttcctttaataactacctcaaagtttatagaattacagatagatgattttctctgct...

Basic information

species Zea mays
transcript GRMZM2G010085_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 4
TCAAAGATGACTGAAGAAGAGGAAGACGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGTACACGTTTAGTTTCACAGCCTTCATgtgagtactttgc---tgactacttgttactaccttgacatgt-aatttcctttaataactacctcaaagtttatagaattacagat-----agatg----attttctctgct------
||||||||||| ||||| |||||||| ||||||||||| ||||| || |||||||||||||||||| ||||||| ||||| ||  ||||||||||||||||||||  | || |   | || | |  ||   ||  |  |||   | | | ||   |  | |   | ||  |   | |||| | | ||     | |||    || || | ||||      
TCAAAGATGACAGAAGAGGAGGAAGATGAAGAATACCTTAAAGAAGAGGAAGATGCCCTTGCTGGTTCAGGGGGAACACGCTTGCTTTCACAGCCTTCATgtgagctcctttcccttcacaattatttgtaactgtatcataagagtatgctgccaccattctgttaatataagttgaataataaattgttaaaatgtaatatattttttgctctgcag

upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 4
TCAAAGATGACTGAAGAAGAGGAAGACGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGTACACGTTTAGTTTCACAGCCTTCATgtgagtactttgctgactacttgttactaccttgacatgtaatttcctttaataactacctcaaagtttatagaattacagatagatgattttctctgct-------
||||||||||| || || || ||||| || || || ||||| ||||| ||||||||||||| ||||||||| || || ||| | |||||||| || ||||||||| | ||   |||  | |   |   |||||    | ||    ||  |  ||| | |     ||||| |  ||  | | || | | |||||   ||         
TCAAAGATGACAGAGGAGGAAGAAGATGAGGAGTATCTCAAGGAGGAGGAAGATGCCCTTGATGGTGCAGGAGGGACCCGTCTGGTTTCACAACCATCATgtgagcatttgcttgatgattctgtcaaaccttttgttttacaagccagtcttaaatgc-----agtttgtgtaacga-aaat-gtttattttgcatggaaggttcg

upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 4
---------TCAAAGATGACTGAAGAAGAGGAAGACGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGTACACGTTTAGTTTCACAGCCTTCATgtgagtact-ttgctgactacttgttactaccttgacatgtaatttcctttaataactacctcaaagtttatagaattacagatagatgattttctctgct
         |||||  | ||||||||||||||||| ||||||||||| |||| ||||||||||| | | ||            |||||| || ||  | || || |||||| |||  | || |    |   |||   ||| | ||   | |  || || || |          |  ||| | |   | |   |   |   |  |  | ||
CGCCATGCATCAAAAGTAACTGAAGAAGAGGAAGATGAAGAATACCTTAAAGGGGAAGAAGATGGCTTAGC---------AAATACACGGTTGGTGACTCAACCATCATgtaagttttctttccttgtttatgtgcatacttggatgggcacattactctactttggttacttacatttgtggctatgcttgtgcctc-ctccccttact

upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G38050.2 (Glycine max), 5'ss of exon 4
---------TCAAAGATGACTGAAGAAGAGGAAGACGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGTACACGTTTAGTTTCACAGCCTTCATgtgagtactttgctgactacttgttactaccttgacatgtaatttcctttaataactacctcaaagttta-tagaattacagatagatgattttctctgct--
         |||||  | ||||||||||||||||| ||||||||||| |||| ||||||||||| | | ||            ||||||  | ||  | || || |||||| |||| | |    | |  || |    |   |  ||| |   |  |  |  | | |  ||||| || |  |  ||||      |      ||    ||    
CGCCATGCATCAAAAGTAACTGAAGAAGAGGAAGATGAAGAATACCTTAAAGGGGAAGAAGATGGCTTAGC---------AAATACACGACTGGTGACTCAACCATCATgtaagtattatttcca-tgtttatgtgcatacttgcatttg--tggccatgctcattttctcaatgtctcctttaattgtgcggaagaatattatgatgtcag

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: 47 (upstream exon), 49 (downstream exon)
Score: 335

TCAAAGATGACTGAAGAAGAGGAAGACGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGTACACGTTTAGTTTCACAGCCTTCATgtgagtactt ... atttctccagGCATCAAGGGAAAGATGCGTGATTACCAGTTGGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 64

TCAAAGATGACTGAAGAAGAGGAAGACGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGTACACGTTTAGTTTCACAGCCTTCATgtgagtactt ... atttctccagGCATCAAGGGAAAGATGCGTGATTACCAGTTGGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 47

TCAAAGATGACTGAAGAAGAGGAAGACGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGTACACGTTTAGTTTCACAGCCTTCATgtgagtactt ... atttctccagGCATCAAGGGAAAGATGCGTGATTACCAGTTGGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 113

TCAAAGATGACTGAAGAAGAGGAAGACGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGTACACGTTTAGTTTCACAGCCTTCATgtgagtactt ... atttctccagGCATCAAGGGAAAGATGCGTGATTACCAGTTGGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG