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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAACTGTTGCGAAATTTCAGgtgagcttctggtattttaattcgacgtatgaagctgttgaggttcatgaacatccttctaatgtcccacctctgcatgtcttcgtaaaccatagtgaat...

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 11
GGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAACTGTTGCGAAATTTCAGgtgagcttctggtattttaattcgacgtatgaagctgttgaggttcatgaacatccttctaatgtcccacctctgcat---gtcttcgtaaaccatagtgaat-----
 ||| ||||||| ||||||||||||||||||||||||||| |||||||||| ||||| || || ||  |  | |||||||| |||||||| ||||||||||||   ||||| |   || |||      |   |||| || |   |  |  || ||| | | |   |     |   |||   ||  |  ||||   |    | |     
AGAATTGTTTGCACAAACAAAATACAAGGAAGCAGCTGAGTTGGCTGCAGAATCTCCTCAAGGTCTTCTCCGAACTCCTGAGACTGTTGCAAAATTTCAGgtgcatttctgct--cttgatt------acagagctattaacacttctttacctccattttacagctatttttcacattctgtactgttaaaagcttaaaattatgtg

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 11
GGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAACTGTTGCGAAATTTCAGgtgagcttctggtattttaattcgacgtatgaagctgttgaggttcatgaacatccttctaatgtcccacctctgcat---gtcttcgtaaaccatagtgaat-----
 ||| ||||||| ||||||||||||||||||||||||||| |||||||||| ||||| || || ||  |  | |||||||| |||||||| ||||||||||||   ||||| |   || |||      |   |||| || |   |  |  || ||| | | |   |     |   |||   ||  |  ||||   |    | |     
AGAATTGTTTGCACAAACAAAATACAAGGAAGCAGCTGAGTTGGCTGCAGAATCTCCTCAAGGTCTTCTCCGAACTCCTGATACTGTTGCAAAATTTCAGgtgcatttctgct--cttgatt------acagagctattaacacttcttcacctccattttacagctatttttcacattctgtactgttaaaagcttaaaattatgtg

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 11
GGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAACTGTTGCGAAATTTCAGgtga-gcttctggtattttaattcgacgtatgaagctgttgaggtt-catgaacatcctt---ctaatgtcccacctctgcatgtcttcgtaaaccatagtgaat--------------------------------------------------------------------------------------
 ||||||||||| |||||||| || || ||||||||||| || ||||| ||||||||||| ||  || |  | || ||||| || ||||| |||||||||||   |  | |   ||         |  |||   | |  ||   || ||| ||||   ||   |||      || || ||| ||| ||     |  |  |  ||                                                                                       
TGAACTGTTTGCCCAAACAAAGTATAAAGAAGCAGCTGAACTTGCTGCTGAGTCTCCGCAAGGAATCCTTCGCACACCTGATACAGTTGCCAAATTTCAGgttttgtatataagatacagccatcaaatattttgttcgtgctctttcatcaacaaatttaacctagacaatcatctttgcttgttttgagggataaaggataaaaggaatttgaactgtttaggtttgttctttttcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatgtggcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 11
GGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAACTGTTGCGAAATTTCAGgt--------gagct-------tctggtattttaattcgacgtatgaagctgttgaggttcatgaacatccttctaatgtcccacctctgcatgtcttc--gtaa-accatagtgaat--------------------------------------------------
 ||||||||||| ||||||||||| |||||||| || ||||| || || || ||||| || ||  || |  | |||||||| || ||||| |||||||||||         || |       ||||| | |||  |    | | |  ||||  |    ||||   | || | | |  ||        |||  || |||   || |   | |  ||  |                                                  
TGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACACAGTTGCCAAATTTCAGgtttcttgataagatgttgctatctgggaattttctcttgcttttttagctacttca-ttcacagagattcattttctggttgtttactgtttgcctttaggtgatgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttatgtggcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 11
GGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAACTGTTGCGAAATTTCAGgtgagcttctggtattttaattcgacgtatgaagctgttgaggttcatgaacatccttcta-atgtcccacctctgca--tgtcttcgtaaaccatagtgaat-------------------------------------------------------------------------------------------------
 ||||||||||| ||||| || || || |||||||||||||| ||||| |||||||| || ||  || |  | || ||||| || ||||| |||||||||||       | |||| | |  |  |   || ||    || ||  |  ||  | | | || | |  |   ||||   ||    |||| ||  |  ||  || ||                                                                                                 
TGAACTGTTTGCCCAAACCAAGTATAAAGAAGCAGCTGAGCTTGCTGCTGAGTCTCCACAAGGAATCCTTCGCACACCTGATACAGTTGCCAAATTTCAGgt------tttgtatataagatatagccatcaaatattttag--ttgtgctctttcatcaacaaatttaacctagacaatcatctttgtggagaatgatggataaaggataaaagagtttgaaatgtttttaggtttgttctttttcttggtcaattaggctgtcatgtttaaagtgtcacgatctgttttatgtggcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 11
GGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAACTGTTGCGAAATTTCAGgtg-agcttctggtattttaattcgacgtat-------gaagctgttgaggttcatgaacatccttctaatgtcccacctctgcatgtcttcgtaaaccatagtgaat
 ||||||||||| || ||||| || |||||||| || ||||| |||||||| ||||| ||||| ||| || | |||||||| |||||||| |||||||||||  | | | ||||    |  ||  | ||||         | |||   |   |||    | ||||| | | ||   || | ||    |||   | ||    ||     
AGAACTGTTTGCTCAGACAAAGTATAAGGAAGCTGCGGAGCTTGCTGCAGAATCTCCACAGGGACTCCTGCGTACTCCTGATACTGTTGCCAAATTTCAGgtatatcatttggttggcttgttt-atgtattttcttaatatctgacaattctcagatgcttccttatgaagttgaacttatgt---tctcatttaatttcagg----

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), 49 (downstream exon)
Score: 232

GGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAACTGTTGCGAAATTTCAGgtgagcttct ... aaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 188

GGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAACTGTTGCGAAATTTCAGgtgagcttct ... aaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 90

GGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAACTGTTGCGAAATTTCAGgtgagcttct ... aaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

GGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAACTGTTGCGAAATTTCAGgtgagcttct ... aaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT