Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctactcaattttagcatcaaaaccttagccctttattaccaaaatgttgtgctttgtgtccttatattggcccttttactgcttttag

Basic information

species Zea mays
transcript GRMZM2G148323_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 5'ss of exon 8
GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctactcaattttagcatcaaaaccttagc-----cctttatta-ccaaaatgttgtgctttgtgtccttatattggcccttttactgcttttag
| ||||  |||| || ||||||||||||||||| || || || |||| |||||| || ||||| || |||||  |||| ||||||||||| ||| ||||||||||| |  || ||| | ||||  | | || ||      ||||  ||  || |||||||||    | | |  |||  | |                   
GTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATATGGAAATCATTCATTAACCTACCGAATCGTTGATAGAATCTTCTCACAGgttagtatgttctattct-gcatacagaactgagatgctgccttagttggcctaaatgttgtttcctatatg-ttacttag-------------------

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G36530.1 (Glycine max), 5'ss of exon 8
GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagt-----ctactcaat--tttagcatcaaaaccttagccctttattaccaaaatgttgtgctttgtgtccttatattggcccttttact--gcttttag----------------------------------------------------------------------------
||||||| |||| |||||||| || || || || || ||||| |||| |||||| |||||| || | |||||| |||| ||||||||||| ||  | |||||| ||      ||||   |  ||  |  |   |   |||    ||||| ||   |        |  | |  || |    |  |      |    |  ||| |                                                                            
GCTGGATACAGATCACGATTTCTTTATAGACAAAGAGAATCTTATCAGATATGGTAACCATGCGCTTACCTATCGAATTGTTGATAGAATATTTTCTCAGgtttgtgtggattacttgttgcttctgtctttgagatttaaatgtttatgacttcagcaacagaccctataccccttctctttctaacgcaagaagtgtttggttcagtgtccatccacttttgtttatcagatcatttattgaagtgcagattctgacttgcttcagtattgtctcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G30930.1 (Glycine max), 5'ss of exon 8
GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagt-----ctactcaat--tttagcatcaaaaccttagccctttattaccaaaatgttgtgctttgtgtccttatattggcccttttact--gcttttag------------------------------------------------------------------------------
||||||| |||| |||||||| || || || || || ||||| |||| |||||| |||||| || | |||||| |||| ||||||||||| ||  | |||||| ||      ||||   |  ||  |  |   |   ||| |  ||| | ||   |        |  | |  || | |  |  |      |    |  ||| |                                                                              
GCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATATGGTAACCATGCGCTTACCTATCGAATTGTTGATAGAATATTTTCTCAGgtttgtgtggattacttgttgcttctgtctttgagatttaactgtttctgacttcagcaacagaccctataccccttttctttctaacgcaagaagtgtttggttcagtgtccattcatttttttttatcagatcattttatagaagatgcagattctgacttgctttattattgtctcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 8
GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctactcaattttagcatcaaaaccttagccctttattaccaaaatgttgtgctttgtgtccttatattggcccttttactgcttttag---------------------------------------------------------------------------------------------------
||||||| |||| || ||||| ||||| || || || |||||||||| |||||| |||||| || | |||||| |||| ||||||||||| ||  | |||||| || |     | | || |||      |||    ||| |  |    | |   |   | |  | ||  | |    ||   |  || |   |                                                                                                     
GCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATATGGTAACCATGCGCTTACCTATCGAATTGTTGATAGAATATTTTCTCAGgttggtgtggattactatatcatgtgttgcttctgtcttaag-atttgacttcagctgtctagggccacagacaacccaaatccctacccctccctccaaatacacatgcactgtcctttcacttatgtttatatgaattaccagagcatttgttgaagatgcagattttgattcactttaatattatctcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G43790.1 (Glycine max), 5'ss of exon 8
GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctactcaattttagcatcaaaaccttagccctttattaccaaaatgttgtgctttgtgtccttatattggcccttttactgcttttag---------------------------------------------------------------------------------------------------
||||||| |||| || ||||| ||||| || || || |||||||||| |||||| |||||| || | |||||| |||| ||||||||||| ||  | |||||| || |     | | || |||      |||    ||| |  |    | |   |   | |  | ||  | |    ||   |  || |   |                                                                                                     
GCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATATGGTAACCATGCGCTTACCTATCGAATTGTTGATAGAATATTTTCTCAGgttggtgtggattactatatcatgtgttgcttctgtcttgag-atttgacttcagctgtctagggccacagacaacccaaatccctacccctcccctccaaataacatgcactgtcctttcacttatgtttatatgaattatcagagcatttgttgaagatgcagattttgattcacttcaatattatctcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT1G03960.1 (Arabidopsis thaliana), 5'ss of exon 8
GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctactcaatt-ttagcatcaaaaccttagccctttattaccaaaatgttgtgctttgtgtccttatattggcccttt-tactgcttttag-----------------
 || ||||  ||||| |||| ||| ||||||||||| ||||||||||||||||| ||  || |  | ||||| || || ||||||||||| ||  |||||||| ||   |  |||| ||     | | |||||         | |   | ||  | || | ||   | || |||| |  ||   | |  ||| | |                 
ACTTGATGGTGACCATGATTGTTTTATTGATAAGGACAATCTCATCAAATATGGTAATAATGCCCTTACCTACAGGATTGTTGATAGAATATTTTCACAGgttggttcccaaaattgttcctgcctagaccttcttaaaagctaagttatatagtatgatgtgatcctttttatttgatctccatgcgtcttgtggctatgtttctcttttag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT5G44090.1 (Arabidopsis thaliana), 5'ss of exon 8
GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtc----tactcaattttagcatcaaaaccttagcc----ctttattaccaaaatgt----tgtgctttgtgtccttata-ttggcccttttactgcttttag-----
 || ||||  ||||| |||||  | ||||||||||||||||||||||||||||| || ||| |  | ||||| || || || || ||||| ||  |||||||| |      |  ||||  |    || || || ||   |    ||| |||   |   | |    |||| ||  |    |  || |||    |    |||  | |       
ACTCGATGGCGACCATGATTTCCTTATTGATAAGGAAAATCTCATCAAATATGGTAATCATGCCCTTACCTACAGGATTGTCGACAGAATATTTTCACAGgttggctccagttgtcaaaatgttaatgaacacttttctcgaaacttaattgttatcttatggagtgtgtttccttctttcttaattgaaattacggctgtctctcactcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|87156079|gb|DY400868.1|DY400868
EST:     ATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAG                         ATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGAC
genomic: ATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctac ... ctgcttttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGAC
EST: gi|23199745|gb|BU582310.1|BU582310
EST:     ATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAG                         ATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGAC
genomic: ATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctac ... ctgcttttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGAC
EST: gi|211505069|gb|FK974737.1|FK974737
EST:     ATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAG                         ATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGAC
genomic: ATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctac ... ctgcttttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGAC
EST: gi|26560172|gb|CA832407.1|CA832407
EST:     ATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAG                         ATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGAC
genomic: ATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctac ... ctgcttttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGAC

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), 48 (downstream exon)
Score: 201

GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctac ... ctgcttttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGACTTTGTTTACTTTATATTATCAGAGGAAGACAAATCATCTGAGCCTAGTC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 143

GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctac ... ctgcttttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGACTTTGTTTACTTTATATTATCAGAGGAAGACAAATCATCTGAGCCTAGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctac ... ctgcttttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGACTTTGTTTACTTTATATTATCAGAGGAAGACAAATCATCTGAGCCTAGTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 181

GCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATATGGGAACCATTCGTTGACCTATAGAATAGTTGATAGAATTTTCGCACAGgttagtctac ... ctgcttttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGACTTTGTTTACTTTATATTATCAGAGGAAGACAAATCATCTGAGCCTAGTC