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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctcgacatcaatttgttttgcccactgcagaagatgttttcgggtgataacatttctgttatcttggttccccag

Basic information

species Zea mays
transcript GRMZM2G082855_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082855_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 6
GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctcgaca-----------tcaatttgttttgcccactgc----agaagatgtttt-cgggtgataacatttctgttatcttggttccccag
||| ||||| |||||| | ||||| ||||| ||||| |||||||| |||||||||||||| || ||||||||||||||   | | |           || |  ||||||  |   |      ||||| | |||| | ||   ||||| ||   || ||||  | |  |||
GGACCTGGCACAGAACCAGCTTACAGGCGATATCCCAAGGCTCATATACTGGAATGAAGTTCTGCAATACCTgtaagaatcctataaaagaaaattgtctaactgttttagctggtagtataagaaggtatttttcaggcattaacactttgcttctcttaat-cttcag

upper sequence: GRMZM2G082855_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv16s0022g02030.t01 (Vitis vinifera), 5'ss of exon 6
GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctcgac--atcaatttgttttgcccactgcagaagatgttttcg-ggtgataacatttctgttatcttggttccc-cag----------------------------------------------------------------------------------
 || ||||| |  ||| | ||||| || || || || ||||| |||||||||||||||||| | |||||||||||||   | | |  ||| |  | |  |    | |    |   || ||      |   | || |  ||   | | ||||     ||                                                                                  
TGACCTGGCTCGAAACCAGCTTACGGGTGAGATACCAAGGCTAATCTACTGGAATGAAGTATTGCAATACCTgtaagtaatagccgaatccaaatatagtcagaattaagaaccttgattctataattccaccagtaatggagtttaggttatggtaggagcctttgatatatttcagtgtttctcatattgaatatacaactgtgctgcttcatccatttgttttgtttaacttcacag
















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|86472326|gb|DY238696.1|DY238696
EST:     ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT                         AGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
genomic: ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
EST: gi|148934014|gb|EC878019.2|EC878019
EST:     ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT                         AGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
genomic: ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
EST: gi|148940443|gb|EC885241.2|EC885241
EST:     ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT                         AGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
genomic: ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
EST: gi|149079906|gb|EE168912.2|EE168912
EST:     ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT                         AGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
genomic: ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
EST: gi|148964982|gb|EC906062.2|EC906062
EST:     ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT                         AGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
genomic: ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
EST: gi|148941048|gb|EC885905.2|EC885905
EST:     ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT                         AGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
genomic: ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
EST: gi|149096378|gb|EE182110.2|EE182110
EST:     ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT                         AGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
genomic: ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
EST: gi|101383199|gb|EB813654.1|EB813654
EST:     ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT                         AGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
genomic: ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
EST: gi|148957491|gb|EC903572.2|EC903572
EST:     ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT                         AGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA
genomic: ACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCA

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: 804

GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCAACTGACTGGCCTGTGGTACTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 85

GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCAACTGACTGGCCTGTGGTACTT


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 1

GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCAACTGACTGGCCTGTGGTACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 514

GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCTgtaagagctc ... ggttccccagAGGCTTGAGGGGTAACTCACTGACTGGAACTTTGTCACCTGACATGTGCCAACTGACTGGCCTGTGGTACTT