Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgattcatccccagttggatcaatctgtacgtcatgcaccactcgtctcacctcgctctcgctctctgtctctgtggcatgtgatttgttgcattgcag

Basic information

species Zea mays
transcript GRMZM2G133844_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133844_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g72950.1 (Oryza sativa), 5'ss of exon 5
ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgattcatccccagttggatcaatctgtacgtcatgcaccactcgtctcacctcgctctcgctctctgtctctgtggcatgtgatttgttgcattgcag
||||||||||| || ||||| || |||||||||||||| ||||| ||||||||||||||||||  |     ||| | |  |  ||||  |  | |  |||   |||     |  |     |  ||  |      ||   |   |      || || ||      
ATCGCTTGGGTTGGAATCCCAACTCCACCGGCATGGCTGCCAACTTACATGCTCATCAAGgtaattacagtatctctaagtccatcacac-atgcagcat-tgccaaaatgcagaatgtaccatcatttgaccacttaatcttaacactatttttacag-----
















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|32842437|gb|CD982118.1|CD982118
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|14529225|gb|BI096358.1|BI096358
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|32842438|gb|CD982119.1|CD982119
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|32842276|gb|CD981957.1|CD981957
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|12971656|gb|BG267591.1|BG267591
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|37380814|gb|CF627243.1|CF627243
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|18179821|gb|BM381031.1|BM381031
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|37378226|gb|CF625789.1|CF625789
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|16379515|gb|BI992998.1|BI992998
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|28982421|gb|BQ539420.2|BQ539420
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|13490470|gb|BG517234.1|BG517234
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|4646657|gb|AI491495.2|AI491495
EST:     TGGGGATCCCGACGCCNCCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|13557973|gb|BG549329.1|BG549329
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
EST: gi|40334773|gb|CK368843.1|CK368843
EST:     TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG                         TCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA
genomic: TGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCA

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: 42 (upstream exon), 42 (downstream exon)
Score: 19

ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCAGGGCACCGTAGCGCCGCCGCCGAATTCATGCTTCATTTCGCATCAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCAGGGCACCGTAGCGCCGCCGCCGAATTCATGCTTCATTTCGCATCAGGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 45

ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCAGGGCACCGTAGCGCCGCCGCCGAATTCATGCTTCATTTCGCATCAGGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 63

ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAGgtagctgatt ... tgcattgcagTCGGACAAGCTCGACTACGAGAGGATATGATGGCCGGCCGGCGGCCTCGCAGGGCACCGTAGCGCCGCCGCCGAATTCATGCTTCATTTCGCATCAGGAG