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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGCCAGGCTCCGGCAAGGCAGGCAGCCCTTGGCGCCGGCTTGCCCAACTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgctactactaccaatatattttgtatattgattgattgttgattagccttgcaagttgcaacctgatagccttatcctggaacgttaccactgacttgttgcag

Basic information

species Zea mays
transcript GRMZM5G860137_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G860137_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g02020.2 (Oryza sativa), 5'ss of exon 2
CTTGGCCAGGCTCCGGCAAGGCAGGCAGCCCTTGGCGCCGGCTTGCCCAACTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgctactactaccaatatattttgtatattgattgattgttgattagccttgcaagttgcaacctgatagccttatcctggaacgttaccactgacttgttgcag---------------------------
|||||||| || ||||| ||||| || ||||| ||||||||||||||| || | ||||| || |||||||||||||||||||| |||||||| |||||||||  |  |  ||| |   |      | | | | |   |   |   |   |  | ||   |||||  || || |     ||  |  | |     |   ||  ||| |                               
CTTGGCCAAGCCCCGGCGAGGCAAGCCGCCCTAGGCGCCGGCTTGCCCGACACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttc-gctattttaacctctctctctctctctctctctctctctctctctttttcagttgttacttgtttctgctactcgaggat-cggcttttgctttgctatctagtgctacttaaaaatgggtcttgcag
















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|71298333|gb|DR785148.1|DR785148
EST:     CTCCGTGCCATGTACCACCATCAACAAAGTTTGCTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTCGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|50337630|gb|CO532756.1|CO532756
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|149110543|gb|EE190473.2|EE190473
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|89760643|gb|DY688974.1|DY688974
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|20803192|gb|BQ294242.1|BQ294242
EST:     CTCCGTGCCATGTACCACCATCAACAAAGTTTGCTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTCGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|149071725|gb|EE160115.2|EE160115
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|93281948|gb|EB674212.1|EB674212
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|149000558|gb|EE037748.2|EE037748
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCCTGTTTTGCGGCTCAAAGTATTCAGCTGGGGATCACCGATGTTGTG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTT-GCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTG
EST: gi|211024306|gb|FL368563.1|FL368563
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|149029957|gb|EE286286.2|EE286286
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|37419864|gb|CF647618.1|CF647618
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|76914731|gb|DV165656.1|DV165656
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|149087112|gb|EE176651.2|EE176651
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|74232957|gb|DT640871.1|DT640871
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|71426143|gb|DR807193.1|DR807193
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|78087866|gb|DV516259.1|DV516259
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|78078473|gb|DV506886.1|DV506886
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|89248149|gb|DY619935.1|DY619935
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|148947617|gb|EC893097.2|EC893097
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAG
EST: gi|148939632|gb|EC884275.2|EC884275
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|149084568|gb|EE174037.2|EE174037
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|91051495|gb|EB161913.1|EB161913
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|149083757|gb|EE173120.2|EE173120
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|211111975|gb|FL386052.1|FL386052
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGCTCCTCGGGAATGAAGG                         CTGTCATGTTTTGCGGCTCAAAGTATTCAGCTGGGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTT-GCGGCTCAAAGTATTCAGCTGGGG
EST: gi|78085615|gb|DV514008.1|DV514008
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|93016086|gb|EB641606.1|EB641606
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCANAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|89248499|gb|DY620285.1|DY620285
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCANAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|71439486|gb|DR820536.1|DR820536
EST:     CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGG                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
genomic: CTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGG
EST: gi|211403233|gb|FL400076.1|FL400076
EST:     CCGTGCCATGTACCACCGTTCA-CAAAGTTTGTTCCTCGGGAATGATAG-                         CTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTG
genomic: CCGTGCCATGTACCACCGT-CAACAAAGTTTGTTCCTCGGGAATGA-AGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTG

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: 43 (upstream exon), 48 (downstream exon)
Score: 17

CTTGGCCAGGCTCCGGCAAGGCAGGCAGCCCTTGGCGCCGGCTTGCCCAACTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGGTCGCCGGTGGCATGGAAAGCATGTCGAATGCCCCAAAATATGTGGCTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 76

CTTGGCCAGGCTCCGGCAAGGCAGGCAGCCCTTGGCGCCGGCTTGCCCAACTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGGTCGCCGGTGGCATGGAAAGCATGTCGAATGCCCCAAAATATGTGGCTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 39

CTTGGCCAGGCTCCGGCAAGGCAGGCAGCCCTTGGCGCCGGCTTGCCCAACTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGGTCGCCGGTGGCATGGAAAGCATGTCGAATGCCCCAAAATATGTGGCTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 26

CTTGGCCAGGCTCCGGCAAGGCAGGCAGCCCTTGGCGCCGGCTTGCCCAACTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgcta ... cttgttgcagCTGTCATGTTTGCGGCTCAAAGTATTCAGCTGGGGATCAACGATGTTGTGGTCGCCGGTGGCATGGAAAGCATGTCGAATGCCCCAAAATATGTGGCTGA