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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCACAGTCCTCCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagcggttctcccctcttctgcccgctctgtgatcccatccgacctcgatctaatgcggggtttgtttttctctctgcttgcgctgtgcag

Basic information

species Zea mays
transcript GRMZM2G131120_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131120_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g05650.1 (Oryza sativa), 5'ss of exon 1
CCTCACAGTCCTCCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagcggttctcccctcttctgcccgctctgtgatcccatccgacctcgatctaatgcggggtttgtttttctctctgcttgcgctgtgcag--------------------
|||||| || || |||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||||||    | | | ||||||  || | |||     ||||| |||||        ||     || | |  | |         | |||||||||                       
CCTCACCGTGCTGCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCCCACGTCACCCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagc----gatccccccctccactcctcgcg----gatccgatccggttggttgcttgcttggtgatcctgtgagctcactcatgcgctgtgttttttttccttttttgtttcag

upper sequence: GRMZM2G131120_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA19G38280.1 (Glycine max), 5'ss of exon 1
CCTCACAGTCCTCCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagcggttctcccctcttctgcccgctctgtgatcccatccgacctcgatctaatgcggggtttgtttttctctctgcttgcgctgtgcag
 ||||| || ||||||||  |||| ||   | |||| || || ||| ||||||||||||| ||| |  |||||||||||||||||||   ||||||||||||      |   || ||     ||||   ||||   |    |  ||    ||| ||||  ||      | ||| |                      
TCTCACGGTGCTCCAGCGAATCGATCCGTTCATCGAAGAGATTCTCTTCACCGCCGCGCATGTCTCCTTCTACGACTTCAACATCGAAAGCAACCAGTGGgt----tcgttcttttctttctttctcttcgcttcttcccactttcttctctc-atcttctgttttactcgttctag--------------------

upper sequence: GRMZM2G131120_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA13G39120.1 (Glycine max), 5'ss of exon 1
CCTCACAGTCCTCCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagcggttctcccctcttctgcccgctctgtgatcccatccgacctcgatctaatgcggggtttgtttttctctctgcttgcgctgtgcag
 ||||| || ||||| ||  ||||||||  ||| || || || |||||||||||||| || |||||  ||||||| ||||||||||||||||  || |||||   |   |  |       ||||    | | | | |  |  ||||| |  ||  ||| ||         | | |  ||   | ||||  | |||||
TCTCACTGTTCTCCAACGAATCGACCCCTTCGTTGAAGAAATTCTCATCACCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGGgttcactctctttctatttttcttacttctgtttt-tattttcatcccat-tctctctcat--------cgctctcttccgcgattgc--tttgcag

upper sequence: GRMZM2G131120_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT1G08370.1 (Arabidopsis thaliana), 5'ss of exon 1
CCTCACAGTCCTCCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagcggttctcccctcttctgcccgctctgtgatcccatccgacctcgatctaatgcggggtttgtttttctctctgcttgcgctgtgcag
 |||||||| ||||||||  |||| ||   | ||||||| ||||||||||| ||||| || |||||| |||| || |||||||| || |||| ||| ||||| || |      ||   | ||   | |    | ||   |    | |     | | ||||||   | | ||| |||     | |             
TCTCACAGTTCTCCAGCGGATCGATCCATACATCGAGGAAATCCTCATCACAGCCGCTCATGTCACTTTCTATGAATTCAACATTGAGCTCAGCCAATGGgttagtc--tcaatcaatcttcgattacataatttgatgtttgcttc----cctacctaatgattgatctgtcttttgtcattcag-----------

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|93282081|gb|EB674345.1|EB674345
EST:     CCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGG                         AGCCGCAAGGACGTGGAAGGGTCCCTGTTCGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagc ... cgctgtgcagAGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG
EST: gi|78086956|gb|DV515349.1|DV515349
EST:     CCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGG                         AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagc ... cgctgtgcagAGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG
EST: gi|148955226|gb|EC900753.2|EC900753
EST:     CCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGG                         AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagc ... cgctgtgcagAGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG
EST: gi|211064273|gb|FK983490.1|FK983490
EST:     CGCCGCGCACGTCASCTCTCTACGACTTCAACATCGACCTCAACCAGTAG                         AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG
genomic: CGCCGCGCACGTCA-CTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagc ... cgctgtgcagAGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG
EST: gi|211064272|gb|FK983489.1|FK983489
EST:     CCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGG                         AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagc ... cgctgtgcagAGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG

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: 48 (upstream exon), 41 (downstream exon)
Score: 65

CCTCACAGTCCTCCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagc ... cgctgtgcagAGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 79

CCTCACAGTCCTCCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagc ... cgctgtgcagAGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 56

CCTCACAGTCCTCCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagc ... cgctgtgcagAGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 83

CCTCACAGTCCTCCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCGCACGTCACTCTCTACGACTTCAACATCGACCTCAACCAGTGGgtgagccagc ... cgctgtgcagAGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG