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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTATTATCTGCATTTGTAATGACCGTTATAGTCAGAAATTGAAGAATCTTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAGgttatttttttttgccatgttcagtcctagtgaagcaatgagcttcagaattactaatgtttccttgaattacaagaacccagcaccacattctttactt...

Basic information

species Zea mays
transcript GRMZM2G457381_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G457381_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os11g36390.1 (Oryza sativa), 5'ss of exon 11
CCCTATTATCTGCATTTGTAATGACCGTTATAGTCAGAAATTGAAGAATCTTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAGgttatttttttttgccatgttcagtcctagtgaagcaatgagcttcagaattactaatgtttccttgaattacaagaacccagcaccacattctttactt--
 ||||| || |||||||| |||||||||||||| |||||||||||||  ||||| ||||||||| |  | |||||||||||||| ||||| || ||||||||||| | ||     |  |     | ||            |  || ||    | | | | | |  |    | ||  |||  |        |  | ||  |  
TCCTATAATTTGCATTTGCAATGACCGTTATAGCCAGAAATTGAAGAGCCTTGTAAATTACTGCTTGCTACTCAACTTCAGAAAACCAACCAAGCAACAGgttatctgttgacctctggacatattctcaatttcttgcaatttttagg--cagttacgatacagttgcatgcagcaacttatttaggggtaatataagtcc

upper sequence: GRMZM2G457381_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA06G46540.2 (Glycine max), 5'ss of exon 12
CCCTATTATCTGCATTTGTAATGACCGTTATAGTCAGAAATTGAAGAATCTTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAGgttatttttt-tttgccat---gttcagtcctagtgaagcaatgagcttcagaattactaatgtttccttgaattacaagaacccagcaccacattctttactt
 ||||||||||||||||| ||||||||||| || |||||| |||| |  |||||||| |||||  |  | || |  ||  | ||||| ||||| ||||||||  || ||| |||   ||       |||  | ||    |  | |  ||   ||||   ||| |||  ||  ||||             |    || |  ||| 
TCCTATTATCTGCATTTGCAATGACCGTTACAGCCAGAAACTGAAAAGCCTTGTGAACTACTGTTTGCTTCTAAGTTTTCGGAAGCCTACAAAGCAACAGgtctttctttgtttattattaaaaaaagttattgtttctcttttacttt---aatttaaaatctttattttgattaggtccttttgttgctctcttttgaact-

upper sequence: GRMZM2G457381_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA12G10230.1 (Glycine max), 5'ss of exon 11
CCCTATTATCTGCATTTGTAATGACCGTTATAGTCAGAAATTGAAGAATCTTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAGgttatttttt-tttgccat---gttcagtcctagtgaagcaatgagcttcagaattactaatgtttccttgaattacaagaacccagcaccacattctttactt
 ||||||||||||||||| ||||||||||| || |||||| |||| |  |||||||| |||||  |  | || |  ||  | ||||| ||||| ||||||||  || ||| |||   ||       |||  | ||    |  | |  ||   ||||   ||| |||  ||  ||||             |    || |  ||| 
TCCTATTATCTGCATTTGCAATGACCGTTACAGCCAGAAACTGAAAAGCCTTGTGAACTACTGTTTGCTTCTAAGTTTTCGGAAGCCTACAAAGCAACAGgtctttctttgtttattattaaaaaaagttattgtttctcttttacttt---aatttaaaatttttattttgattaggtccttttgttgctctcttttgaact-

upper sequence: GRMZM2G457381_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT5G22010.1 (Arabidopsis thaliana), 5'ss of exon 12
CCCTATTATCTGCATTTGTAATGACCGTTATAGTCAGAAATTGAAGAATCTTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAGgtt--attt------ttttttgccatgttcagtcctagtgaagcaatgagcttcagaattac---taatgtttccttga-attacaagaacccagcaccacattctttactt--------------
 ||||| |||||||||||||||||||| |||||||| ||| |||||| | | || || ||||| |||   ||||| | | | ||||| || ||||| ||||||  ||||      || |||| | | |       |  | ||| | |  ||    || || |     ||||  | ||   | | |  || | |  ||  |  || |  | ||              
TCCTATCATCTGCATTTGTAATGACCGATATAGTCAAAAACTGAAGAGTTTAGTAAACTACTGTCTTCCCCTCAATTACCGGAAGCCCACGAAACAGCAGgttggatttagatgattgtttgtcctttctgcgtttttttaaggattatgcacaggattttcattctatgtaccattattagtccttgagctcttcattatcttttcgatttgtcttttattgcag

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|160481320|gb|EY254484.1|EY254484
EST:     TTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAG                         ATGGGTAAAAGATTGA-GAAAAATTGCCAAA
genomic: TTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAGgttatttttt ... tacttgacagATGGGTAAAAGATTGATGGAAA-TTGCCAAA
EST: gi|160481307|gb|EY254481.1|EY254481
EST:     TTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAG                         ATGGGTAAAAGATTGATGGAAATTGCCAAAAAGGAAGGTATTCAAGCTCAA
genomic: TTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAGgttatttttt ... tacttgacagATGGGTAAAAGATTGATGGAAATTGCCAAAAAGGAAGGTATTCAAGCTCAA

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), 47 (downstream exon)
Score: 314

CCCTATTATCTGCATTTGTAATGACCGTTATAGTCAGAAATTGAAGAATCTTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAGgttatttttt ... tacttgacagATGGGTAAAAGATTGATGGAAATTGCCAAAAAGGAAGGTATTCAAGCTCAAGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 124

CCCTATTATCTGCATTTGTAATGACCGTTATAGTCAGAAATTGAAGAATCTTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAGgttatttttt ... tacttgacagATGGGTAAAAGATTGATGGAAATTGCCAAAAAGGAAGGTATTCAAGCTCAAGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 95

CCCTATTATCTGCATTTGTAATGACCGTTATAGTCAGAAATTGAAGAATCTTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAGgttatttttt ... tacttgacagATGGGTAAAAGATTGATGGAAATTGCCAAAAAGGAAGGTATTCAAGCTCAAGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 118

CCCTATTATCTGCATTTGTAATGACCGTTATAGTCAGAAATTGAAGAATCTTGTGAATTACTGCCTTATGCTCAACTTCAGAAAGCCAACAAAACAACAGgttatttttt ... tacttgacagATGGGTAAAAGATTGATGGAAATTGCCAAAAAGGAAGGTATTCAAGCTCAAGAG