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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCTCATCTCCGCTTGAGGGATCCTACAGTACCCGAACGAGTAAATGTTGCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaactagccactccttgttgaattcccgttgctcccttcatgcatcaatgactcaaagctttagtggccaagagttttctgatcactactgtgtctgttttcatgtag

Basic information

species Zea mays
transcript GRMZM2G032222_T02
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032222_T03 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os10g37210.1 (Oryza sativa), 5'ss of exon 16
CGCCTCATCTCCGCTTGAGGGATCCTACAGTACCCGAACGAGTAAATGTTGCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaactagccactccttgttgaattcccgttgctcccttcatgcatcaatgactcaaagctttagtggccaagagttttctgatcactactg---tgtctgttttcatgtag
| ||||||||||| |||||||||||||||||||| ||  |||||||| || | |||||||| |  ||||| ||||  ||||| ||||| || ||||||||||| | ||| | |||  || |  ||||||    | |    ||| ||   || ||  ||| || ||   |       |  | || || |||||| |||   |   |||| ||||| ||
CTCCTCATCTCCGTTTGAGGGATCCTACAGTACCGGAGAGAGTAAATCTTCCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaattggcctttcttacttgaatgaaagataa--cctaca---attaagtactgaatgcccaaac-----aaggattgctaatcacttctgccatacatgttctcatgcag

upper sequence: GRMZM2G032222_T03 (Zea mays), 5'ss of exon 16
lower sequence: AT2G43400.1 (Arabidopsis thaliana), 5'ss of exon 16
CGCCTCATCTCCGCTTGAGGGATCCTACAGTACCCGAACGAGTAAATGTTGCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaactagccactccttgttgaattcccgttgctcccttca--tgcatcaatgactcaaagctttagtggccaagagttttctgatcactactgtgtctgttttca-tgtag-----
|  ||||| | ||||||||||||||||   | || |||   |||||  || ||  |||||| |||||||| ||||| || ||||||||||| |||||||||||  |||  |     |||     |   || |  |  |    |  |  |  ||||||   ||||   ||   ||  |||||   |  |  ||  | |||| |   ||   |   ||      
CATCTCATTTGCGCTTGAGGGATCCTAAGATTCCAGAAAAGGTAAACTTTCCAGAGTATGCTGCGCCAGAGTCACGTTACTGCCCAGCCCGTGTTTACGAgta-ataacttcctttctctaccctctctttctctcaccatatgaaatttgatcaatatatcaag--ttccttgaacaagatactcatcttcgtttctgtattgattcaaaacataaaaaag
















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|78120295|gb|DV538679.1|DV538679
EST:     GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTTCGA                         ATATATTTTTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
genomic: GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
EST: gi|94479206|gb|EB708164.1|EB708164
EST:     GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGA                         ATATATCTTTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
genomic: GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
EST: gi|71756373|gb|DR954310.1|DR954310
EST:     GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGA                         ATATATCTTTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
genomic: GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
EST: gi|87157160|gb|DY401949.1|DY401949
EST:     GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGA                         ATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
genomic: GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
EST: gi|161593692|gb|EY964319.1|EY964319
EST:     CGGGTTTACGA                         ATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
genomic: CGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
EST: gi|31353246|gb|CD437603.1|CD437603
EST:     GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGA                         ATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
genomic: GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
EST: gi|76020278|gb|DT947448.1|DT947448
EST:     GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGA                         ATATATCTTTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
genomic: GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
EST: gi|21809980|gb|BQ668298.1|BQ668298
EST:     GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGA                         ATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA
genomic: GCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAA

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), 49 (downstream exon)
Score: 49

CGCCTCATCTCCGCTTGAGGGATCCTACAGTACCCGAACGAGTAAATGTTGCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 92

CGCCTCATCTCCGCTTGAGGGATCCTACAGTACCCGAACGAGTAAATGTTGCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

CGCCTCATCTCCGCTTGAGGGATCCTACAGTACCCGAACGAGTAAATGTTGCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

CGCCTCATCTCCGCTTGAGGGATCCTACAGTACCCGAACGAGTAAATGTTGCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaac ... tttcatgtagATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAG