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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTATATTTGCTTTGATGGAGCGTAGTGAGGCCGAGTTGGCAGAACCCATTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaagcatcctgtagatatggttctgatttcgaattaataatttgctgctaggcttagcatatccatctaaagtattgcttgttgcttctaatt...

Basic information

species Zea mays
transcript GRMZM2G155384_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T03 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 17
TATTATATTTGCTTTGATGGAGCGTAGTGAGGCCGAGTTGGCAGAACCCATTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactct-aagcatcctgtagatatggttctgatttcgaattaataatttgctgctaggcttagca-tatccatctaaagtattgcttgttgcttctaatt
||| |||||||| ||||||||||| |||||||| ||| |||||||||||||||||||  ||||||||||||||||||| ||| | ||||||||||| ||||||  | |  |||| |||  |    | ||||   ||| || | | |  |||   |||  |   |  |  ||     ||||  |   |  ||     ||  ||
TATCATATTTGCCTTGATGGAGCGCAGTGAGGCTGAGCTGGCAGAACCCATTATACGCCTGCTTCCTGTTGCGCTTGGTCTTCTGTATCTTGGAAAGCAGgtactttttgagcaaccttgaagcttagttcc--ttttgattcattttttttgggctgtgtgcactagcatttgcttaaaaaaaatccagtattccctgctt

upper sequence: GRMZM2G155384_T03 (Zea mays), 5'ss of exon 17
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 5'ss of exon 15
TATTATATTTGCTTTGATGGAGCGTAGTGAGGCCGAGTTGGCAGAACCCATTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaagcatcctgta-gatatggttctgatttcgaattaataatttgctgctaggcttagc--atatccatctaaagtattgcttgttgcttctaatt
||||||||||||||||||||| || |||||||| ||  |||  ||  || | |  || ||  | ||  |||  ||||| ||| |||| || || |||||||| |  | | |  |  |  |  || | | |||   |||| ||  || |||   |||   ||||  |  | ||| |  |     | |   |             
TATTATATTTGCTTTGATGGATCGAAGTGAGGCAGAACTGGGTGATGCCCTCACTCGTTTCTTGCCACTTGGTCTTGGACTTCTATACCTGGGCAAACAGgttag-caatgtgttttacataatctcgctctttgttcgtat--atcattatttgcattgcttgaccaacatcaacttgttccaatatctaccag--------
















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|32940220|gb|CF045039.1|CF045039
EST:     TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAG                         GATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATA
genomic: TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATA
EST: gi|18659836|gb|BM500547.1|BM500547
EST:     TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAG                         GATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATA
genomic: TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATA
EST: gi|32943723|gb|CF048542.1|CF048542
EST:     TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAG                         GATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATA
genomic: TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATA
EST: gi|32929231|gb|CF034043.1|CF034043
EST:     TATACGGTTGCTTCCTGAAGCAGCTTGGCCTTTTATATCTTGGAAAACAG                         GATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATA
genomic: TATACGGTTGCTTCCTGTTGC-GCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATA
EST: gi|32848175|gb|CD987856.1|CD987856
EST:     TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAG                         GATAGTGTGGAGGCTACCGCACAGGTCTCTAAAACATTTGATGAGAAGATA
genomic: TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATA
EST: gi|32928692|gb|CF033504.1|CF033504
EST:     TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAG                         GATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATA
genomic: TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATA

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: 49 (upstream exon), 39 (downstream exon)
Score: 348

TATTATATTTGCTTTGATGGAGCGTAGTGAGGCCGAGTTGGCAGAACCCATTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATAGGGAAGTACTGTGATGTAACACTTATGTCACTGGCATATGCCGGGACAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 260

TATTATATTTGCTTTGATGGAGCGTAGTGAGGCCGAGTTGGCAGAACCCATTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATAGGGAAGTACTGTGATGTAACACTTATGTCACTGGCATATGCCGGGACAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 175

TATTATATTTGCTTTGATGGAGCGTAGTGAGGCCGAGTTGGCAGAACCCATTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATAGGGAAGTACTGTGATGTAACACTTATGTCACTGGCATATGCCGGGACAG


Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 229

TATTATATTTGCTTTGATGGAGCGTAGTGAGGCCGAGTTGGCAGAACCCATTATACGGTTGCTTCCTGTTGCGCTTGGCCTTTTATATCTTGGAAAACAGgtaactctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAGAAGATAGGGAAGTACTGTGATGTAACACTTATGTCACTGGCATATGCCGGGACAG