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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGGCGGTGATCCACTTCTAGAGCTACTTGCGGTCGATTGGTTCAAAGTTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAAgtaagcttgtctgataaactttaccattatccctcattgacgggcattagttacttaattgtgggcgtgattgcctcgatttttcttattcttgttcaat...

Basic information

species Zea mays
transcript GRMZM2G160927_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160927_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g34060.2 (Oryza sativa), 5'ss of exon 17
TGTTGGCGGTGATCCACTTCTAGAGCTACTTGCGGTCGATTGGTTCAAAGTTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAAgtaagcttgtctga-taaactttaccattatccctcattgacg--ggcattagttacttaattgtgggcgtgattgcctcgatttttcttattcttgttcaat
|||||| |||||||| |||||| ||||  |||| ||||||||||| || | | |||| || |||||||||||||||||||| ||||| ||||| || || ||||    |  |   | | |   |||| ||||||  | | | |    ||    || ||  ||  ||    |   |  || ||   |   ||| | | ||||| 
TGTTGGAGGTGATCCCCTTCTAAAGCTTATTGCTGTCGATTGGTTTAAGGCTGATGAGCGTTTTGATTCAGTTGCCTTACACCCCAAGAGCCTCGTTCAGgtaaaaaaggttacctgaccaccaccaatatcccaaagtaatgcaaccagctttttctctatcatgtttttatgtaact-gagaatcaatatgcct-ttcaa-
















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|60397419|gb|DN230235.1|DN230235
EST:     TTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAA                         TCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG
genomic: TTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAAgtaagcttgt ... tacattacagTCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG
EST: gi|211510092|gb|FL332408.1|FL332408
EST:     TTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAA                         TCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG
genomic: TTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAAgtaagcttgt ... tacattacagTCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG
EST: gi|71439002|gb|DR820052.1|DR820052
EST:     TTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAA                         TCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG
genomic: TTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAAgtaagcttgt ... tacattacagTCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG
EST: gi|211488642|gb|FL313368.1|FL313368
EST:     TTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAA                         TCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG
genomic: TTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAAgtaagcttgt ... tacattacagTCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG
EST: gi|33942624|gb|CF349224.1|CF349224
EST:     TTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAA                         TCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG
genomic: TTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAAgtaagcttgt ... tacattacagTCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG

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: 322

TGTTGGCGGTGATCCACTTCTAGAGCTACTTGCGGTCGATTGGTTCAAAGTTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAAgtaagcttgt ... tacattacagTCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 147

TGTTGGCGGTGATCCACTTCTAGAGCTACTTGCGGTCGATTGGTTCAAAGTTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAAgtaagcttgt ... tacattacagTCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 145

TGTTGGCGGTGATCCACTTCTAGAGCTACTTGCGGTCGATTGGTTCAAAGTTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAAgtaagcttgt ... tacattacagTCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 175

TGTTGGCGGTGATCCACTTCTAGAGCTACTTGCGGTCGATTGGTTCAAAGTTAATGAACGCTTTGATTCAGTTGCCTTACATCCCAAAAGCCTTGTGCAAgtaagcttgt ... tacattacagTCAGAAGCTGCAAAGAAACTTCCTTTCATATTGGTTATAAATTTGCAG