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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagtagctagttgcatacttgcatcttcttctgcatcccattttctgcttatggtttatctaactggtgatgttcccttttttcttgtctagATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGATTGG

Basic information

species Zea mays
transcript GRMZM2G108416_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108416_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g24460.2 (Oryza sativa), 3'ss of exon 9
gtgcagtagctagttgcatacttgcatcttcttctgcatcccattttctgcttatggtttatctaactggtgatgttcccttttttcttgtctagATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGATTGG
            ||   |||  |   |||   | | ||| |  |||||||||| || | |||   |     |||  ||| | | || || ||||| ||||||||||||||||||||||||||||||||||||||||||| ||||||||||
------------gtgcaataactatttctgtatttccattcttttttctgcttgtgatatatgagaa----gattgtccttatgtttttatctagGTTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTAGTCGTGATTGG
















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|78087292|gb|DV515685.1|DV515685
EST:     TTACGTATATATGATGGAAAAGTATTCAAATTAGATGAACATTTGGACAG                         ATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGA
genomic: TTACGTATATATGATGGAAAAGTATTCAAATTAGATGAACATTTGGACAGgtgcagtagc ... tcttgtctagATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGA
EST: gi|211301117|gb|FL169205.1|FL169205
EST:     TTACGTATATATGATGGAAAAGTATTCAAATTAGATGAACATTTGGACAG                         ATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGA
genomic: TTACGTATATATGATGGAAAAGTATTCAAATTAGATGAACATTTGGACAGgtgcagtagc ... tcttgtctagATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGA
EST: gi|78115926|gb|DV534314.1|DV534314
EST:     TTACGTATATATGATGGAAAAGTATTCAAATTAGATGAACATTTGGACAG                         ATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGA
genomic: TTACGTATATATGATGGAAAAGTATTCAAATTAGATGAACATTTGGACAGgtgcagtagc ... tcttgtctagATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGA

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: 118

TTTCAGTGTTTGATTCAGTTGTACAAGGAGGAGATGCTGTTTGGGAAGGTTTACGTATATATGATGGAAAAGTATTCAAATTAGATGAACATTTGGACAGgtgcagtagc ... tcttgtctagATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGATTGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 119

TTTCAGTGTTTGATTCAGTTGTACAAGGAGGAGATGCTGTTTGGGAAGGTTTACGTATATATGATGGAAAAGTATTCAAATTAGATGAACATTTGGACAGgtgcagtagc ... tcttgtctagATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGATTGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 160

TTTCAGTGTTTGATTCAGTTGTACAAGGAGGAGATGCTGTTTGGGAAGGTTTACGTATATATGATGGAAAAGTATTCAAATTAGATGAACATTTGGACAGgtgcagtagc ... tcttgtctagATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGATTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 167

TTTCAGTGTTTGATTCAGTTGTACAAGGAGGAGATGCTGTTTGGGAAGGTTTACGTATATATGATGGAAAAGTATTCAAATTAGATGAACATTTGGACAGgtgcagtagc ... tcttgtctagATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGATTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattttctgcttatggtttatctaactggtgatgttcccttttttcttgtctagATTGTTTGATTCTGCAAAAGCTATGGCCTTCAGCAATGTGCCTACTCGTGATTGG
                    atctaac  putative branch site (score: 167)
                                 tgttcccttttttctt  putative PPT
                 tttatctaa  TA-rich tract