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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggcgatcgagcaaatgatctgtgcaatcgtattgttgtacaaaatacatgtagtttcttggcgtgcccctcaccagtgtagacgattacattaatttttgttgcttttatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGA

Basic information

species Zea mays
transcript GRMZM2G348675_T02
intron # 46
splice site 3'
intron type U2

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|33095263|gb|CF055257.1|CF055257
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|33098458|gb|CF058418.1|CF058418
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCGG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|71444755|gb|DR825805.1|DR825805
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGAGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|31406262|gb|CD484994.1|CD484994
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|211436987|gb|FL183985.1|FL183985
EST:     GGCTGTGTCGAAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGT

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), 49 (downstream exon)
Score: 289

TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcccctcaccagtgtagacgattacattaatttttgttgcttttatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGA
                          cattaat  putative branch site (score: 91)
                                tttttgttgctttt  CT-rich tract
                      attacattaatttttg  TA-rich tract