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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtggggccgttttttgattaatcacgcctccatcataataatgtattgcttttttattttggccgagaacaccatgtcatgggatgcatcatgcatgcgcctttaatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTTGACTTGACCGACCCTGTATCATGTAATTTGTATGCCACTCATTTGTGGT

Basic information

species Zea mays
transcript GRMZM2G151268_T01
intron # 7
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|12971760|gb|BG267644.1|BG267644
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|4647161|gb|AI622236.1|AI622236
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|32833706|gb|CD973384.1|CD973384
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|32834914|gb|CD974592.1|CD974592
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|91049337|gb|EB159755.1|EB159755
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|32909956|gb|CF014768.1|CF014768
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|60348471|gb|DN215444.1|DN215444
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|74239381|gb|DT647295.1|DT647295
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|21809549|gb|BQ667867.1|BQ667867
EST:     GAAAGTGTTCAAATAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|47961828|gb|CN844537.1|CN844537
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGNGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGCGTTGCT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTG-GTTGCT
EST: gi|94478768|gb|EB707726.1|EB707726
EST:     GAAAGTGTTCCGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|60399998|gb|DN232805.1|DN232805
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|15323531|gb|BI478753.1|BI478753
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|211191649|gb|FL029190.1|FL029190
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|32938881|gb|CF043700.1|CF043700
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|60400202|gb|DN233009.1|DN233009
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|45847355|gb|CN071298.1|CN071298
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT

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: 722

ATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATCGACTGCCCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTTGACTTGACCGACCCTGTATCATGTAATTTGTATGCCACTCATTTGTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 299

ATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATCGACTGCCCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTTGACTTGACCGACCCTGTATCATGTAATTTGTATGCCACTCATTTGTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

ATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATCGACTGCCCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTTGACTTGACCGACCCTGTATCATGTAATTTGTATGCCACTCATTTGTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 290

ATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATCGACTGCCCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTTGACTTGACCGACCCTGTATCATGTAATTTGTATGCCACTCATTTGTGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggccgagaacaccatgtcatgggatgcatcatgcatgcgcctttaatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTTGACTTGACCGACCCTGTATCATGTAATTTGTATGCCACTCATTTGTGGT
                                          ctttaat  putative branch site (score: 290)
                                       cgccttt  CT-rich tract
                                           tttaattt  TA-rich tract