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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgtgataaactttaaaattttcagaatattaactgagccatattaactaatttatttttcgcagGAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACC

Basic information

species Zea mays
transcript GRMZM2G121210_T02
intron # 8
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|32930587|gb|CF035399.1|CF035399
EST:     TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCCTGAAAACAAA
genomic: TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAGgtatatgtga ... tttttcgcagGAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|166672199|gb|EG171329.1|EG171329
EST:     CTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAA
genomic: CTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAGgtatatgtga ... tttttcgcagGAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|32934519|gb|CF039331.1|CF039331
EST:     TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAA
genomic: TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAGgtatatgtga ... tttttcgcagGAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|32931356|gb|CF036168.1|CF036168
EST:     TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAA
genomic: TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAGgtatatgtga ... tttttcgcagGAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAA
EST: gi|166472322|gb|EG045877.1|EG045877
EST:     ACTTGAGGAGTTCTGTCATTTAAGGACTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAAAGC
genomic: ACTTGAGGAGTTCTGTCATTTAAGG-CTTGAATTCTATTGTAAGAGAAAGgtatatgtga ... tttttcgcagGAAGCATTGTTGAAAAGC
EST: gi|32930092|gb|CF034904.1|CF034904
EST:     TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAG                         GAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAA
genomic: TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAGgtatatgtga ... tttttcgcagGAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAA

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: 778

TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAGgtatatgtga ... tttttcgcagGAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 71

TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAGgtatatgtga ... tttttcgcagGAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAGgtatatgtga ... tttttcgcagGAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 34

TACTTGAGGAGTTCTGTCATTTAAGGCTTGAATTCTATTGTAAGAGAAAGgtatatgtga ... tttttcgcagGAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttaaaattttcagaatattaactgagccatattaactaatttatttttcgcagGAAGCATTGTTGAAAAGCATCAAGTTGGACTTAAAGAAGCTTGAAAACAAAGTTAGGTTTATCCGCTGTGTTGTTGATAATGAAATTATAGTTAACAACC
                                         tttatttttc  CT-rich tract
                              atattaactaatttat  TA-rich tract