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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatatgataccctagtttgtttttttcttctagtgttgctgcagatgactcattgttatcctgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACTGTTAAGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCA

Basic information

species Zea mays
transcript GRMZM2G049141_T02
intron # 11
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|211176318|gb|FL281704.1|FL281704
EST:     TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAG                         GTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
genomic: TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
EST: gi|211174649|gb|FL281699.1|FL281699
EST:     TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAG                         GTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
genomic: TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
EST: gi|211174646|gb|FL281696.1|FL281696
EST:     TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAG                         GTCAACATTTGTAACTTANAAGAGTATATTTCTTTGGTTGTGGATGCTACT
genomic: TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
EST: gi|211176315|gb|FL281701.1|FL281701
EST:     TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAG                         GTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
genomic: TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
EST: gi|211176317|gb|FL281703.1|FL281703
EST:     TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAG                         GTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
genomic: TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
EST: gi|20301115|gb|BQ164058.1|BQ164058
EST:     TGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAG                         GTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
genomic: TGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
EST: gi|67039619|gb|CO465874.1|CO465874
EST:     TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAG                         GTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
genomic: TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
EST: gi|20299937|gb|BQ162880.1|BQ162880
EST:     TGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAG                         GTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
genomic: TGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
EST: gi|67021475|gb|CO450224.1|CO450224
EST:     TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAG                         GTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT
genomic: TTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACT

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: 127

TCTATGTTTCCGTGGTGCTCCCGTTGAAGATTTATATTTGGACTTCACTCTTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACTGTTAAGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

TCTATGTTTCCGTGGTGCTCCCGTTGAAGATTTATATTTGGACTTCACTCTTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACTGTTAAGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 52

TCTATGTTTCCGTGGTGCTCCCGTTGAAGATTTATATTTGGACTTCACTCTTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACTGTTAAGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 99

TCTATGTTTCCGTGGTGCTCCCGTTGAAGATTTATATTTGGACTTCACTCTTCCGGGCTATCCTGAATATGTTCTCAAGGAAGGTGGAGAGAATGCAGAGgtaagttata ... tgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACTGTTAAGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttttttcttctagtgttgctgcagatgactcattgttatcctgtcttatagGTCAACATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACTGTTAAGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCA
                                          tcctgtctt  CT-rich tract
     tttttctt  TA-rich tract