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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaggagaaacaatttccatttgttttctttattttgattctgagatatgagtagctgagtaggtacttgaaatgcttaaacttcagaaatttatctttgtttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG

Basic information

species Zea mays
transcript GRMZM2G137707_T01
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|67012698|gb|CO441447.1|CO441447
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGG-TTGCCGAG
EST: gi|149107024|gb|EE188919.2|EE188919
EST:     TGTTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|71774748|gb|DR972626.1|DR972626
EST:     TGTTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|89106092|gb|DY576309.1|DY576309
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|88747666|gb|DY531807.1|DY531807
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|78108108|gb|DV526526.1|DV526526
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|32936074|gb|CF040886.1|CF040886
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|71442203|gb|DR823253.1|DR823253
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|33093800|gb|CF053794.1|CF053794
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|14204187|gb|BG837864.1|BG837864
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|32937138|gb|CF041957.1|CF041957
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|91874804|gb|EB404761.1|EB404761
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|18172389|gb|BM347777.1|BM347777
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|78122709|gb|DV541093.1|DV541093
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|17932241|gb|BM269201.1|BM269201
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
EST: gi|74232442|gb|DT640356.1|DT640356
EST:     TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG                         CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
genomic: TGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG

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), 41 (downstream exon)
Score: 76

CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 30

CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 61

CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAGgtcaggagaa ... tttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagtaggtacttgaaatgcttaaacttcagaaatttatctttgtttcttgcagCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG
                                   tttatctttgtttctt  CT-rich tract
                                aaatttatctttgttt  TA-rich tract