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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagtctccccatgctattcccttgttctctttatcgtattacgctagtagctacgggatttggtggtgatgtctcactaatctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGACCTTTATTTAAGGCGCAGGGCTGCAGGCCCGTTCCCTCAGCTGACCATAC

Basic information

species Zea mays
transcript GRMZM5G802854_T01
intron # 1
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|211385473|gb|FL080439.1|FL080439
EST:     CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCG                         GTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
genomic: CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCGgtaaaagtct ... tctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
EST: gi|211385475|gb|FL080441.1|FL080441
EST:     CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCG                         GTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
genomic: CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCGgtaaaagtct ... tctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
EST: gi|71434798|gb|DR815848.1|DR815848
EST:     CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCG                         GTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
genomic: CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCGgtaaaagtct ... tctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
EST: gi|71433727|gb|DR814777.1|DR814777
EST:     CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCG                         GTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
genomic: CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCGgtaaaagtct ... tctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
EST: gi|211385472|gb|FL080438.1|FL080438
EST:     CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCG                         GTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
genomic: CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCGgtaaaagtct ... tctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
EST: gi|211385474|gb|FL080440.1|FL080440
EST:     CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCG                         GTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
genomic: CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCGgtaaaagtct ... tctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
EST: gi|211385470|gb|FL080436.1|FL080436
EST:     CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCG                         GTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC
genomic: CGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCGgtaaaagtct ... tctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGAC

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: 47 (upstream exon), 49 (downstream exon)
Score: 141

GGATTGATGGCAGGTGACGCGTGAATTTGTCGTCGGAGTTGAAGCTCCGCCGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCGgtaaaagtct ... tctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGACCTTTATTTAAGGCGCAGGGCTGCAGGCCCGTTCCCTCAGCTGACCATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

GGATTGATGGCAGGTGACGCGTGAATTTGTCGTCGGAGTTGAAGCTCCGCCGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCGgtaaaagtct ... tctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGACCTTTATTTAAGGCGCAGGGCTGCAGGCCCGTTCCCTCAGCTGACCATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

GGATTGATGGCAGGTGACGCGTGAATTTGTCGTCGGAGTTGAAGCTCCGCCGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCGgtaaaagtct ... tctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGACCTTTATTTAAGGCGCAGGGCTGCAGGCCCGTTCCCTCAGCTGACCATAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 75

GGATTGATGGCAGGTGACGCGTGAATTTGTCGTCGGAGTTGAAGCTCCGCCGTGACCGCGCTCACTGCCGTGGCCCGGAACATTTGCGCTACTAACCTCGgtaaaagtct ... tctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGACCTTTATTTAAGGCGCAGGGCTGCAGGCCCGTTCCCTCAGCTGACCATAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattacgctagtagctacgggatttggtggtgatgtctcactaatctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGACCTTTATTTAAGGCGCAGGGCTGCAGGCCCGTTCCCTCAGCTGACCATAC
                                       cactaat  putative branch site (score: 75)
                                               tcaaata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagtctccccatgctattcccttgttctctttatcgtattacgctagtagctacgggatttggtggtgatgtctcactaatctcaaatagGTGGAGGTGGTTCTCAAATCTCAAGTCCATCCACGCGGAATCGGACTTGACCTTTATTTAAGGCGCAGGGCTGCAGGCCCGTTCCCTCAGCTGACCATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
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