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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatggggtcagtttggcttgtcatttttttcatatataaaataaatatgacatacatctgatattgtattaccattgtcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG

Basic information

species Zea mays
transcript GRMZM2G114220_T02
intron # 4
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|76909136|gb|DV163240.1|DV163240
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211392498|gb|FL156787.1|FL156787
EST:     CCACACCTGGAAG-CGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211392504|gb|FL156793.1|FL156793
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211395124|gb|FL156801.1|FL156801
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211389877|gb|FL156782.1|FL156782
EST:     CCACACCTGGAAG-CGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211392507|gb|FL156796.1|FL156796
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|91873355|gb|EB403312.1|EB403312
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|14242735|gb|BG840580.2|BG840580
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211392505|gb|FL156794.1|FL156794
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|71417924|gb|DR804257.1|DR804257
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|50338446|gb|CO533572.1|CO533572
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211392501|gb|FL156790.1|FL156790
EST:     CCMCACCTGGAAGGCGGKGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTGCT
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTGCT
EST: gi|211389876|gb|FL156781.1|FL156781
EST:     CCACACCTGGAAG-CGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211392496|gb|FL156785.1|FL156785
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|93015584|gb|EB641104.1|EB641104
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211389879|gb|FL156784.1|FL156784
EST:     CCACACCTGGAAG-CGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|32862738|gb|CF002420.1|CF002420
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211392502|gb|FL156791.1|FL156791
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|91049005|gb|EB159423.1|EB159423
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|6637070|gb|AW261342.1|AW261342
EST:     CCACACCTGGAAGGCGGCGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211395123|gb|FL156800.1|FL156800
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211392503|gb|FL156792.1|FL156792
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211392499|gb|FL156788.1|FL156788
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|211392510|gb|FL156799.1|FL156799
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|213183590|gb|FM196389.1|FM196389
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
EST: gi|32859779|gb|CD999460.1|CD999460
EST:     CCACACCTGGAAGGCGGTGATAAAG                         TAATAATGCCACCTTCTGCCCTTGATCGTCTTG
genomic: CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG

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), 48 (downstream exon)
Score: 72

CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 106

CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 122

CCACACCTGGAAGGCGGTGATAAAGgtaaggatgg ... tcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatataaaataaatatgacatacatctgatattgtattaccattgtcaaatgtagTAATAATGCCACCTTCTGCCCTTGATCGTCTTG
                       atctgat  putative branch site (score: 122)
     aaaataaatatgacat  TA-rich tract