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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCTCCGTTAGGGTTGTTTTTGCTACTCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGgtaaaatccacgtcttttagcgagagaattcgtgtcttgatttctgtcgttcgcctgttcgtgtttgatgtcactgattttttggttgctggtgtgcag

Basic information

species Zea mays
transcript GRMZM2G134582_T01
intron # 1
splice site 5'
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|211419497|gb|FK986932.1|FK986932
EST:     TCTGCCTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: TCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|211299931|gb|FL223399.1|FL223399
EST:     GCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCG                         ATCTGAGATCGAGCG-A-MKAAGCTTTTTCATCGAGATGGTGCTT
genomic: GCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGgtaaaatcca ... tggtgtgcagATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT
EST: gi|211419502|gb|FK986937.1|FK986937
EST:     TCTGCCTCTGCTTTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: TCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|17930924|gb|BM267884.1|BM267884
EST:     TCTGCTTCTGCTCT-ACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCG                         ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT
genomic: TCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGgtaaaatcca ... tggtgtgcagATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT
EST: gi|15053873|gb|BI359418.1|BI359418
EST:     TTCGCTGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: TTCGCTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|211269911|gb|FK986926.1|FK986926
EST:     TCTGCCTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: TCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|31354444|gb|CD438801.1|CD438801
EST:     CTGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: CTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|50333934|gb|CO529060.1|CO529060
EST:     CTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCG                         ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT
genomic: CTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGgtaaaatcca ... tggtgtgcagATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT
EST: gi|211269910|gb|FK986925.1|FK986925
EST:     TCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCG                         ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT
genomic: TCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGgtaaaatcca ... tggtgtgcagATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT
EST: gi|21891605|gb|BQ744818.1|BQ744818
EST:     CACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCG                         ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGG-GCTT
genomic: CACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGgtaaaatcca ... tggtgtgcagATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT
EST: gi|211244386|gb|FL238837.1|FL238837
EST:     TCTGCCTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: TCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|211269915|gb|FK986930.1|FK986930
EST:     TCTGCCTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: TCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|60398445|gb|DN231261.1|DN231261
EST:     TTCGCTGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: TTCGCTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|211512831|gb|FL354907.1|FL354907
EST:     GCTGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: GCTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|31354453|gb|CD438810.1|CD438810
EST:     TCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: TCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|67020169|gb|CO448918.1|CO448918
EST:     TGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: TGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|60399613|gb|DN232423.1|DN232423
EST:     CTGCTCGCCCGATCTCGCGCTGCCGGCAGCG                    
genomic: CTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg
EST: gi|6020992|gb|AW065920.1|AW065920
EST:     CACCTGTTTCGCTGCTCACCCGATCTCGCGCTGCCGGCAGCG                    
genomic: CACCTGTTTCGCTGCTCGCCCGATCTCGCGCT----GC--CGgtaaaatcca ... tggtg

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), 46 (downstream exon)
Score: 127

ATGGCTCCGTTAGGGTTGTTTTTGCTACTCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGgtaaaatcca ... tggtgtgcagATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 191

ATGGCTCCGTTAGGGTTGTTTTTGCTACTCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGgtaaaatcca ... tggtgtgcagATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 188

ATGGCTCCGTTAGGGTTGTTTTTGCTACTCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGgtaaaatcca ... tggtgtgcagATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 172

ATGGCTCCGTTAGGGTTGTTTTTGCTACTCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGgtaaaatcca ... tggtgtgcagATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT


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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGCTCCGTTAGGGTTGTTTTTGCTACTCTGCTTCTGCTCTCACCTGTTTCGCTGCTCGCCCGATCTCGCGCTGCCGgtaaaatccacgtcttttagcgagagaattcgtgtcttgatttctgtcgttcgcctgttcgtgtttgatgtcactgattttttggttgctggtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT