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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaatgcttttattatagttctactactatcatgctggcatggcggggacacggtgccgtggttggcacacatccgagaacgtgatccttatag...

Basic information

species Zea mays
transcript GRMZM2G017584_T01
intron # 6
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|50333059|gb|CO528185.1|CO528185
EST:     GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTG                         GGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
genomic: GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
EST: gi|149088812|gb|EE177939.2|EE177939
EST:     GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTG                         GGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
genomic: GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
EST: gi|148954015|gb|EC899413.2|EC899413
EST:     GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTG                         GGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
genomic: GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
EST: gi|32165048|gb|CD670366.1|CD670366
EST:     GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTG                         GGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
genomic: GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
EST: gi|30032130|gb|CB833981.1|CB833981
EST:     GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTG                         GGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
genomic: GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
EST: gi|71326297|gb|DR799838.1|DR799838
EST:     GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTG                         GGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
genomic: GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
EST: gi|31910411|gb|CD651410.1|CD651410
EST:     GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTG                         GGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
genomic: GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCA
EST: gi|78116765|gb|DV535152.1|DV535152
EST:     GGTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTG                         GGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGG
genomic: GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGG

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: 46 (upstream exon), 49 (downstream exon)
Score: 92

GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCAGAAGCAAAGGAACTGGCCCTTGCAG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 24

GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCAGAAGCAAAGGAACTGGCCCTTGCAG


Block sizes: 46 (upstream exon), 42 (downstream exon)
Score: 15

GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCAGAAGCAAAGGAACTGGCCCTTGCAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 26

GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaa ... cttcctgtagGGTGCTGAGTTCGAGCTTGATACCATCAAAAAATTGTCAAAGGAGTATGCAGAAGCAAAGGAACTGGCCCTTGCAG


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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTTGCAAATAGCCAAGCAGAAAGATATATGCACATGGACTTGgtaagttcaatgcttttattatagttctactactatcatgctggcatggcggggacacggtgccgtggttggcacacatccgagaacgtgatccttatag

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