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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCTGATACAAGAGCAGGAGCAGAAAGGAAAAAAGAAGACATCTGATGATTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtattatactctgatttgagctgtctgccatttcatgaatgctaccagattttttcacatattttctatggtagatttattcattgcaattttcac...

Basic information

species Zea mays
transcript GRMZM2G081924_T01
intron # 5
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|211412951|gb|FL027551.1|FL027551
EST:     TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTG                         GCATTCCATATCCTGAAAAGGAAGAAGTCCGTATCCTTCTAAGGCAG
genomic: TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtatta ... ctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG
EST: gi|42492027|gb|CK701073.1|CK701073
EST:     TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTG                         GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG
genomic: TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtatta ... ctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG
EST: gi|76292397|gb|DV031965.1|DV031965
EST:     GATAAACGATACTGTG                         GCATACCATATCCTGAAAAGGAAGAAGTTGGTATCCTTCTAAGGCAG
genomic: GATAAACGATACTGTGgtatgtatta ... ctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG
EST: gi|166687876|gb|EG207911.1|EG207911
EST:     TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTG                         GCATTCCATATCCTGAAAAGGAAGAAGTCCGTATCCTTCTAAGGCAGG
genomic: TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtatta ... ctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGG
EST: gi|76292398|gb|DV031966.1|DV031966
EST:     TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTG                         GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG
genomic: TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtatta ... ctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG
EST: gi|22491227|gb|BU051150.1|BU051150
EST:     TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTG                         GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG
genomic: TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtatta ... ctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG
EST: gi|87152125|gb|DY396914.1|DY396914
EST:     TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTG                         GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG
genomic: TTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtatta ... ctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG

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: 122

TCTCTGATACAAGAGCAGGAGCAGAAAGGAAAAAAGAAGACATCTGATGATTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtatta ... ctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 97

TCTCTGATACAAGAGCAGGAGCAGAAAGGAAAAAAGAAGACATCTGATGATTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtatta ... ctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 117

TCTCTGATACAAGAGCAGGAGCAGAAAGGAAAAAAGAAGACATCTGATGATTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtatta ... ctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 118

TCTCTGATACAAGAGCAGGAGCAGAAAGGAAAAAAGAAGACATCTGATGATTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtatta ... ctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCTGATACAAGAGCAGGAGCAGAAAGGAAAAAAGAAGACATCTGATGATTACAATTACATATCTTTTGTCAGTCTTCTTGCTGATAAACGATACTGTGgtatgtattatactctgatttgagctgtctgccatttcatgaatgctaccagattttttcacatattttctatggtagatttattcattgcaattttcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT