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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCACTTGGCCACCATAACCACAACCTCTTCTCCCCTGTTTCCTCTCGTGCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtgaatgagaagagaaagggttggaggaaatatttccgaatctgtttccattacgattttggtggcgtagaatttggtttcaaacgcgcagtt...

Basic information

species Zea mays
transcript GRMZM2G006765_T02
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|211179264|gb|FL010862.1|FL010862
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|32907965|gb|CF012778.1|CF012778
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|32868978|gb|CF008660.1|CF008660
EST:     GCGTTCTCCGCGGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|211179259|gb|FL010857.1|FL010857
EST:     CAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGCAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: CAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|78117775|gb|DV536162.1|DV536162
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|71315363|gb|DR794285.1|DR794285
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|6695747|gb|AW288825.1|AW288825
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|211179261|gb|FL010859.1|FL010859
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCATAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|211179263|gb|FL010861.1|FL010861
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAKCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|211179260|gb|FL010858.1|FL010858
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|12045697|gb|BF727836.1|BF727836
EST:     TTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: TTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|101383600|gb|EB813855.1|EB813855
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|22546788|gb|BU099099.1|BU099099
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|32865168|gb|CF004850.1|CF004850
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|32906739|gb|CF011552.1|CF011552
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
EST: gi|78179272|gb|DV549645.1|DV549645
EST:     GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGG                         TGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC
genomic: GCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGC

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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 42

CCTCACTTGGCCACCATAACCACAACCTCTTCTCCCCTGTTTCCTCTCGTGCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG


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

CCTCACTTGGCCACCATAACCACAACCTCTTCTCCCCTGTTTCCTCTCGTGCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 450

CCTCACTTGGCCACCATAACCACAACCTCTTCTCCCCTGTTTCCTCTCGTGCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtg ... ctcctcctagTGTTTTTGTTCCAGAATCTGTAGCAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCACTTGGCCACCATAACCACAACCTCTTCTCCCCTGTTTCCTCTCGTGCGTTCTCCGCAGGAGCGAGGAGGGCTCGCGGCAGCGGCAGGGTCTCCGGgtacgtcgtgaatgagaagagaaagggttggaggaaatatttccgaatctgtttccattacgattttggtggcgtagaatttggtttcaaacgcgcagtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagagaaa