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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatgaattctctgtagagttcagatgactactttatcccacaaatgaccataaatgctatcccctctgtattttatataaatgttacaacagaa...

Basic information

species Zea mays
transcript GRMZM2G381933_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|211076371|gb|FL154531.1|FL154531
EST:     GAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCTGAGAAGCTGACAAGCAGCTTTGAA
genomic: GAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|50332159|gb|CO527285.1|CO527285
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|211222853|gb|FL456563.1|FL456563
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTCTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|4628225|gb|AI619099.1|AI619099
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|60359540|gb|DN226513.1|DN226513
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|60396268|gb|DN229137.1|DN229137
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|71767359|gb|DR965296.1|DR965296
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|5706282|gb|AI942058.1|AI942058
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGCCAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|60351624|gb|DN218597.1|DN218597
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|71756800|gb|DR954737.1|DR954737
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|31628473|gb|CD526625.1|CD526625
EST:     AGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: AGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|60394781|gb|DN227651.1|DN227651
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|56382643|gb|CV985312.1|CV985312
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTGCTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|74242521|gb|DT650435.1|DT650435
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|37386793|gb|CF630585.1|CF630585
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|211222854|gb|FL456564.1|FL456564
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTCTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|8665487|gb|BE186303.1|BE186303
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|60351898|gb|DN218871.1|DN218871
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
EST: gi|211035729|gb|FL441186.1|FL441186
EST:     GTCATCGGATATCAAGAGCTGGTCCTTTGGTTCTGAATCTTACTGGAAAG                         GATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA
genomic: GTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAA

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: 74

GGTGTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAAGGACAATTTTCCCAACTTAACAGTTGCAAATAAGCTGTCAGAGACACCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 107

GGTGTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAAGGACAATTTTCCCAACTTAACAGTTGCAAATAAGCTGTCAGAGACACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

GGTGTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAAGGACAATTTTCCCAACTTAACAGTTGCAAATAAGCTGTCAGAGACACCC


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 144

GGTGTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatg ... ataatttcagGATAACCAGAGGGTAGATGCGGCTGCCGAGAAGCTGACAAGCAGCTTTGAAGGACAATTTTCCCAACTTAACAGTTGCAAATAAGCTGTCAGAGACACCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGTCATCGGATATCAAGAGCTGGTCCTTTGGTTGTGAATCTTACTGGAAAGgtagatgatgaattctctgtagagttcagatgactactttatcccacaaatgaccataaatgctatcccctctgtattttatataaatgttacaacagaa

- - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctctg