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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttctatgtattaattacaaaaaaacacgccttttgcatttacgtgatgctctggagacattattggaggaagcaacttatggttggctattattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTCATGAATCATTTGCTGGATGGTAAAGAATAGCCGATGCTTGCAAGTCAGC

Basic information

species Zea mays
transcript GRMZM2G147726_T03
intron # 5
splice site 3'
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|211217104|gb|FL383487.1|FL383487
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAA
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAA
EST: gi|18181584|gb|BM382794.1|BM382794
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|60396369|gb|DN229238.1|DN229238
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|32945768|gb|CF050587.1|CF050587
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|5456152|gb|AI833842.1|AI833842
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|211104194|gb|FL471169.1|FL471169
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|31611779|gb|CD568401.1|CD568401
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|149086485|gb|EE176030.2|EE176030
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|60346093|gb|DN213066.1|DN213066
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|29946538|gb|CB816199.1|CB816199
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|6994080|gb|AW453294.1|AW453294
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|44901570|gb|CK828115.1|CK828115
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|14646131|gb|BI180320.1|BI180320
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|71426509|gb|DR807559.1|DR807559
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|12973349|gb|BG268436.1|BG268436
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|14203130|gb|BG836807.1|BG836807
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|211068733|gb|FL060710.1|FL060710
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|60399097|gb|DN231911.1|DN231911
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|32906937|gb|CF011750.1|CF011750
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTTCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|71775316|gb|DR973194.1|DR973194
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|29544164|gb|CB604544.1|CB604544
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|78110076|gb|DV528491.1|DV528491
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|18175608|gb|BM350861.1|BM350861
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|21809994|gb|BQ668312.1|BQ668312
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
EST: gi|33092385|gb|CF052379.1|CF052379
EST:     TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTG                         GCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC
genomic: TTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTC

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 1 RNA-Seqlibrary.


Block sizes: 19 (upstream exon), 8 (downstream exon)
Score: 1

TTACAGAGTCATTAGAACTACACAAAATTAAGAGCCGCCAATGGGCGATTTTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtgggg ... attattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTCATGAATCATTTGCTGGATGGTAAAGAATAGCCGATGCTTGCAAGTCAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgctctggagacattattggaggaagcaacttatggttggctattattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTCATGAATCATTTGCTGGATGGTAAAGAATAGCCGATGCTTGCAAGTCAGC
                                            tattatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttctatgtattaattacaaaaaaacacgccttttgcatttacgtgatgctctggagacattattggaggaagcaacttatggttggctattattgcagGCTCAGTAACACGCTCAAATCTGGAAGCAGCTAAGGAGCCTCCGCCTCGTCATGAATCATTTGCTGGATGGTAAAGAATAGCCGATGCTTGCAAGTCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA