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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttgtgaaccttaggctagtacttactatgtttatggtcctactagcactcctgaagtcctattttgtttatggtcttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGTTTGTTTGACCCTATTAAAGCTACAGAAGAAGGCCGAGCTGTGTACTTTA

Basic information

species Zea mays
transcript GRMZM2G075488_T01
intron # 7
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|37377171|gb|CF625167.1|CF625167
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|37377054|gb|CF625098.1|CF625098
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|32928448|gb|CF033260.1|CF033260
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGTACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|32928122|gb|CF032934.1|CF032934
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|60358578|gb|DN225551.1|DN225551
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|32928342|gb|CF033154.1|CF033154
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|211492404|gb|FL232704.1|FL232704
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|67011936|gb|CO440685.1|CO440685
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT

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: 49 (upstream exon), 43 (downstream exon)
Score: 91

TTCGAAATGTGGCTAGATTTTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGTTTGTTTGACCCTATTAAAGCTACAGAAGAAGGCCGAGCTGTGTACTTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

TTCGAAATGTGGCTAGATTTTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGTTTGTTTGACCCTATTAAAGCTACAGAAGAAGGCCGAGCTGTGTACTTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

TTCGAAATGTGGCTAGATTTTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGTTTGTTTGACCCTATTAAAGCTACAGAAGAAGGCCGAGCTGTGTACTTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

TTCGAAATGTGGCTAGATTTTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGTTTGTTTGACCCTATTAAAGCTACAGAAGAAGGCCGAGCTGTGTACTTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatggtcctactagcactcctgaagtcctattttgtttatggtcttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGTTTGTTTGACCCTATTAAAGCTACAGAAGAAGGCCGAGCTGTGTACTTTA
                             tattttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttgtgaaccttaggctagtacttactatgtttatggtcctactagcactcctgaagtcctattttgtttatggtcttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGTTTGTTTGACCCTATTAAAGCTACAGAAGAAGGCCGAGCTGTGTACTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG