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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggatgcctgctatccaatacttcaaattttcatgtagtccctagaacatttcattttactcatttttggtttgcaaatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAAGGGGAGAGGAGGAATGCAAAACCAGCTAGTGAACAGAGCTTTTGAAGGA

Basic information

species Zea mays
transcript GRMZM2G059039_T01
intron # 15
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|32844847|gb|CD984528.1|CD984528
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGT
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGT
EST: gi|37398128|gb|CF636373.1|CF636373
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|9732110|gb|BE510862.1|BE510862
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|26558849|gb|CA831084.1|CA831084
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|60347979|gb|DN214952.1|DN214952
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|87156817|gb|DY401606.1|DY401606
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|29544218|gb|CB604598.1|CB604598
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|29544428|gb|CB604808.1|CB604808
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|71766574|gb|DR964511.1|DR964511
EST:     GCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: GCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|32844395|gb|CD984076.1|CD984076
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGT
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGT
EST: gi|60352216|gb|DN219189.1|DN219189
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|29544594|gb|CB604974.1|CB604974
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|22546055|gb|BU098376.1|BU098376
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|211193672|gb|FL124549.1|FL124549
EST:     TCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: TCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|32843825|gb|CD983506.1|CD983506
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTA
EST: gi|67024010|gb|CO452759.1|CO452759
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|31357379|gb|CD441736.1|CD441736
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|50326789|gb|CO521915.1|CO521915
EST:     GTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: GTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|149105665|gb|EE291221.2|EE291221
EST:     ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: ACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
EST: gi|211462540|gb|FL444815.1|FL444815
EST:     CAACAAAGCAGCAGCTACGAAAGCAGG                         GGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA
genomic: CAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAA

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: 192

TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAAGGGGAGAGGAGGAATGCAAAACCAGCTAGTGAACAGAGCTTTTGAAGGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 66

TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAAGGGGAGAGGAGGAATGCAAAACCAGCTAGTGAACAGAGCTTTTGAAGGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 74

TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAAGGGGAGAGGAGGAATGCAAAACCAGCTAGTGAACAGAGCTTTTGAAGGA


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 45

TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGGgtgggatgcc ... aatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAAGGGGAGAGGAGGAATGCAAAACCAGCTAGTGAACAGAGCTTTTGAAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtagtccctagaacatttcattttactcatttttggtttgcaaatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAAGGGGAGAGGAGGAATGCAAAACCAGCTAGTGAACAGAGCTTTTGAAGGA
                      attttactcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggatgcctgctatccaatacttcaaattttcatgtagtccctagaacatttcattttactcatttttggtttgcaaatcattcagGGGGAAGAGGTCACAACCTAGTACAAATGGGAATGACCCTGCAAACAAGAAGGGGAGAGGAGGAATGCAAAACCAGCTAGTGAACAGAGCTTTTGAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG