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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaaccacttctacccttgacctgtatatatagatagatagatagattcagtttggatgtttgcgagtagcagcaggaacttaatcgaatttcctcactgcttaattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCATTCAGGGCTGCGGCTAAGAAGGCCTGCAAATTCGATGTCAACAGAGCAA

Basic information

species Zea mays
transcript GRMZM2G085711_T02
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|76013367|gb|DT940537.1|DT940537
EST:     GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|76011900|gb|DT939070.1|DT939070
EST:     GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|67027734|gb|CO456483.1|CO456483
EST:     GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|78120621|gb|DV539005.1|DV539005
EST:     GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|24764671|gb|CA399835.1|CA399835
EST:     ACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGATTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCACCTGCCGCA
genomic: ACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|71323602|gb|DR798473.1|DR798473
EST:     GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|86474415|gb|DY240785.1|DY240785
EST:     GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|93283843|gb|EB676107.1|EB676107
EST:     GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|91876115|gb|EB406072.1|EB406072
EST:     TCGCGTCAGGTTTCTATTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: TCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|78120471|gb|DV538855.1|DV538855
EST:     GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|93283595|gb|EB675859.1|EB675859
EST:     CAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: CAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|78120185|gb|DV538569.1|DV538569
EST:     GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|76910374|gb|DV163830.1|DV163830
EST:     GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
EST: gi|94472513|gb|EB701471.1|EB701471
EST:     GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACAT                         GTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA
genomic: GCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCA

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: 37 (upstream exon), 40 (downstream exon)
Score: 6

AGCAAAGAACTGCACCTTCTGTGGTGTGTGGAAAGGGGGAGGTGGAGCTGGCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCATTCAGGGCTGCGGCTAAGAAGGCCTGCAAATTCGATGTCAACAGAGCAA


Block sizes: 29 (upstream exon), 21 (downstream exon)
Score: 1

AGCAAAGAACTGCACCTTCTGTGGTGTGTGGAAAGGGGGAGGTGGAGCTGGCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCATTCAGGGCTGCGGCTAAGAAGGCCTGCAAATTCGATGTCAACAGAGCAA


Block sizes: 44 (upstream exon), 35 (downstream exon)
Score: 9

AGCAAAGAACTGCACCTTCTGTGGTGTGTGGAAAGGGGGAGGTGGAGCTGGCCAAAACGACATCTACGTCGCGTCAGGTTTCTACTACCTTGCCTCACATgtaggaacca ... aattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCATTCAGGGCTGCGGCTAAGAAGGCCTGCAAATTCGATGTCAACAGAGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgcgagtagcagcaggaacttaatcgaatttcctcactgcttaattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCATTCAGGGCTGCGGCTAAGAAGGCCTGCAAATTCGATGTCAACAGAGCAA
                   aacttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggaaccacttctacccttgacctgtatatatagatagatagatagattcagtttggatgtttgcgagtagcagcaggaacttaatcgaatttcctcactgcttaattggcaagGTTGGGTTCATAGATAGCAAAGCTCCAAGCGCAAAGGCCCCTCCTGCCGCATTCAGGGCTGCGGCTAAGAAGGCCTGCAAATTCGATGTCAACAGAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA