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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttccacacactttaaatctacatgttcagatgctcttctcacctgttatgcttattgtttcagcattttgtacatcaaagccttttctttcttgtgaatcag

Basic information

species Zea mays
transcript GRMZM2G131667_T01
intron # 3
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|37381281|gb|CF627515.1|CF627515
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|20208213|gb|BQ134302.1|BQ134302
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTTCATCACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|211365709|gb|FL031158.1|FL031158
EST:     TGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|91877199|gb|EB407156.1|EB407156
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|4776649|gb|AI665652.1|AI665652
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTCGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|5006220|gb|AI712282.1|AI712282
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGNAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACNCA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|21987668|gb|BQ779196.1|BQ779196
EST:     -ATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|30160506|gb|CB924235.1|CB924235
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATAGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|44900457|gb|CK827002.1|CK827002
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|60343398|gb|DN210371.1|DN210371
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|60351758|gb|DN218731.1|DN218731
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATAGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|5895985|gb|AW037231.1|AW037231
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|38229665|gb|CF919978.1|CF919978
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATAGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA

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), 48 (downstream exon)
Score: 159

ACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 330

ACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 267

ACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 555

ACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttccacacactttaaatctacatgttcagatgctcttctcacctgttatgcttattgtttcagcattttgtacatcaaagccttttctttcttgtgaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA