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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCCGTGGTAATGCTTCAAAAAAGCGGAAGGAGGTCACTGATGCAGCTGCGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatcatatccttttagcaagatccatatccctaaatggggaggcggtgggtttattctgcagacactaaatgccctaaaattcttcttaaccat...

Basic information

species Zea mays
transcript GRMZM2G414496_T07
intron # 17
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|37377775|gb|CF625524.1|CF625524
EST:     CGCAGATAAGTGCTGCTTATGACTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|71312125|gb|DR792591.1|DR792591
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|14245465|gb|BG874047.1|BG874047
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|60400302|gb|DN233109.1|DN233109
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|71312126|gb|DR792592.1|DR792592
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|32937939|gb|CF042758.1|CF042758
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|76285513|gb|DV025081.1|DV025081
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAAT
EST: gi|21331411|gb|BQ486792.1|BQ486792
EST:     CGCAGATAAGTGCTGCTTATGACTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCCCGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|211402618|gb|FL252146.1|FL252146
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|78544440|gb|DV621938.1|DV621938
EST:     CGCAGATAAGTGCTGCTTATGACTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|71446738|gb|DR827788.1|DR827788
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|211424705|gb|FL442294.1|FL442294
EST:     ATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGMCAATGGAAAA                         CTGAAGGAAATGMCCMCGGTGGAATTGAGATCCTACCTGMCCGCGCATGAT
genomic: ATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|37383098|gb|CF628530.1|CF628530
EST:     CGCAGATAAGTGCTGCTTATGACTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|60338376|gb|DN205349.1|DN205349
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|60347385|gb|DN214358.1|DN214358
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|101382023|gb|EB813067.1|EB813067
EST:     CGCAGATAAGTGCTGTTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGCCCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|33097000|gb|CF056960.1|CF056960
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|71761431|gb|DR959368.1|DR959368
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|24768047|gb|CA403179.1|CA403179
EST:     CGCAGATAAGTGCTGCTTATGACTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|211405145|gb|FL252147.1|FL252147
EST:     AGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGATATCCTACCTGACCGCGCATGAT
genomic: AGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|211157517|gb|FL458094.1|FL458094
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
EST: gi|211424706|gb|FL442295.1|FL442295
EST:     CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAA                         CTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT
genomic: CGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGAT

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), 49 (downstream exon)
Score: 299

TTCCCGTGGTAATGCTTCAAAAAAGCGGAAGGAGGTCACTGATGCAGCTGCGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGATCTCCCGGTTTCTGGTAAGAAAGATGTACTTATCAGCAGGATCTTGACTC


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 37

TTCCCGTGGTAATGCTTCAAAAAAGCGGAAGGAGGTCACTGATGCAGCTGCGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGATCTCCCGGTTTCTGGTAAGAAAGATGTACTTATCAGCAGGATCTTGACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 30

TTCCCGTGGTAATGCTTCAAAAAAGCGGAAGGAGGTCACTGATGCAGCTGCGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGATCTCCCGGTTTCTGGTAAGAAAGATGTACTTATCAGCAGGATCTTGACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

TTCCCGTGGTAATGCTTCAAAAAAGCGGAAGGAGGTCACTGATGCAGCTGCGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatc ... tcatttgcagCTGAAGGAAATGACCACGGTGGAATTGAGATCCTACCTGACCGCGCATGATCTCCCGGTTTCTGGTAAGAAAGATGTACTTATCAGCAGGATCTTGACTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCCGTGGTAATGCTTCAAAAAAGCGGAAGGAGGTCACTGATGCAGCTGCGCAGATAAGTGCTGCTTATGATTGGGCAGAACTTGCAGACAATGGAAAAgtgagtaatcatatccttttagcaagatccatatccctaaatggggaggcggtgggtttattctgcagacactaaatgccctaaaattcttcttaaccat

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT