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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctaatgcttgaatttctatatgcagtttatagagatcgcttgttcatcaactaattcactttacttgctgattgcttgttcatcaattctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA

Basic information

species Zea mays
transcript GRMZM2G134770_T03
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|5005812|gb|AI711874.1|AI711874
EST:     CACAGTCTGTAATATGAGAAAGTGCAACACACCTAGGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: CACAGTCTGTAATATGAGAAAGTGCAACACACCTA-GACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|71428348|gb|DR809398.1|DR809398
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|12970927|gb|BG267228.1|BG267228
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|32943442|gb|CF048261.1|CF048261
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|94474683|gb|EB703641.1|EB703641
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|78112738|gb|DV531132.1|DV531132
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|32841271|gb|CD980952.1|CD980952
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|32839908|gb|CD979589.1|CD979589
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGTCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|88752563|gb|DY536704.1|DY536704
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATTTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|211158909|gb|FK993540.1|FK993540
EST:     GTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGWTCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|32841323|gb|CD981004.1|CD981004
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|32835369|gb|CD975047.1|CD975047
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|32840727|gb|CD980408.1|CD980408
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|78026571|gb|DV494958.1|DV494958
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|31350190|gb|CD434547.1|CD434547
EST:     ACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: ACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|32841497|gb|CD981178.1|CD981178
EST:     GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: GCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
EST: gi|89247194|gb|DY618980.1|DY618980
EST:     AGACCTGAAAACCAG                         GGATCTAAGCCTGATGGTTTAAGAGGGTCAA
genomic: AGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA

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: 48 (upstream exon), 47 (downstream exon)
Score: 168

TGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACTTTGGCTTCCGCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 88

TGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACTTTGGCTTCCGCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA


Block sizes: 49 (upstream exon), 31 (downstream exon)
Score: 135

TGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACTTTGGCTTCCGCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 65

TGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACTTTGGCTTCCGCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACCTGAAAACCAGgttagagact ... ctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcaactaattcactttacttgctgattgcttgttcatcaattctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA
                                           ttctttgt  CT-rich tract
     aactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctaatgcttgaatttctatatgcagtttatagagatcgcttgttcatcaactaattcactttacttgctgattgcttgttcatcaattctttgtgcagGGATCTAAGCCTGATGGTTTAAGAGGGTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - tgcttga
- - - - - - - - - -atatgca
- - - - - - - - - - - - - - - - - - - - - - - - -caactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgt