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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgcaacaattctcatggagaaattgtttaatgatatcctgatttcttaatctgatcatctgtgcaattaaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAGCAGCAGCTAATTATGCTGTCATAGCATGGACTAAATTTTGCCTGTCTTT

Basic information

species Zea mays
transcript GRMZM2G078756_T01
intron # 9
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|32856608|gb|CD996289.1|CD996289
EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
EST: gi|211308521|gb|FL467499.1|FL467499
EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
EST: gi|76910024|gb|DV163657.1|DV163657
EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
EST: gi|31072245|gb|BQ479053.1|BQ479053
EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
EST: gi|78113854|gb|DV532243.1|DV532243
EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
EST: gi|71762613|gb|DR960550.1|DR960550
EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
EST: gi|78079223|gb|DV507635.1|DV507635
EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
EST: gi|60395362|gb|DN228231.1|DN228231
EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
EST: gi|71310636|gb|DR791614.1|DR791614
EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
EST: gi|211026939|gb|FL261356.1|FL261356
EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG

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: 195

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAGCAGCAGCTAATTATGCTGTCATAGCATGGACTAAATTTTGCCTGTCTTT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 227

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAGCAGCAGCTAATTATGCTGTCATAGCATGGACTAAATTTTGCCTGTCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAGCAGCAGCTAATTATGCTGTCATAGCATGGACTAAATTTTGCCTGTCTTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 143

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAGCAGCAGCTAATTATGCTGTCATAGCATGGACTAAATTTTGCCTGTCTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttaatgatatcctgatttcttaatctgatcatctgtgcaattaaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAGCAGCAGCTAATTATGCTGTCATAGCATGGACTAAATTTTGCCTGTCTTT
                                          aattaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgcaacaattctcatggagaaattgtttaatgatatcctgatttcttaatctgatcatctgtgcaattaaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAGCAGCAGCTAATTATGCTGTCATAGCATGGACTAAATTTTGCCTGTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA