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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacagggtaaacgactattaggagaagagtggctgtagcaaaatttatgttgtttgagagtcttctaatgtcaatttattttgtttttcctttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCTTCTGGCACAGAAATTGGCAAGAAAGCAAAAGAATACATGGACAATGGAA

Basic information

species Zea mays
transcript GRMZM2G030628_T01
intron # 2
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|148967472|gb|EE018708.2|EE018708
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211468826|gb|FL048935.1|FL048935
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211468828|gb|FL048937.1|FL048937
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211468823|gb|FL048932.1|FL048932
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|93014324|gb|EB639844.1|EB639844
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211468834|gb|FL048943.1|FL048943
EST:     GAGCTCCCGCCTCGGGAAAAGGGACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211468829|gb|FL048938.1|FL048938
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211468825|gb|FL048934.1|FL048934
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|76282827|gb|DV022395.1|DV022395
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|91874212|gb|EB404169.1|EB404169
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211471358|gb|FL048948.1|FL048948
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211184345|gb|FL140051.1|FL140051
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211468836|gb|FL048945.1|FL048945
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211471359|gb|FL048949.1|FL048949
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211468827|gb|FL048936.1|FL048936
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211468824|gb|FL048933.1|FL048933
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|71301850|gb|DR786994.1|DR786994
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
EST: gi|211468831|gb|FL048940.1|FL048940
EST:     GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAG                         TATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT
genomic: GAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCT

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), 36 (downstream exon)
Score: 29

GGCACCACCGCCGGCGCGGGGTAAGACTTCGCTCAAGGTGATGATTTCGGGAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCTTCTGGCACAGAAATTGGCAAGAAAGCAAAAGAATACATGGACAATGGAA


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 96

GGCACCACCGCCGGCGCGGGGTAAGACTTCGCTCAAGGTGATGATTTCGGGAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCTTCTGGCACAGAAATTGGCAAGAAAGCAAAAGAATACATGGACAATGGAA


Block sizes: 30 (upstream exon), 36 (downstream exon)
Score: 2

GGCACCACCGCCGGCGCGGGGTAAGACTTCGCTCAAGGTGATGATTTCGGGAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCTTCTGGCACAGAAATTGGCAAGAAAGCAAAAGAATACATGGACAATGGAA


Block sizes: 42 (upstream exon), 36 (downstream exon)
Score: 47

GGCACCACCGCCGGCGCGGGGTAAGACTTCGCTCAAGGTGATGATTTCGGGAGCTCCCGCCTCGGGAAAAGGAACGCAATGCCGCATGATCGTCGAGAAGgtgaaatgtt ... tttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCTTCTGGCACAGAAATTGGCAAGAAAGCAAAAGAATACATGGACAATGGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttgtttgagagtcttctaatgtcaatttattttgtttttcctttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCTTCTGGCACAGAAATTGGCAAGAAAGCAAAAGAATACATGGACAATGGAA
                             tttattttgtttttcc  CT-rich tract
                           aatttattttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacagggtaaacgactattaggagaagagtggctgtagcaaaatttatgttgtttgagagtcttctaatgtcaatttattttgtttttcctttgatttagTATGGTTTAGTTCACATATCAACTGGTGATCTTCTGCGAGCTGAAGTATCTTCTGGCACAGAAATTGGCAAGAAAGCAAAAGAATACATGGACAATGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - aaacgac
- - - - - - - - - - - - - - - -gctgtag
- - - - - - - - - - - - - - - - - - - - - - - -tgttgtt