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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagattatatatgatgcatcattcagatgctgcttatgccattttcagctaatgcttacactttataagtttcaatgtttactttcttttatttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG

Basic information

species Zea mays
transcript GRMZM2G080722_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080722_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G22430.1 (Glycine max), 3'ss of exon 4
----tagattatatatgatgcatcattcagatgctgcttatgccattttcagctaatgcttacactttataagtttcaatgtttactttcttttatttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG
     |  ||  ||    ||  || || | | | |   ||    |||   |  ||| | ||    |    |  |   | ||||  |  | || | | | |||||||||||||| || ||||| ||||| || ||||| ||||||||  |||| ||||| |||||  | ||||  |||||||||
cttccaagtttaatcacttgtttcctttaaaagtttaata----attaataaataacgatttttttaatgatatcctactgttctccctgttctttctgtgcagTAACTGGCCAACATTTCCTCAAATTTTCATCAAGGGAGAGTTTATTGGTGGATCAGATATTGTTCTCAATATGCACCAG

upper sequence: GRMZM2G080722_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g06040.t01 (Vitis vinifera), 3'ss of exon 5
tagattatatatgatgcatcattcagatgctgcttatgccattttcagctaatgcttacactttataagtttcaatgttt--actttctttt-atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG
   |  |       ||  |   | | || |    |     |     || | ||   |      |  | |||||| |  |   ||  ||| |  || |||||||  ||||||| || |||||||||||||| || || || |||||| | |||||||||||||| || |||| ||||||||||
---aacaccctcattggcttcataaaataccaaattattaaaaaatagatgatttgtgatgcctgcatgtttcactaatcgaacactctctccatctctgcagCCACTGGCCCACATTTCCACAAATATTCATAAAGGGGGAGTTCATAGGGGGATCTGATATTATTCTCAACATGCACCAG
















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|6587608|gb|AW244926.1|AW244926
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGNTAAAGCATACAG                         TAANNCTG-CCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAA--CTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCG
EST: gi|71772931|gb|DR970854.1|DR970854
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|211393122|gb|FK956090.1|FK956090
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTAAAAGCATACAG                         TAACTGGCCTACGTTTTCACAAATATTTATCAAAAGAGAGTTCGGTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|149072625|gb|EE160853.2|EE160853
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|5819352|gb|AI987558.1|AI987558
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTGCGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|84980246|gb|DW530595.1|DW530595
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|116818678|gb|EC861726.1|EC861726
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGACAGTTCGA-GGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|76019176|gb|DT946346.1|DT946346
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|31348993|gb|CD433350.1|CD433350
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|18649501|gb|BM498320.1|BM498320
EST:     TCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: TCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|6827118|gb|AW330761.1|AW330761
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|89252698|gb|DY624484.1|DY624484
EST:     AAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|108954172|gb|EC365037.1|EC365037
EST:     GAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCTTAGCAGAGTTCGTTGGGGG
genomic: GAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|149076048|gb|EE164622.2|EE164622
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|211208256|gb|FL334762.1|FL334762
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|71772930|gb|DR970853.1|DR970853
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|32934185|gb|CF038997.1|CF038997
EST:     AGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|211393127|gb|FK956095.1|FK956095
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACCTGGCCTACGTTTTCCACAA-TATTTATCAAAGGAGAGTTCGGTTGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAAC-TGGCCTACGTTT-CCACAAATATTTATCAAAGGAGAGTTCG-TTGG
EST: gi|149072626|gb|EE160854.2|EE160854
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|76019175|gb|DT946345.1|DT946345
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|31364491|gb|CD448846.1|CD448846
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|6020541|gb|AW065469.1|AW065469
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGGGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|18450417|gb|BM428695.1|BM428695
EST:     TAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCATAAGGTAGAGTTCGTTGGT
genomic: TAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCA-AAGG-AGAGTTCGTTGG-
EST: gi|71771232|gb|DR969169.1|DR969169
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|32908664|gb|CF013477.1|CF013477
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|149051827|gb|EE155954.2|EE155954
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|211395747|gb|FK956104.1|FK956104
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|149051826|gb|EE155953.2|EE155953
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
EST: gi|149076047|gb|EE164621.2|EE164621
EST:     AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG                         TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG
genomic: AGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAGgtaagtatct ... atttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagctaatgcttacactttataagtttcaatgtttactttcttttatttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG
       tgcttac  putative branch site (score: 2)
                              tgtttactttctttta  putative PPT
                            aatgtttactttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagattatatatgatgcatcattcagatgctgcttatgccattttcagctaatgcttacactttataagtttcaatgtttactttcttttatttctgcagTAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA