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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgctcatgtttggaaccatagaacaatgccaatatatggtccgcttacagtatagtgatattgtccag

Basic information

species Zea mays
transcript GRMZM2G158097_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158097_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g36062.2 (Oryza sativa), 5'ss of exon 10
TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgctcatgtttggaacc--atagaacaatgccaatatatggtccgcttacagtata----gtgatattgtccag--------------------
||||||||||||||||||||| ||| | |||||||| |||||||| || |||||||||||||| || |||||||||||||||||||||||||||||||||||| ||||  ||| | |   | |  | ||||      |   |||  |    |||| | |||     |   ||    |                       
TCTTAACCTTATTGGAGGTGACACATTGTTTGGCCGCTTATGGGGCTGTCTGCCAGATGCTTATTTCCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtaatttgtgcatctctcagagcttacagaatgtgaacttcataatggaaacttataatatgtattgcagtagcacctgaatatgtttcaaaaccatttc

upper sequence: GRMZM2G158097_T03 (Zea mays), 5'ss of exon 10
lower sequence: Vv12s0035g01750.t01 (Vitis vinifera), 5'ss of exon 10
TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtat---tttgctcatgtttggaaccatagaac--aatgccaatatat----ggtccgcttacagtatagtgatattgtccag------------------
||| || ||||||||||| |||||  |||| ||||| ||||||||||| || |||   ||||| | ||| |  |||||||||||||| |||||||| ||||| |   | ||    ||||   | |  || | |  ||  | |   |      || ||  ||| | |  ||  |||||  |  |                  
TCTCAATCTTATTGGAGGAGATACTTTATTCGGCCGCTTATGGGGATGTCTCCCACGAGCTTATTATCCTAGCTTGCATTTTGAAGCATGCTATTACCAGgtttggatctgactttgttctcatcagtaaagctgaactctatggtccaccaggaccatttaaaatg-agaaatattagctggtaacttttttttttttga
















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|78124181|gb|DV542565.1|DV542565
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|71766886|gb|DR964823.1|DR964823
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841492|gb|CD981173.1|CD981173
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|71766748|gb|DR964685.1|DR964685
EST:     TTTGAAGCTTGCTATTTTCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGGGGAGGCAGGTGCT
genomic: TTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841296|gb|CD980977.1|CD980977
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|50325271|gb|CO520397.1|CO520397
EST:     CATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAACCCTGAGTAAGGTGGAGGCAGGTGCT
genomic: CATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|89249944|gb|DY621730.1|DY621730
EST:     TACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841005|gb|CD980686.1|CD980686
EST:     CATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: CATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32840850|gb|CD980531.1|CD980531
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|71766749|gb|DR964686.1|DR964686
EST:     TTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841147|gb|CD980828.1|CD980828
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32840869|gb|CD980550.1|CD980550
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841261|gb|CD980942.1|CD980942
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|13389377|gb|BG462692.1|BG462692
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGA
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGA
EST: gi|32841581|gb|CD981262.1|CD981262
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|16379420|gb|BI992935.1|BI992935
EST:     TACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841639|gb|CD981320.1|CD981320
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgctcatgtttggaaccatagaacaatgccaatatatggtccgcttacagtatagtgatattgtccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC