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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcttttttctggtgaccctccttttgcagctagattttttctctgctgaaacgttatctgataaaccaatcaaactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG

Basic information

species Zea mays
transcript GRMZM5G848768_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G848768_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g57260.1 (Oryza sativa), 3'ss of exon 9
--------------gtattgcttttttctggtgaccctccttttgcagctagattttttctctgc------tgaaacgtta--------------tctgataaaccaatcaaactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG
               ||    ||||||||| |||| || || ||||| | ||  ||| | | | |      ||  || ||               | |  |||   ||  || || ||||||||| || ||||||||||| ||||||||||||||||||||||||||||  ||    || ||  ||||||| || || || |||||||||||||||||
gtattgcagcactcttagcttttttttctgctgacactactattgcaaccaggctttgtttgtccattgcttgttacattgtgtatgtgttttttttttttaatttaacgaatctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGAGGGACGTAGCGATGAAGAAGGGACTTCCTATTCTTGGTGTTTTCAG

upper sequence: GRMZM5G848768_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 9
gtattgcttttttctggtgaccctccttttgcagctagattttttctctgctgaaacgtta--tctgataaaccaatcaaactg-tgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG
    |      |  |    ||| |  |  |        ||  |||||  | |||      |  | | || |    ||     || | |||| ||||| ||||| |||||||||||||||| ||||||||| || |||||||||  ||| ||  || | || ||||| |||||||||||||| |||||
---gtataagatcataaaaaccttgttcatttcctctaatcctttcta-gttgatgtaccaagtttaatcatatgatgcctgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG

upper sequence: GRMZM5G848768_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv05s0051g00720.t01 (Vitis vinifera), 3'ss of exon 9
gtattgcttttttctg-gtgaccctccttttgcagctagattttttctctgctgaaacgttatctgataaaccaatcaaactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG
|||||         |   | |      | || ||    |||| ||| |    |   |  |||     |    |  |      ||||||| ||||| || ||||||||||||||||||||||||||||| |||||||| |||  ||| ||  ||   |||||| | || ||||||||||| |||||
gtattagacggccatatataatttctttctttcaaaatgattgtttgttccattccattttactatttggtgcttttg----gtgtagGGAATTCTAGCCAAGTGAGTGATGGTGCTGGAGCTGTTCTCCTCATGAAGAGAAGTGTTGCAATGCGTAAAGGGTTACCTATTCTTGGTGTATTCAG

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|71769910|gb|DR967847.1|DR967847
EST:     CCAGTTTTTAAAAA-GATGGGACTACAACTGCAG                         GCAATCCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: CCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|60346439|gb|DN213412.1|DN213412
EST:     TTTAAAAAGGATGGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: TTTAAAAAGGAT-GGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|32868231|gb|CF007913.1|CF007913
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGAACTACAACTGCAG                         GCAATTCCAGTCAAGGGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|6994094|gb|AW453308.1|AW453308
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGAACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|149076676|gb|EE165319.2|EE165319
EST:     TTTTAAAAAGGATGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: TTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|91874450|gb|EB404407.1|EB404407
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|213184067|gb|FM191388.1|FM191388
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGAACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|211292683|gb|FL176851.1|FL176851
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGAACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|74238395|gb|DT646309.1|DT646309
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|33942354|gb|CF348954.1|CF348954
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGAACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|148946680|gb|EC891943.2|EC891943
EST:     AAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: AAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|149100616|gb|EE186704.2|EE186704
EST:     TGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: TGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|32859198|gb|CD998879.1|CD998879
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGAACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|60672291|gb|DN475055.1|DN475055
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGAACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCCTGGAGCTGTTCTTCTCATGAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGC-TGGAGCTGTTCTTCTCATGAAA
EST: gi|78074202|gb|DV502636.1|DV502636
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|88752432|gb|DY536573.1|DY536573
EST:     CGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: CGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|32859848|gb|CD999529.1|CD999529
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGAACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|149101630|gb|EE187762.2|EE187762
EST:     CAGTTTTTAAAAAGGATGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: CAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|101388206|gb|EB816117.1|EB816117
EST:     CAGTTTTTAAAAAGGATGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: CAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|6012216|gb|AW061758.1|AW061758
EST:     ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGAACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: ATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|60345789|gb|DN212762.1|DN212762
EST:     AAAGGATGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
genomic: AAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA
EST: gi|101394624|gb|EB819247.1|EB819247
EST:     CCAGTTTTTAAAAAGGATGGGACTACAACTGCAG                         GCAATTCCAGTCAAGTGAGTGATGGTGCGGGAGCTGTTCTTCTCATGAAAA
genomic: CCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgcttt ... aactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctagattttttctctgctgaaacgttatctgataaaccaatcaaactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG
                            atctgat  putative branch site (score: 4)
      attttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgcttttttctggtgaccctccttttgcagctagattttttctctgctgaaacgttatctgataaaccaatcaaactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA