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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATCTGCTTCAGTGTGAGTGGAGCTTTGTTTGCTTCAGCTGGTGATGACAAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccacagtatattcttggactctgttccattgcaataattatatttcacagttgatgttatttaagcgaaaagacatattcattacatagttctgtccgtgaatttcacacttttgagaatgtaatttgaataaggatttgttgcaatgttttttattgcag

Basic information

species Zea mays
transcript GRMZM2G131998_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131998_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g53530.1 (Oryza sativa), 5'ss of exon 2
CTATCTGCTTCAGTGTGAGTGGAGCTTTGTTTGCTTCAGCTGGTGATGACAAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccacagtatattcttggactctgttccattgcaataattatatttcacagttgatgttatttaagcgaaaagacatattcattacatagttctgtccgtgaatttcacacttttgagaatgtaatttgaataaggatttgttgcaatgttttttattgcag
||||||  || ||||  |  || ||| |||| || || |||||||||||||| ||||| ||||| |||||||||||||| ||| | ||||| | ||| ||||||| |||        | ||   | ||||  ||||  | ||  ||| |  |   || |    |||  || | |      |||| || |  || ||| ||  || ||| |   ||| |                                                
CTATCTCGTTTAGTGCAAACGGTGCTCTGTTCGCATCCGCTGGTGATGACAAGCTTGTTAAGGTCTGGAAGACTGATTCATGGTGCTGCATTCGGACCATgtaagtcac--------cctg---tttgttttattgtga-aagcataatgga---ttaaccaaatt--agtgtaccattttatttatcatgta-ttcagtgagtcaatctacaactat------------------------------------------------
















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|211048672|gb|FL294333.1|FL294333
EST:     AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTAT                         AACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
genomic: AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccaca ... tttattgcagAACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
EST: gi|211051626|gb|FL294345.1|FL294345
EST:     AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTAT                         AACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
genomic: AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccaca ... tttattgcagAACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
EST: gi|211051623|gb|FL294342.1|FL294342
EST:     AAACTTGTGAAGGGTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTAT                         AACTTCGGAGAAAGAGG-TCAGTGCAGTTGTTTAT-AGCCACGATG
genomic: AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccaca ... tttattgcagAACTTCGGAGAA-GAGGGTCAGTGCAGTTGTT-ATTAGCAACGATG
EST: gi|211048680|gb|FL294341.1|FL294341
EST:     AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTAT                         AACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
genomic: AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccaca ... tttattgcagAACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
EST: gi|211048669|gb|FL294330.1|FL294330
EST:     AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTAT                         AACTTCGGAGAAGAG
genomic: AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccaca ... tttattgcagAACTTCGGAGAAGAG
EST: gi|211048668|gb|FL294329.1|FL294329
EST:     AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTAT                         AACTTCGGAGAARAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
genomic: AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccaca ... tttattgcagAACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
EST: gi|211048676|gb|FL294337.1|FL294337
EST:     AAACTTGTGAAGTTTTGAAAGACTGATTCGTGNCGTTGCATCCAGACTAT                         AACTTCGGAGAAGAGGGTCAGTGCAGTTGTTAATAACCACGATGACCT
genomic: AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccaca ... tttattgcagAACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
EST: gi|211048673|gb|FL294334.1|FL294334
EST:     AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTAT                         AACTTCGGAGAAGAGGGTCAGTGCAGTTGTTA
genomic: AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccaca ... tttattgcagAACTTCGGAGAAGAGGGTCAGTGCAGTTGTTA
EST: gi|211051633|gb|FL294352.1|FL294352
EST:     AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTAT                         AACTTCGGAGAAGACGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
genomic: AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccaca ... tttattgcagAACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
EST: gi|211051625|gb|FL294344.1|FL294344
EST:     AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTAT                         AACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
genomic: AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccaca ... tttattgcagAACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGACCT
EST: gi|211048667|gb|FL294328.1|FL294328
EST:     AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTAT                         AACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGAC
genomic: AAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccaca ... tttattgcagAACTTCGGAGAAGAGGGTCAGTGCAGTTGTTATTAGCAACGATGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATCTGCTTCAGTGTGAGTGGAGCTTTGTTTGCTTCAGCTGGTGATGACAAACTTGTGAAGGTTTGGAAGACTGATTCGTGGCGTTGCATCCAGACTATgtaagccacagtatattcttggactctgttccattgcaataattatatttcacagttgatgttatttaagcgaaaagacatattcattacatagttctgtccgtgaatttcacacttttgagaatgtaatttgaataaggatttgttgcaatgttttttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA