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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttattagattaaccatggaaagcaccttcaatgtctttaatcttctttatattcattcacatatgttgtttgtcagtctgattttgtgagcatgcagACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACATTACGGTCATCAGTAGAATGAAACAGTTCAGGGCAATGAACAAGCTCAA

Basic information

species Zea mays
transcript GRMZM5G856738_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856738_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g43410.1 (Oryza sativa), 3'ss of exon 3
atgttattagattaaccatggaaagcaccttcaatgtctttaatcttctttatattcattcacatatgttgtttgtcagtctgattttgtgagcatgcagACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACATTACGGTCATCAGTAGAATGAAACAGTTCAGGGCAATGAACAAGCTCAA
 | ||| ||||| |    ||          |  ||      | |  || || |     ||  || || | |||  |    || ||  | | |  || ||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| || ||||| || ||||| ||||||||||||||||||||||| ||
tttttaatagataatttctgctcttgtttctatataaaccgagttatcatttttactgtttgcaaatatagttaatgcacctaatactttaaatatacagACCACCCATGGATTAGAGAGGATGGAGAAGCCCCAGACAAGCCACTTGACATTACAGTTATCAGCAGGATGAAGCAGTTCAGGGCAATGAACAAGCTTAA
















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|32930571|gb|CF035383.1|CF035383
EST:     GATGCTGCGACAAGACCCAAAAGAACGCCTGACTGCTGCTGAAATTTTGA                         ACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACA
genomic: GATGCTGCGACAAGACCCAAAAGAACGCCTGACTGCTGCTGAAATTTTGAgtaaggctac ... gagcatgcagACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACA
EST: gi|94476938|gb|EB705896.1|EB705896
EST:     GATGCTGCGACAAGACCCAAAAGAACGCCTGACTGCTGCTGAAATTTTGA                         ACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACA
genomic: GATGCTGCGACAAGACCCAAAAGAACGCCTGACTGCTGCTGAAATTTTGAgtaaggctac ... gagcatgcagACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACA
EST: gi|6952611|gb|AW424679.1|AW424679
EST:     GATGCTGCGACAAGACCCAAAAGAACGCCTGACTGCTGCTGAAATTTTGA                         ACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACA
genomic: GATGCTGCGACAAGACCCAAAAGAACGCCTGACTGCTGCTGAAATTTTGAgtaaggctac ... gagcatgcagACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACA
EST: gi|78181002|gb|DV551375.1|DV551375
EST:     GATGCTGCGACAAGACCCAAAAGAACGCCTGACTGCTGCTGAAATTTTGA                         ACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACA
genomic: GATGCTGCGACAAGACCCAAAAGAACGCCTGACTGCTGCTGAAATTTTGAgtaaggctac ... gagcatgcagACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttatattcattcacatatgttgtttgtcagtctgattttgtgagcatgcagACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACATTACGGTCATCAGTAGAATGAAACAGTTCAGGGCAATGAACAAGCTCAA
                                 gtctgat  putative branch site (score: 4)
     tatattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttattagattaaccatggaaagcaccttcaatgtctttaatcttctttatattcattcacatatgttgtttgtcagtctgattttgtgagcatgcagACCACCCATGGATTAGAGAGGATGGAGAGGCCCCAGATAAGCCACTTGACATTACGGTCATCAGTAGAATGAAACAGTTCAGGGCAATGAACAAGCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA