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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacatgtcagtggcacattttgggattgcaaaattttgcaatggcgaataactaacctctttctgcacaaaggtaactccatgttcatgtatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTG

Basic information

species Zea mays
transcript GRMZM2G435373_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G435373_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 3'ss of exon 5
ccacatgtcagtggcacattttgggattgcaaaattttgcaatggcgaataactaacctctttctgcacaaaggtaactccatgttcatgta-------tatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTG
     |  |    |    |     ||| ||||||   |  |     |  |   | |||| |||||||| | |  ||||||  | | ||| |        | || ||||||||||||||||||||| ||||| ||||||||||| || |||||||||||||||||||||||||||||||| ||| ||||||| ||| ||||||| || 
-----taccttcagtctttcacatgat-gcaaaaggatatatctatgcttcttttacct-tttctgcatataaataactctgtttccatttgccctttcttttccagAAAATATGGTTTAAGTGACGATACCGTGGATTTCATCGGTCATGCACTTGCTCTTCATAGAGATGATCGCTACCTTAATGAACCAGCAATTGATACTGTA

upper sequence: GRMZM2G435373_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 3'ss of exon 5
ccacatgtcagtggcacattttgggattgcaaaattttgcaatggcgaataactaacctctttctgcacaaaggtaactccatgttcatgtat-----atttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTG
 |      |  | | |||| |||  |    ||  || | |    ||  ||   ||   | | | || ||| | || ||||  | | ||||| |      || ||||||||||||||||||||| ||||| ||||||||||| || ||||||||||||||||||||||||||||| || ||  ||||||| ||| ||||||| || 
gccttcaaccttag-acatgttgcaa----aaggttatacctgtgcttattgttacattttatttgaacataagtgactctgtttccatgtgtcttcttttccagAAAATATGGTTTAAGTGACGATACTGTGGATTTCATCGGCCATGCACTTGCTCTTCATAGAGATGATCGTTACCTAAATGAACCAGCAATTGATACTGTA
















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|32846965|gb|CD986646.1|CD986646
EST:     ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
genomic: ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagcacct ... tatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
EST: gi|6031345|gb|AW076202.1|AW076202
EST:     GATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGNTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
genomic: GATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagcacct ... tatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
EST: gi|32938598|gb|CF043417.1|CF043417
EST:     ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
genomic: ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagcacct ... tatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
EST: gi|33094579|gb|CF054573.1|CF054573
EST:     ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
genomic: ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagcacct ... tatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
EST: gi|32850140|gb|CD989821.1|CD989821
EST:     ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
genomic: ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagcacct ... tatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
EST: gi|32939909|gb|CF044728.1|CF044728
EST:     ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
genomic: ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagcacct ... tatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
EST: gi|32932660|gb|CF037472.1|CF037472
EST:     ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
genomic: ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagcacct ... tatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
EST: gi|211034436|gb|FL381555.1|FL381555
EST:     GTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
genomic: GTGACAACTAGAGAACTTATAGCgttagcacct ... tatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
EST: gi|32932658|gb|CF037470.1|CF037470
EST:     ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
genomic: ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagcacct ... tatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
EST: gi|33104315|gb|CF064275.1|CF064275
EST:     ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
genomic: ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagcacct ... tatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
EST: gi|32939179|gb|CF043998.1|CF043998
EST:     ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC
genomic: ACACATCAAGGATTAGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagcacct ... tatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaataactaacctctttctgcacaaaggtaactccatgttcatgtatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTG
                                          atgtatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacatgtcagtggcacattttgggattgcaaaattttgcaatggcgaataactaacctctttctgcacaaaggtaactccatgttcatgtatatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG