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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcgtctccaacttctgggttttctgttccctgtcatgctacattcaattttgagttttttatttgacgttctctaagtcttgatggagatttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTGCCAAAGAAAATGGAAACGTCGGATGTGGTGCTGGTTACTGGAGCCACCG

Basic information

species Zea mays
transcript GRMZM2G019358_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019358_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 2
gtttcgtctccaacttctgggttttctgttccctgtcatgctacattcaattttgagttttttatttgacgttctctaagtcttgatggagatttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTGCCAAAGAAAATGGAAACGTCGGATGTGGTGCTGGTTACTGGAGCCACCG
||||  || |    ||  |  |||| |   ||   ||  | |||| | | |||    |||   |||    || ||| | || |||   |     | ||||||||||||| || ||  | ||||||||||||||  ||||| || |||| |||||||||||||||||| | || |||||||||||||| |||||||| ||||
gtttactcactgtattgggattttttttcacctcttctcgttacagtta-tttcacatttggcatt----gtgctc-atgttttgtctgttcaatctgtagATTGTAGAGTCCATTCTTAGCAGTTTCACTGGCTCTGCTCCTGGTGAGGTGCCAAAGAAAATGGAATCTTCTGATGTGGTGCTGGTCACTGGAGCTACCG
















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|211345090|gb|FL234331.1|FL234331
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|211345086|gb|FL234327.1|FL234327
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|211349887|gb|FL234353.1|FL234353
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|211345091|gb|FL234332.1|FL234332
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAGACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|148936820|gb|EC880961.2|EC880961
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|211345089|gb|FL234330.1|FL234330
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|211349889|gb|FL234355.1|FL234355
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|71440788|gb|DR821838.1|DR821838
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|211347484|gb|FL234337.1|FL234337
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|91055536|gb|EB165954.1|EB165954
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|211349882|gb|FL234348.1|FL234348
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|211345082|gb|FL234323.1|FL234323
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGG
EST: gi|211345087|gb|FL234328.1|FL234328
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
EST: gi|211349886|gb|FL234352.1|FL234352
EST:     GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAG                         ATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG
genomic: GATTTGTCAAGACGCTGTATTTCTTCAACGGGCCTCCAAACCTTCTCAAGgtttcgtctc ... atttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattttgagttttttatttgacgttctctaagtcttgatggagatttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTGCCAAAGAAAATGGAAACGTCGGATGTGGTGCTGGTTACTGGAGCCACCG
                                  tcttgat  putative branch site (score: 4)
     tttgagttttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcgtctccaacttctgggttttctgttccctgtcatgctacattcaattttgagttttttatttgacgttctctaagtcttgatggagatttgtgtagATTGTAGAATCTATCATCAGCAGTTTCACTGGACCTGCTTCTAGTGAAGTGCCAAAGAAAATGGAAACGTCGGATGTGGTGCTGGTTACTGGAGCCACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA