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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATGCATATGAAGTGAAGAAACAAGAGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAGgtaaaagaaatgtggtgttaagttttactcccttcttttgtatcttataatgcatgctcggaagtcagaactggattcatattccttgtaatgtctgcat...

Basic information

species Zea mays
transcript GRMZM2G147500_T05
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147500_T04 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 5'ss of exon 9
GTTGATGCATATGAAGTGAAGAAACAAGAGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAGgtaaaagaaatgtggtgttaagttttactcccttcttttgtatcttataatgcatgctcggaagtcagaactggattcatattccttgtaatgtctgcat
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GTTGATGCCTATGAGGTAAAGAAGCAAGAGTTGATGCAAGAAAATGCTGATTTGCGAGCACTATTGCGTTCGATGCAGgtaaaaccataaaaggatgccacttccacatcatattattcctttcatgctagacaaatatacgctagccattccttagatctcagtggacaatggggaa

upper sequence: GRMZM2G147500_T04 (Zea mays), 5'ss of exon 9
lower sequence: PP1S23_191V6.1 (Physcomitrella patens), 5'ss of exon 11
GTTGATGCATATGAAGTGAAGAAACAAGAGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAGgtaaaagaaatgtggtgttaagttttactcccttcttttgtatcttataatgcatgct-cggaagtca---gaactggattcatattccttgtaatgtctgcat
|||||||||||||| ||||||||| ||||| || |||||||| |||||||| ||| ||||||| || ||||||||| | ||| | ||| | || || | | | | | | | ||| | || | | | | | |||| ||
GTTGATGCATATGAGTCGAAGAAACAGGAGCTAGTGGCTGAGAATGCGGATTTACGTGCATTGTTACGATCCATGCAGgtatgtcat-catggcct--ggttgtggctatttgcgagatacataaaagtaagtcttgttggagttacttattcttaaggtgaaggcgaggaatagtctaca-
















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|74237135|gb|DT645049.1|DT645049
EST:     AGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAG                         ATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCTACT
genomic: AGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAGgtaaaagaaa ... tttacctcagATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCTACT
EST: gi|211359662|gb|FL110321.1|FL110321
EST:     AGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAG                         ATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCTACT
genomic: AGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAGgtaaaagaaa ... tttacctcagATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCTACT
EST: gi|76923168|gb|DV169366.1|DV169366
EST:     GCTGATGNCA-GAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAG                         ATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCTACT
genomic: GCTGATG-CAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAGgtaaaagaaa ... tttacctcagATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCTACT
EST: gi|60347145|gb|DN214118.1|DN214118
EST:     AGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAG                         ATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCTACT
genomic: AGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAGgtaaaagaaa ... tttacctcagATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCTACT
EST: gi|24765838|gb|CA400997.1|CA400997
EST:     AGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAG                         ATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCTACT
genomic: AGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAGgtaaaagaaa ... tttacctcagATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCTACT
EST: gi|149081286|gb|EE170399.2|EE170399
EST:     GCTGATGNCA-GAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAG                         ATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCT
genomic: GCTGATG-CAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAGgtaaaagaaa ... tttacctcagATGGACATGCGTGACTTTCTCAATGCCCCGAATGGGTCATCACAATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATGCATATGAAGTGAAGAAACAAGAGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAGgtaaaagaaatgtggtgttaagttttactcccttcttttgtatcttataatgcatgctcggaagtcagaactggattcatattccttgtaatgtctgcat

- - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - GCAGAT