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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcatttctgtaaattatgtttacatattgtaaaatagttgtcagcttgtcacatcttagcaactaaaagtggatttgatagtagtttttctgat...

Basic information

species Zea mays
transcript GRMZM5G815009_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G815009_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g59440.2 (Oryza sativa), 5'ss of exon 3
TTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat-ttctgtaaattatgtttacatattgtaaaatagttgtcagcttgtcacatcttagcaactaaaagtggatttgatagtagtttttctgat-----
||||||||||||||||||| |||||||||||| ||||||||||||||||||| ||||| ||||||||  | ||||| || || |  |||||||||||| ||||||||  | || |  |||| || |      |||||||||||||| | || |  |||||| ||||| ||| |           |||      ||    ||     
TTGGTAATTTGAAGAATCTTATAAGCTTGGACCTGTACAAGAACAACATTTCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgtgttattcaaatgatctc-----attgtaaaatagttctaagttc-tcacatgttagctactgatttcatgccgtatatgcacattctgcatacttc
















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|166561397|gb|EG084590.1|EG084590
EST:     TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCA-GGGAACTTTCTGG
genomic: TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
EST: gi|149104284|gb|EE289722.2|EE289722
EST:     TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAAGGAACTTTCTGG
genomic: TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
EST: gi|89756077|gb|DY686250.1|DY686250
EST:     TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGGGGCGATCCCAAGGGAACTTTCTGG
genomic: TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
EST: gi|93284383|gb|EB676647.1|EB676647
EST:     TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
genomic: TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
EST: gi|89249279|gb|DY621065.1|DY621065
EST:     GGGGACAATACCTCCTTCCCCTTGGAAAGTTGAAATCCCCTTGTATTCCT                         GCGGGTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
genomic: GGGGACAATACCTCCTTCCC-TTGGAAAGTTGAAATCCC-TTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
EST: gi|91054725|gb|EB165143.1|EB165143
EST:     TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
genomic: TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
EST: gi|91051618|gb|EB162036.1|EB162036
EST:     TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCCAAGG-AACTTTCTG
genomic: TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCC-AAGGGAACTTTCTG
EST: gi|149101778|gb|EE287382.2|EE287382
EST:     TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
genomic: TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
EST: gi|50336224|gb|CO531350.1|CO531350
EST:     TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
genomic: TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
EST: gi|211004201|gb|FL095595.1|FL095595
EST:     TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
genomic: TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
EST: gi|149106063|gb|EE291719.2|EE291719
EST:     TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
genomic: TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
EST: gi|211001424|gb|FL095584.1|FL095584
EST:     CGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGNTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGG
genomic: CGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTG-TATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGG
EST: gi|74240378|gb|DT648292.1|DT648292
EST:     TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCT                         GCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG
genomic: TCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcat ... cgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGGACAATACCTCCTTCCCTTGGAAAGTTGAAATCCCTTGTATTCCTgtaagttcatttctgtaaattatgtttacatattgtaaaatagttgtcagcttgtcacatcttagcaactaaaagtggatttgatagtagtttttctgat

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