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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgatttgcttcactcatcgttaacaagtgatataacactttagcttgtcgtgctggcaactgaggccaggtgtgatccgatttctctctcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAG

Basic information

species Zea mays
transcript GRMZM2G090647_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090647_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g37832.1 (Oryza sativa), 3'ss of exon 8
aatgatttgcttcactcatc--gttaa--caagtgatataacactttagcttgtcgtgctggcaactgaggccaggtgtgatccgatttctctctcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAG
  || ||   | ||    ||  ||| |    | ||  || |  ||||||| | ||  |||  |||     | ||| | | ||   || || ||||    |||||||| || |||||||||||||| |||||||||||||| |||||| |||   |    
-ctgtttccatgcaaatgtcttgttgaactcattgtcattattctttagcatctcccgcttccaatatcaggcagctcttat---atctccctctgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCAG---
















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|47962698|gb|CN845407.1|CN845407
EST:     GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAA                         AACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
genomic: GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAAgtaagctttg ... tcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
EST: gi|5686889|gb|AI939803.1|AI939803
EST:     GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATC-CAA                         AACAAAATCTGAGACTGGAGGAGGTTTNTGGCATGTGGAGTAGACATCATC
genomic: GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAAgtaagctttg ... tcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
EST: gi|71770109|gb|DR968046.1|DR968046
EST:     GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAA                         AACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
genomic: GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAAgtaagctttg ... tcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
EST: gi|30705964|gb|CD058985.1|CD058985
EST:     GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAA                         AACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
genomic: GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAAgtaagctttg ... tcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
EST: gi|76918843|gb|DV167481.1|DV167481
EST:     GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAA                         AACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
genomic: GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAAgtaagctttg ... tcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
EST: gi|5018209|gb|AI714402.1|AI714402
EST:     GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAA                         AACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
genomic: GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAAgtaagctttg ... tcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
EST: gi|211242536|gb|FL481660.1|FL481660
EST:     GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAA                         AACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
genomic: GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAAgtaagctttg ... tcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
EST: gi|211164192|gb|FL363087.1|FL363087
EST:     GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAA                         AACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
genomic: GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAAgtaagctttg ... tcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA
EST: gi|60336843|gb|DN203816.1|DN203816
EST:     GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCGTCCGATCACAA                         AACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTCGAGTAGACATCATA
genomic: GTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAAgtaagctttg ... tcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtcgtgctggcaactgaggccaggtgtgatccgatttctctctcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAG
                                tccgatttctctctcc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgatttgcttcactcatcgttaacaagtgatataacactttagcttgtcgtgctggcaactgaggccaggtgtgatccgatttctctctcccgtgcagAACAAAATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG