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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacaactgaattgcttcatttctccaactgtatgactgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA

Basic information

species Zea mays
transcript GRMZM2G440916_T02
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G440916_T01 (Zea mays), 3'ss of exon 26
lower sequence: LOC_Os05g51790.1 (Oryza sativa), 3'ss of exon 26
------------------gtaacacaactgaattgcttcatttctccaactgtatgactgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA
                  ||       |   ||    ||| | ||   |    |||| | |||  ||||  | | |||     |||   |    ||   |||||  |||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||| ||||| ||    ||||| || ||
gcaagccaaccctcacaagtttttgttccctatgcactcaatgctgttataaaatgattactagtttgttgaagcattacaaaggt---aactgtttccccgaaattgcagGAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAGCCAGTCAGCCAAACACTCCACA

upper sequence: GRMZM2G440916_T01 (Zea mays), 3'ss of exon 26
lower sequence: LOC_Os05g51790.2 (Oryza sativa), 3'ss of exon 26
------------------gtaacacaactgaattgcttcatttctccaactgtatgactgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA---------------------------
                  ||       |   ||    ||| | ||   |    |||| | |||  ||||  | | |||     |||   |    ||   |||||  |||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||| ||||| ||    ||||| || ||                           
gcaagccaaccctcacaagtttttgttccctatgcactcaatgctgttataaaatgattactagtttgttgaagcattacaaaggt---aactgtttccccgaaattgcagGAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAGCCAGTCAGCCAAACACTCCACAGTTTGTGACAGTACTCTTAGCATTTCA
















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|32794483|gb|CD946719.1|CD946719
EST:     GATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: GATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|33097205|gb|CF057165.1|CF057165
EST:     GAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: GAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|32930688|gb|CF035500.1|CF035500
EST:     TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|211323885|gb|FK953781.1|FK953781
EST:     TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|33092036|gb|CF052030.1|CF052030
EST:     TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|211323884|gb|FK953780.1|FK953780
EST:     TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|78075393|gb|DV503827.1|DV503827
EST:     TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA
         ttgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacacaactgaattgcttcatttctccaactgtatgactgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC