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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACTGCATTTGCGTGTACCTTGGCAAAGCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAGgtcagtaggttcgccatactctcatgcacacatatgcctcttattttactcattaattttcaatttgatatcttgcag

Basic information

species Zea mays
transcript GRMZM2G002276_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002276_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g62820.1 (Oryza sativa), 5'ss of exon 5
GTGACTGCATTTGCGTGTACCTTGGCAAAGCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAGgtcagtaggttcgccatactctcatgcacacatatgcctcttattttactcattaattttcaatttgatatcttgcag
||||||||||||||||||||| | || ||||| ||||||||||||||  | |||||||||||||| ||||||||| |||||   ||      |    |||| |||   | | |  |  |||  ||| || ||||| | | ||| |  | || |||||
GTGACTGCATTTGCGTGTACCCTTGCGAAGCATAGGAAATCATCAGTCCTGGAAGCCAAGGATGTATTGCTGCACCTAGgttgataaccctcct---ctctgatgtg-atagaatcaactttatttgcttattaaatctgaatatattttcatgcag
















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|71299025|gb|DR785503.1|DR785503
EST:     GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAG                         AAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC
genomic: GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAGgtcagtaggt ... tatcttgcagAAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC
EST: gi|71426365|gb|DR807415.1|DR807415
EST:     GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAG                         AAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAAAT
genomic: GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAGgtcagtaggt ... tatcttgcagAAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAA-T
EST: gi|409610|gb|T12672.1|T12672
EST:     GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAG                         AAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC
genomic: GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAGgtcagtaggt ... tatcttgcagAAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC
EST: gi|71328191|gb|DR800734.1|DR800734
EST:     GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAG                         AAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC
genomic: GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAGgtcagtaggt ... tatcttgcagAAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC
EST: gi|211197974|gb|FL446526.1|FL446526
EST:     ACAGGAAATCATCAGTTGTCGAAGCCAAAGGATGTGTTGCTGCACTTAG                         AAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC
genomic: ACAGGAAATCATCAGTTGTCGAAGCC-AAGGATGTGTTGCTGCACTTAGgtcagtaggt ... tatcttgcagAAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC
EST: gi|71756862|gb|DR954799.1|DR954799
EST:     GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAG                         AAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC
genomic: GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAGgtcagtaggt ... tatcttgcagAAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC
EST: gi|86473700|gb|DY240070.1|DY240070
EST:     GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAG                         AAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC
genomic: GCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAGgtcagtaggt ... tatcttgcagAAAGAAATTGGCATTTATCTGTTCCTGGTTTCTCAAGGGAGGATAAGAATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACTGCATTTGCGTGTACCTTGGCAAAGCACAGGAAATCATCAGTTGTCGAAGCCAAGGATGTGTTGCTGCACTTAGgtcagtaggttcgccatactctcatgcacacatatgcctcttattttactcattaattttcaatttgatatcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC