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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatatttggcagcgcatctgacatctgccccctccattccccgcttggatatgcagaacactcataccttgtcacctaaagcggggttatactcaaagtaccattgaaattcttttgtgtgttctgttacttgtggaatatgcag

Basic information

species Zea mays
transcript GRMZM5G870572_T03
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G870572_T03 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os08g25060.1 (Oryza sativa), 5'ss of exon 18
GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatatttggcagcgcatctgacatctgccccctccattccccgcttggatatgcagaacactcataccttgtcacctaaagcggggttatactcaaagtaccattgaaattcttttgtgtgttctgttacttgtggaatatgcag
||||||||| |||| || || ||||| ||||||||||||||| |||||||||    |   || | ||  || |      |     | |   |   ||    |||  ||  ||       ||  |   |  |||  |  | |||| | |  |  || |                                       
GTTCAAAGAATTAAGGATGCAATGACCCAGATATATCAAAAGTTGCAGgtaa----tctccatcacaattgcc-----tctttatcttcttcgagttcatcatgtggagtaccttagtttttaccttttgagcatgagt-tactgataagatgatagc--------------------------------------
















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|148959669|gb|EE010942.2|EE010942
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATTTCGGTTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|29946463|gb|CB816162.1|CB816162
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|89247122|gb|DY618908.1|DY618908
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|74239224|gb|DT647138.1|DT647138
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|71433412|gb|DR814462.1|DR814462
EST:     GAGTTAAAGAAGCTTTGACCCAGATATTTCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|71301572|gb|DR786840.1|DR786840
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|5607882|gb|AI901549.1|AI901549
EST:     AGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCNCAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: AGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|24763305|gb|CA398481.1|CA398481
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|4967176|gb|AI691877.1|AI691877
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatatttggcagcgcatctgacatctgccccctccattccccgcttggatatgcagaacactcataccttgtcacctaaagcggggttatactcaaagtaccattgaaattcttttgtgtgttctgttacttgtggaatatgcag

- - - - - - AAAGAA
- - - - - -  AAGAAG
- - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - CTGCAG