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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgttcatgcatgcaaatagattttccagactatctccctgttacttgttagcctaaaacttgttgcttctcagGTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGGCCTGTCGAGGGAGATGAGGCTGTGCAGGAGGTTGCTGCTGCCGAGTAG

Basic information

species Zea mays
transcript GRMZM2G030915_T09
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030915_T09 (Zea mays), 3'ss of exon 4
lower sequence: PP1S17_306V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------gtaattgttcatgcatg-caaatagattttcca----gactatctccctgttact--tgttagcctaaaacttgttgcttctcagGTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGGCCTGTCGAGGGAGATGAGGCTGTGCAGGAGGTTGCTGCTGCCGAGTAG-------
               ||  ||  |    | ||     | ||||||       ||  |  | ||   | ||  | ||   |||     | | | |   ||||||||||| |||||||  ||||| || |||| |||| ||||||||||||| | ||  ||||  |      | |  | |||||| ||||||          
actcagaatgagctcgtggtttctttatcgtgatgtgtcgattttttcatgtgatgaggttccacatgctgatattgttctatggtatttggttcgacagGTTCATGGGGACTACAGCGAGGAAGTCGGTGCGAAGATTGAGAGGCCTGTTGGGGACGATGCCGAAACCGATGCTGCTGCTGCCGCCGAGCCAGTTCCCG
















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|5439403|gb|AI820324.1|AI820324
EST:     AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAG                         GTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGGCCTGTC
genomic: AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAGgtaattgttc ... tgcttctcagGTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGGCCTGTC
EST: gi|166624052|gb|EG316033.1|EG316033
EST:     AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAG                         GTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGC
genomic: AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAGgtaattgttc ... tgcttctcagGTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGC
EST: gi|29543599|gb|CB603979.1|CB603979
EST:     AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAG                         GTTCATGGCGA-TACAAAGAGGATGTTGGTGTGAAG
genomic: AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAGgtaattgttc ... tgcttctcagGTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAG
EST: gi|31664634|gb|CD573567.1|CD573567
EST:     AGGTGAAGATACTCAAGGCCCCCCAGTTCGATCTTGGGAAGCTCATGGAG                         GTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGGCCTGTC
genomic: AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAGgtaattgttc ... tgcttctcagGTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGGCCTGTC
EST: gi|211501448|gb|FL027595.1|FL027595
EST:     AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAG                         GTTCACGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGGCCTGTC
genomic: AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAGgtaattgttc ... tgcttctcagGTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGGCCTGTC
EST: gi|113671990|gb|DW823470.1|DW823470
EST:     AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAG                         GTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGC
genomic: AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAGgtaattgttc ... tgcttctcagGTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGC
EST: gi|78027339|gb|DV495726.1|DV495726
EST:     AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAG                         GTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGCCCTGTC
genomic: AGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAGgtaattgttc ... tgcttctcagGTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGGCCTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttccagactatctccctgttacttgttagcctaaaacttgttgcttctcagGTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGGCCTGTCGAGGGAGATGAGGCTGTGCAGGAGGTTGCTGCTGCCGAGTAG
                                gcctaaa  putative branch site (score: 3)
                                            ttgcttctc  putative PPT
                                   taaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgttcatgcatgcaaatagattttccagactatctccctgttacttgttagcctaaaacttgttgcttctcagGTTCATGGCGACTACAAAGAGGATGTTGGTGTGAAGCTTGAGAGGCCTGTCGAGGGAGATGAGGCTGTGCAGGAGGTTGCTGCTGCCGAGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC