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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcctgcgatcatcatttttgtgattatccttccaatatcttctttacatgatgcactggttttcctctatgattgtttttctcttacattagcaaagATATTTAAACAAGAAGAAGGCGGCTGAAGAGATGATTCAGCATTATGAGAAGCAATCTTCAGTGGATTACAGCCTCAAAGAAGGGGAGACATTGGTTCTT

Basic information

species Zea mays
transcript GRMZM2G040401_T03
intron # 7
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040401_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g42830.1 (Oryza sativa), 3'ss of exon 6
atttcctgcgatcatcatttttgtgattatcct--tccaatatcttctttacatgatgcactggttttcctctatgattgtttttctcttacattagcaaagATATTTAAACAAGAAGAAGGCGGCTGAAGAGATGATTCAGCATTATGAGAAGCAATCTTCAGTGGATTACAGCCTCAAAGAAGGGGAGACATTGGTTCTT
 ||| | |   |  |  | | ||  | |||  |  |||||||  ||||||  || | | ||   ||||||  |||||||  || | |||||||| | ||||||||| |||||||||| ||| | |||||||||||| | || || ||||||||   ||| ||||||||||||||||||||||||||||| || |||||| | 
-tttgcagttgtagttgtgtatggtaatatttttatccaataagttctttttataacggacca-ttttccggtatgatttgttatttcttacatcatcaaagATATCTAAACAAGAAAAAGACTGCTGAAGAGATGGTACAACACTATGAGAAATCATCATCAGTGGATTACAGCCTCAAAGAAGGGGAAACTTTGGTTTTG
















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|5455978|gb|AI833668.1|AI833668
EST:     GAAAGACCTGAAGCATATGACTTCCAAGCTGCCCTACATGATCATATGAA                         ATATTTAAACAAGAAGAAGGCGGCTGAAGAGATGATTCAGCATTATGAGAA
genomic: GAAAGACCTGAAGCATATGACTTCCAAGCTGCCCTACATGATCATATGAAgtatccttct ... attagcaaagATATTTAAACAAGAAGAAGGCGGCTGAAGAGATGATTCAGCATTATGAGAA
EST: gi|32847568|gb|CD987249.1|CD987249
EST:     GAAAGACCTGAAGCATATGACTTCCAAGCTGCCCTACATGATCATATGAA                         ATATTTAAACAAGAAGAAGGCCGCTGAAGAGATGATTCAGCATTATGAGAA
genomic: GAAAGACCTGAAGCATATGACTTCCAAGCTGCCCTACATGATCATATGAAgtatccttct ... attagcaaagATATTTAAACAAGAAGAAGGCGGCTGAAGAGATGATTCAGCATTATGAGAA
EST: gi|211053449|gb|FL366040.1|FL366040
EST:     GAAAGACCTGAAGCATATGACTTCCAAGCTGCCCTACATGATCATATGAA                         ATATTTAAACAAGAAGAAGGCGGCTGAAGAGATGATTCAGCATTATGAGAA
genomic: GAAAGACCTGAAGCATATGACTTCCAAGCTGCCCTACATGATCATATGAAgtatccttct ... attagcaaagATATTTAAACAAGAAGAAGGCGGCTGAAGAGATGATTCAGCATTATGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacatgatgcactggttttcctctatgattgtttttctcttacattagcaaagATATTTAAACAAGAAGAAGGCGGCTGAAGAGATGATTCAGCATTATGAGAAGCAATCTTCAGTGGATTACAGCCTCAAAGAAGGGGAGACATTGGTTCTT
                   ttcctctat  putative branch site 
                                 tttttctcttacatt  putative PPT
                             attgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcctgcgatcatcatttttgtgattatccttccaatatcttctttacatgatgcactggttttcctctatgattgtttttctcttacattagcaaagATATTTAAACAAGAAGAAGGCGGCTGAAGAGATGATTCAGCATTATGAGAAGCAATCTTCAGTGGATTACAGCCTCAAAGAAGGGGAGACATTGGTTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG