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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAACCTCAGTTGATTTTAAGCCATACATTGGTCCAATCTATAATGCAATACTGGGACGTTTGGCCAATCAAGATCAGGATCAGgtttggcaaaattctcttttctcactccctctcttgtgtgcttgcagtgcactctcatttatcatgcaaatttgtgttctcccag

Basic information

species Zea mays
transcript GRMZM2G168629_T04
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168629_T04 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 16
ACAACCTCAGTTGATTTTAAGCCATACATTGGTCCAATCTATAATGCAATACTGGGACGTTTGGCCAATCAAGATCAGGATCAGgtttggcaaaattctcttttctcactccctctcttgtgtgcttgcagtgcactctcatttatcatgcaaatttgtgttctcccag
 ||  | |  | ||||  | |||||| ||||||||||||||||| || ||  |||  || ||||| ||||| |||||||||||||||  ||||||||  |   || |  ||    ||| || |  ||      | |||   | | | ||| |||| | ||||       
GCACGCACTCTAGATTACAGGCCATATATTGGTCCAATCTATAAGGCTATCTTGGCCCGCTTGGCAAATCAGGATCAGgatcaggttgagcaaaattaacacctccctatcttcatct-gtctctttct----ctctcaggtctcttatggaaatatttgtttcag---

upper sequence: GRMZM2G168629_T04 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g07340.1 (Oryza sativa), 5'ss of exon 12
ACAACCTCAGTTGATTTTAAGCCATACATTGGTCCAATCTATAATGCAATACTGGGACGTTTGGCCAATCAAGATCAGGATCAGgttt-ggcaaaattctcttttctcactccctctcttgtgtgcttgcagtgcactctcatttatcatgcaaatttgtgttctcccag
 ||  |||    ||||  | |||||| ||||||||||||||||| || ||  |||  || ||||| ||||| ||||||||||||| |  ||   |      ||  | |   ||    ||  | ||  |      | |||   | | | ||| |||| | ||||       
CCACACTCTCCAGATTACAGGCCATATATTGGTCCAATCTATAAGGCTATCTTGGCCCGCTTGGCAAATCAGGATCAGgatcaggatcaggttgagcaaaattaacacctccctatcctcatctgtctctttctctctcaggtctcttatggaaatatttgtttcag---
















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|22489194|gb|BU049130.1|BU049130
EST:     GGCCAATCAAGATCAGGATCAG                         GAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT
genomic: GGCCAATCAAGATCAGGATCAGgtttggcaaa ... gttctcccagGAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT
EST: gi|211432450|gb|FL213954.1|FL213954
EST:     CAATCTATAATGCAATACTGGGACGTTTGGCCAATCAAGATCAGGATCAG                         GAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT
genomic: CAATCTATAATGCAATACTGGGACGTTTGGCCAATCAAGATCAGGATCAGgtttggcaaa ... gttctcccagGAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT
EST: gi|87298767|gb|DY470770.1|DY470770
EST:     GGCCAATCAAGATCAGGATCAG                         GAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT
genomic: GGCCAATCAAGATCAGGATCAGgtttggcaaa ... gttctcccagGAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT
EST: gi|61118518|gb|DN559479.1|DN559479
EST:     CAATCTATAATGCGATACTGGGACGTTTGGCCAATCAAGATCAGGATCAG                         GAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT
genomic: CAATCTATAATGCAATACTGGGACGTTTGGCCAATCAAGATCAGGATCAGgtttggcaaa ... gttctcccagGAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT
EST: gi|32859371|gb|CD999052.1|CD999052
EST:     CAATCTATAATGCGATACTGGGACGTTTGGCCAATCAAGATCAGGATCAG                         GAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT
genomic: CAATCTATAATGCAATACTGGGACGTTTGGCCAATCAAGATCAGGATCAGgtttggcaaa ... gttctcccagGAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT
EST: gi|211432451|gb|FL213955.1|FL213955
EST:     CAATCTATAATGCAATACTGGGACGTTTGGCCAATCAAGATCAGGATCAG                         GAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT
genomic: CAATCTATAATGCAATACTGGGACGTTTGGCCAATCAAGATCAGGATCAGgtttggcaaa ... gttctcccagGAGGTAAAAGAATGCGCCATATCTTGCATGAGTTTGGTGGTCTCTACTTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAACCTCAGTTGATTTTAAGCCATACATTGGTCCAATCTATAATGCAATACTGGGACGTTTGGCCAATCAAGATCAGGATCAGgtttggcaaaattctcttttctcactccctctcttgtgtgcttgcagtgcactctcatttatcatgcaaatttgtgttctcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA