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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAATTGCTTGGGTCCTTTGGGGACAATGAACTATCTCCGGAGTGTCTGGATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggaccttttcttatacatatattttctcaattcctgatgccaaaaacattttaaatatcatttgattgtctgcttatgtttctttgcag

Basic information

species Zea mays
transcript GRMZM2G011456_T03
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011456_T03 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g04660.2 (Oryza sativa), 5'ss of exon 11
GTGAATTGCTTGGGTCCTTTGGGGACAATGAACTATCTCCGGAGTGTCTGGATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggaccttt---tcttatacatatattttctcaattcctgatgccaaaaacattttaaatatcatttgatt--------gtctg----cttatgtttctttgcag
|||| |||||||| |||||||| || |||||||| ||||| |||||||| |||||||||||  ||||||||||||| ||||||||||| |||||||||||||||||  | |||   || |     |||||||||    ||| ||    |||  | ||   | ||||| |||  ||         | ||    |||||||| ||||||||
GTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGTCTAGATGGTGCTCAGAGATTCTTGAAGCCAGATGGGATTTCTATTCCTTCATCgtactgaccttttctgtccttagtctatattttcatctttcttgg-atcaattaaatcccagatatccttttgttcttatatcatttgataacttatgttcctttgcag
















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|20803221|gb|BQ294271.1|BQ294271
EST:     TATGGTGCTCAACTATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATC                         ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
genomic: GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggacc ... ttctttgcagATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
EST: gi|21843268|gb|BQ703849.1|BQ703849
EST:     GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATC                         ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
genomic: GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggacc ... ttctttgcagATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
EST: gi|211483571|gb|FL225316.1|FL225316
EST:     GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATC                         ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
genomic: GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggacc ... ttctttgcagATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
EST: gi|60340216|gb|DN207189.1|DN207189
EST:     GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATC                         ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
genomic: GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggacc ... ttctttgcagATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
EST: gi|71300981|gb|DR786519.1|DR786519
EST:     GGATTTCCATTCCTTCATC                         ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
genomic: GGATTTCCATTCCTTCATCgtactggacc ... ttctttgcagATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
EST: gi|26456816|gb|CA828399.1|CA828399
EST:     GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATC                         ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
genomic: GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggacc ... ttctttgcagATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
EST: gi|31558384|gb|CD527596.1|CD527596
EST:     GATGG-GCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATC                         ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
genomic: GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggacc ... ttctttgcagATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
EST: gi|26557923|gb|CA830158.1|CA830158
EST:     GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATC                         ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
genomic: GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggacc ... ttctttgcagATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
EST: gi|60397916|gb|DN230732.1|DN230732
EST:     GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATC                         ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
genomic: GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggacc ... ttctttgcagATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
EST: gi|71311076|gb|DR791852.1|DR791852
EST:     GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATC                         ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC
genomic: GATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggacc ... ttctttgcagATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAATTGCTTGGGTCCTTTGGGGACAATGAACTATCTCCGGAGTGTCTGGATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTTCATCgtactggaccttttcttatacatatattttctcaattcctgatgccaaaaacattttaaatatcatttgattgtctgcttatgtttctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC