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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaacacagcgagctccggttctaacatctggttgctcagcagttaaaacttaaagtttggtaccccagtccccttttctcatcattatcttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG

Basic information

species Zea mays
transcript GRMZM2G003692_T02
intron # 7
splice site 3'
intron type U2

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|12968787|gb|BG265824.1|BG265824
EST:     GCTGCAGCTTTTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACCATT
genomic: GCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|91875090|gb|EB405047.1|EB405047
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|113703640|gb|EE681144.1|EE681144
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|32940746|gb|CF045565.1|CF045565
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|88757473|gb|DY541614.1|DY541614
EST:     CACTACAATCTTCTGTTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|32909212|gb|CF014024.1|CF014024
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|88757474|gb|DY541615.1|DY541615
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|6101980|gb|AW126450.1|AW126450
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|37390564|gb|CF632514.1|CF632514
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|31362808|gb|CD447165.1|CD447165
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAGCGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|6022668|gb|AW067596.1|AW067596
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|211078663|gb|FL128724.1|FL128724
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|78021266|gb|DV489653.1|DV489653
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|211495955|gb|FL480154.1|FL480154
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATTGCAAACACATTTTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|5915523|gb|AW053164.1|AW053164
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|211078661|gb|FL128722.1|FL128722
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|71767908|gb|DR965845.1|DR965845
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|60353742|gb|DN220715.1|DN220715
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaacttaaagtttggtaccccagtccccttttctcatcattatcttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG
                        tccccttttctcatca  CT-rich tract
     ttaaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaacacagcgagctccggttctaacatctggttgctcagcagttaaaacttaaagtttggtaccccagtccccttttctcatcattatcttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA