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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacagcgagctccggttctaacatctggttgctcagcagttaaaacttaaagtttggtaccccagtccccttttctcatcattatcttcctcacagcagAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG

Basic information

species Zea mays
transcript GRMZM2G003692_T01
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|31362808|gb|CD447165.1|CD447165
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGCAG                       
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G-AGgttatccctg ... ctcacagc
EST: gi|32940746|gb|CF045565.1|CF045565
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         C
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcag-
EST: gi|32940746|gb|CF045565.1|CF045565
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         C
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcag-
EST: gi|211495955|gb|FL480154.1|FL480154
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATTGCAAACACATTTTGCTGAG                         AAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcagAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
EST: gi|211078663|gb|FL128724.1|FL128724
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         AAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcagAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
EST: gi|60353742|gb|DN220715.1|DN220715
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         AAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcagAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
EST: gi|5915523|gb|AW053164.1|AW053164
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGCAG                       
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G-AGgttatccctg ... ctcacagc
EST: gi|88757474|gb|DY541615.1|DY541615
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         AAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcagAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
EST: gi|32909212|gb|CF014024.1|CF014024
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         AAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcagAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
EST: gi|6022668|gb|AW067596.1|AW067596
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGCAG                       
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G-AGgttatccctg ... ctcacagc
EST: gi|12968787|gb|BG265824.1|BG265824
EST:     GCTGCAGCTTTTTCATCGCAAACACATTCTGCTGAGCAG                       
genomic: GCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G-AGgttatccctg ... ctcacagc
EST: gi|113703640|gb|EE681144.1|EE681144
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         AAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcagAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
EST: gi|78021266|gb|DV489653.1|DV489653
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGCAG                       
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G-AGgttatccctg ... ctcacagc
EST: gi|211078661|gb|FL128722.1|FL128722
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGCAG                       
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G-AGgttatccctg ... ctcacagc
EST: gi|6101980|gb|AW126450.1|AW126450
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGCAG                       
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G-AGgttatccctg ... ctcacagc
EST: gi|71767908|gb|DR965845.1|DR965845
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         C
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcag-
EST: gi|71767908|gb|DR965845.1|DR965845
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         C
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcag-
EST: gi|91875090|gb|EB405047.1|EB405047
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         AAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcagAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
EST: gi|37390564|gb|CF632514.1|CF632514
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGCAG                       
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G-AGgttatccctg ... ctcacagc
EST: gi|88757473|gb|DY541614.1|DY541614
EST:     CACTACAATCTTCTGTTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         AAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ctcacagcagAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttaaagtttggtaccccagtccccttttctcatcattatcttcctcacagcagAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG
                                           tcctcac  putative branch site (score: 2)
                     tccccttttctcatca  CT-rich tract
                                 atcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacagcgagctccggttctaacatctggttgctcagcagttaaaacttaaagtttggtaccccagtccccttttctcatcattatcttcctcacagcagAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - -gctccgg
- - - - - - - - - - - - - tggttgc
- - - - - - - - - - - - - - - - -tcagcag