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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattccgataagcttttttcttgtagattcttatgcttgtatcactctgcatcaccagagcatctactttattctactaataacaagtattgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG

Basic information

species Arabidopsis thaliana
transcript AT3G04820.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04820.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 12
gtaaattccgataagcttttttcttgtagattcttatgcttgtatcactctgcatcaccagagcatctactttattctactaataacaagtattgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG
||| ||| |  | | |||||       | | || || |      ||||||     | |||        ||| || | || | |||  |    || | | ||||||||||||||||| | ||||||||| |||| |||  | |||||||| || ||||| |||||||||||
gtatattac--tcaacttttcctc---aaaatcctacg------tcactc-----ccccatcctggtcactgtagt-tattcatatgactgtttttcttagGGAATTCTCAATAACCAACATGACTGGAGGTTTTAGGAGGGTTTTCCAAAAGCCAATCGACTTTGAATG
















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|116457912|gb|EG500504.1|EG500504
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGAC
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGAC
EST: gi|116457909|gb|EG500501.1|EG500501
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
EST: gi|116457905|gb|EG500497.1|EG500497
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTT
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTT
EST: gi|116457913|gb|EG500505.1|EG500505
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
EST: gi|116457903|gb|EG500495.1|EG500495
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCC
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCC
EST: gi|116462939|gb|EG505531.1|EG505531
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
EST: gi|116457908|gb|EG500500.1|EG500500
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
EST: gi|116457917|gb|EG500509.1|EG500509
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
EST: gi|116457902|gb|EG500494.1|EG500494
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
EST: gi|116457914|gb|EG500506.1|EG500506
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
EST: gi|116457920|gb|EG500512.1|EG500512
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
EST: gi|116457916|gb|EG500508.1|EG500508
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
EST: gi|116457919|gb|EG500511.1|EG500511
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
EST: gi|116457911|gb|EG500503.1|EG500503
EST:     GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAA                         GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA
genomic: GACGGTATCAGCCTAACTGAGAGCATTCACGGTGTAAAgtaaattccg ... attgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actctgcatcaccagagcatctactttattctactaataacaagtattgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG
                                  taataac  putative branch site (score: 1)
                                              ttgtttc  putative PPT
                        tttattctactaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattccgataagcttttttcttgtagattcttatgcttgtatcactctgcatcaccagagcatctactttattctactaataacaagtattgtttcagGGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG