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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagtttcgaaagcctcagcgagagctaattggcgtagaaaacctcataatcttgttaaattctaagactctcacttttgttgttgtttttgtggtgtagGCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGG

Basic information

species Arabidopsis thaliana
transcript AT1G21190.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G21190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G28300.1 (Glycine max), 3'ss of exon 1
tcagtttcgaaagcc-tcagcgagagctaattgg-cgtagaaaacctcataatcttgttaaattctaagactctcacttttgttgttgtttttgtggtgtagGCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGG
  |||| |    |   | |    || ||  |      | |    | | ||||   | ||   || |   | | |    |  ||| |   |||     || |||||| |||||||||| | ||||||||||| ||||||||||||||  || |||| ||  | |||||||| || |||||||| ||||| |||||  ||
--agttcccttggtgattattttgatcttttaaaatatcgttggcttgataagtattttcctttttcttattttgcactgggttttcaatttgaatttgcagGCTTATGATCAGCATCTTAATATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG

upper sequence: AT1G21190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G09090.1 (Glycine max), 3'ss of exon 1
tcagtttcgaaagcctcagcgagagctaattgg--cgtagaaaacctcataatcttgtta--aattctaagactctcacttt-tgtt--gttgtttttgtgg---tgtagGCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGG
          |||   |   |     || || |  | |  ||||  || |    ||| ||   ||| |     ||| | ||| |  |  ||| | | | |||   ||||||||| |||||||||| | ||||||||||| || |||||||||||  | ||||| ||  | |||||||| || |||||||| ||||| |||||  ||
----------aagtgcccttggtgattattttgatcttttaaaatttcgttggtttgatattgattttccttttcttattttgtactgggttttctatttgggtttgtagGCTTATGATCAGCATCTTAATATGATTCTTGGCGATGTTGAAGAAATCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG

upper sequence: AT1G21190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0072g00710.t01 (Vitis vinifera), 3'ss of exon 1
tcagtttcgaaagcctcagcgagagctaattggcg-tagaaaacctcataatcttgttaaattctaagactctcacttttgttgtt----gtttttgtggtgtagGCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGG
       | |||   |  |    |  || |       | | ||  |   |||| |  | ||   || |  |||   || ||| |||      | | ||  |  |||| | ||||||||||||||| |||||||| ||||||||||||||  || |||| ||  ||||||||||||| || || |||||||| |||||||| 
----aaccaaaaagtttggacttatttattacataacaaagaagtttgcaatcctcattaaca-tatgtttcttctttgtgtggtttggcaatctggtttttcagGCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGA

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|164127766|gb|ES164040.1|ES164040
EST:     CTCCGCGGCAAGCTTCAC                         GCTTTTGATCAGCTATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTAT
genomic: CTCCGCGGCAAGCTTCACgtacgttctt ... tgtggtgtagGCTTTTGATCAGC-ATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTAT
EST: gi|86083319|gb|DR379078.1|DR379078
EST:     GGATCTATKTCAAGCTCCGATCTGACCGTGAACTCCGCGGCAAGCTTCAC                         GCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATT
genomic: GGATCTATGTCAAGCTCCGATCTGACCGTGAACTCCGCGGCAAGCTTCACgtacgttctt ... tgtggtgtagGCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATT
EST: gi|125189351|gb|EL204305.1|EL204305
EST:     CTATGTCAAGCTCCGATCTGACCGTGAACTCCGCGGCAAGCTTCAC                         GCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGG
genomic: CTATGTCAAGCTCCGATCTGACCGTGAACTCCGCGGCAAGCTTCACgtacgttctt ... tgtggtgtagGCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGG
EST: gi|19740683|gb|AU226036.1|AU226036
EST:     GGATCTATGTCAAGCTCCGATCTGACCGTGAACTCCCCGGCAAGCTTCAC                         GCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATT
genomic: GGATCTATGTCAAGCTCCGATCTGACCGTGAACTCCGCGGCAAGCTTCACgtacgttctt ... tgtggtgtagGCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATT
EST: gi|19874534|gb|AU235365.1|AU235365
EST:     GGATCTATGTCAAGCTCCGATCTGACCGTGAACTCCGCGGCAAGCTTCAC                         GCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATT
genomic: GGATCTATGTCAAGCTCCGATCTGACCGTGAACTCCGCGGCAAGCTTCACgtacgttctt ... tgtggtgtagGCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataatcttgttaaattctaagactctcacttttgttgttgtttttgtggtgtagGCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGG
                       ctctcac  putative branch site (score: 3)
                                      ttgttttt  putative PPT
       ttgttaaattctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagtttcgaaagcctcagcgagagctaattggcgtagaaaacctcataatcttgttaaattctaagactctcacttttgttgttgtttttgtggtgtagGCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - -cgaaagc
- - - - - - - - - - - - - - - - - - - aaaacct
- - - - - - - - - - - - - - - - - - - - - - -cataatc