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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTAAGAAGCCCTCTTCTCCTTCGTCTTCTATGAAATCGAAAGTTTACCGCTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagtttttctccgatctggttttactttcatatatttgtgtgtgttgtggcttgatctgttttcttatatgtgttgtttggtttattctttcattttg...

Basic information

species Arabidopsis thaliana
transcript AT4G23630.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23630.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv02s0025g00640.t01 (Vitis vinifera), 5'ss of exon 1
---ACTAAGAAGCCCTCTTCTCCTTCGTCTTCTATGAAATCGAAAGTTTACCGCTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagtt---tttctccgatc--tggttttactttcatatatttgtgtgtgttgtggcttgatctgttttcttatatgtgttgtttggtttattctttcattttg
      ||  ||   || ||||| ||  |||  |   || | || ||||| ||  | |||||  | ||  |||||||||| |||||||||||||||||||| |||| ||    | |   | |||  || | ||  |||  | | ||| | | | |||||   |     |       | ||| |  | |||    | |     |||   
TCCGACAACGAGAAATCGTCTCCCTCAGCTTTCA---AAGCCAAGGTTTATCGGATCTTCGGCAGGGAAAAGCCTGTTCACAAGGTTCTCGGCGGTGGAAAACgtacgtaaagtgtacaccatcgatgatctttttttttttttttttttttttttgtgtggttgctaggaaaaaaaaatgcg--gcttgagaaaatggga-attc--
















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|116428045|gb|EG470637.1|EG470637
EST:     CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGC                         CGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
genomic: CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagttttt ... ctatttgcagCGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
EST: gi|116431244|gb|EG473836.1|EG473836
EST:     CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGC                         CGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
genomic: CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagttttt ... ctatttgcagCGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
EST: gi|116437736|gb|EG480328.1|EG480328
EST:     CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGC                         CGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
genomic: CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagttttt ... ctatttgcagCGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
EST: gi|86028442|gb|DR324195.1|DR324195
EST:     CTTNNNCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGCGGAAAGC                         CGGCTGATATATTCATGTGGAAGAACAAGAAGAT
genomic: CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagttttt ... ctatttgcagCGGCTGATATATTCATGTGGAAGAACAAGAAGAT
EST: gi|86028443|gb|DR324196.1|DR324196
EST:     CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGC                         CGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
genomic: CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagttttt ... ctatttgcagCGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
EST: gi|116425192|gb|EG467784.1|EG467784
EST:     CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGC                         CGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
genomic: CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagttttt ... ctatttgcagCGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
EST: gi|116437696|gb|EG480288.1|EG480288
EST:     CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGC                         CGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
genomic: CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagttttt ... ctatttgcagCGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
EST: gi|116437735|gb|EG480327.1|EG480327
EST:     CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGC                         CGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
genomic: CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagttttt ... ctatttgcagCGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
EST: gi|116437695|gb|EG480287.1|EG480287
EST:     CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGC                         CGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
genomic: CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagttttt ... ctatttgcagCGGCTGATATATTCATGTGGAAGAACAAGAAGATGTCTGGTGGTGTACTTG
EST: gi|164180442|gb|ES089510.1|ES089510
EST:     CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTCCTCGGCGGTGGAAAGC                         CGGCTGATATATTCATGTGGAAGAAC
genomic: CTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagttttt ... ctatttgcagCGGCTGATATATTCATGTGGAAGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTAAGAAGCCCTCTTCTCCTTCGTCTTCTATGAAATCGAAAGTTTACCGCTTGTTCGGACGAGAGCAGCCTGTTCATAAGGTTCTCGGCGGTGGAAAGCgtaagtttttctccgatctggttttactttcatatatttgtgtgtgttgtggcttgatctgttttcttatatgtgttgtttggtttattctttcattttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttttctc