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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagaaaaaacattttgtgcaaagtttagaatcttttttagtttcatgaaccattgacgcgatttaggttttatcaaatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCCAAAGAAACTGCACCGTGCAAAGAGATTCCGTCTCTGCAACTCATCAACC

Basic information

species Arabidopsis thaliana
transcript AT1G64520.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0025g02010.t01 (Vitis vinifera), 3'ss of exon 5
-----gtaagagaaaaaacattttgtgcaaagtt-----tagaatcttttttagtttcatg-aaccattgacgcgatttaggttttatcaaat-cttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCCAAAGAAACTGCACCGTGCAAAGAGATTCCGTCTCTGCAACTCATCAACC
      ||  |   |  | | ||     | ||||     |  | |||||  |   |  | | || | |||| | |  || |  || ||||  | |||  |||||||||||||||||||  | ||| | ||   |||  | |||||||  || |||||| ||||||| ||||||||||||||||||||||||||||| ||||
cacacatatcatgcaccagaattgcaatacagttgctcttgtactctttactgaatgaagggaatctttgatgagcatttgaatt-atcatctgcttgcagGAGCATCCTGAGTGGGAGATAAAGAACGGCCATGTGTTTTTCCAGAGGGCGAAAGAATCTGCACCCTGCAAAGAGATTCCGTCTCTGCAACTCATTAACC
















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|164224596|gb|EL993610.1|EL993610
EST:     GTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGAT                         GAGCATCCCGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
genomic: GTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGATgtaagagaaa ... aatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
EST: gi|116478804|gb|EG521396.1|EG521396
EST:     AGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGAT                         GAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
genomic: AGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGATgtaagagaaa ... aatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
EST: gi|125213473|gb|EL228305.1|EL228305
EST:     AGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGAT                         GAGCATCCTGAGTGGGAAGTGAAGGAAGG
genomic: AGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGATgtaagagaaa ... aatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGG
EST: gi|86064683|gb|DR360440.1|DR360440
EST:     AGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGAT                         GAGCATCCCGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCANAAAGCC
genomic: AGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGATgtaagagaaa ... aatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
EST: gi|116446013|gb|EG488605.1|EG488605
EST:     AGATGTTGTTGNNNNNNNCTGATCAAGAACTCTTAACCTATGTCACAGAT                         GAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
genomic: AGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGATgtaagagaaa ... aatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
EST: gi|125071398|gb|EL136460.1|EL136460
EST:     GTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGAT                         GAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
genomic: GTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGATgtaagagaaa ... aatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
EST: gi|124778158|gb|EH868101.1|EH868101
EST:     AGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGAT                         GAGCATCCTGGGTGGGAAG
genomic: AGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGATgtaagagaaa ... aatcttatagGAGCATCCTGAGTGGGAAG
EST: gi|163996987|gb|ES065557.1|ES065557
EST:     AGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGAT                         GAGCATCCCGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
genomic: AGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGATgtaagagaaa ... aatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
EST: gi|125260032|gb|EL274117.1|EL274117
EST:     AACTCTTAACCTATGTCACAGAT                         GAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
genomic: AACTCTTAACCTATGTCACAGATgtaagagaaa ... aatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
EST: gi|124893082|gb|EH971984.1|EH971984
EST:     TGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGAT                         GAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
genomic: TGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACCTATGTCACAGATgtaagagaaa ... aatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
EST: gi|124955091|gb|EL030131.1|EL030131
EST:     GTTGTTCTCTTCTGATCAAGAACTCTTAACCTTATGTCACAGAT                         GAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC
genomic: GTTGTTCTCTTCTGATCAAGAACTCTTAACC-TATGTCACAGATgtaagagaaa ... aatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttttagtttcatgaaccattgacgcgatttaggttttatcaaatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCCAAAGAAACTGCACCGTGCAAAGAGATTCCGTCTCTGCAACTCATCAACC
                    cattgac  putative branch site (score: 3)
                                     ttttatcaaatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagaaaaaacattttgtgcaaagtttagaatcttttttagtttcatgaaccattgacgcgatttaggttttatcaaatcttatagGAGCATCCTGAGTGGGAAGTGAAGGAAGGGTTTGTTGTCTTCCAGAAAGCCAAAGAAACTGCACCGTGCAAAGAGATTCCGTCTCTGCAACTCATCAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA