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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacactcaaaccctttttccaaagtttgattatttgtttactcagaatcacaaaggaggtttctcacagtggcagaaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTGAGATTGAAAGAAGAATATGTTGAAGGTATGCTTGAAACTCCAACAGTCA

Basic information

species Arabidopsis thaliana
transcript AT2G42130.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42130.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G17130.1 (Glycine max), 3'ss of exon 4
--gtaacacactcaaa----ccctttttccaaagtttgattat-ttgt--ttactcagaatcacaaaggaggt--ttctcacagtggcagaaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTGAGATTGAAAGAAGAATATGTTGAAGGTATGCTTGAAACTCCAACAGTCA
   |  || | |  ||     | | ||| || | | || || | |  |  ||||||     |  |  |    |   | | |   |       ||||| ||||||||| |||| ||||||| ||| | |||||  |||| ||||| ||||| ||| |||||||||| |||||||||||  |  | |  || |||||| | |
atatggcatattttaaattgtcttctttgcagattgtgtttgtgtcattattactccctcccttagtgttattgactattaactttttgatcaaatgtagATAGAAAACAAAGTCATTCTCTCAACCAAATTATCTGTGGAGGGGCCACTTAGAATGAAAGAAGAGTATGTTGAAGGGGTTTTCGTGACACCAACAATTA

upper sequence: AT2G42130.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G29260.1 (Glycine max), 3'ss of exon 4
----gtaacacactcaa----accctttttccaaagtttgattatt-tgtttactcagaatcacaaaggaggt--ttctcacagtggcagaaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTGAGATTGAAAGAAGAATATGTTGAAGGTATGCTTGAAACTCCAACAGTCA
     |  || | |  |      | | ||| |  | | || || || |  ||||||     |  |  |    |   | | |   |       || || ||||||||| |||| ||||||| ||| | |||||  |||| ||||| ||||| ||| |||||||||| |||||||||||  | ||||  || |||||| | |
ttatatgccatattttatattgtcttctttgctgattgtgtttgttattattactccttcccttagtgctattgactattaactttttgatcaagtgtagATAGAAAACAAAGTCATTCTCTCAACCAAATTATCTGTGGAGGGGCCACTTAGAATGAAAGAAGAGTATGTTGAAGGGGTTCTTGTGACACCAACAATTA

upper sequence: AT2G42130.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g06480.t01 (Vitis vinifera), 3'ss of exon 4
------gtaacacactcaaaccctttttccaaagtttgatta---tttgtttactcagaatcacaaaggaggtttctcacagtg----gcagaaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTGAGATTGAAAGAAGAATATGTTGAAGGTATGCTTGAAACTCCAACAGTCA
       |  | ||||        |  | |  | |    |||   ||| || | | | ||    | |  ||  ||      |||    |  | |||||| || ||||||| |||||  |||||      |  ||  ||||||||||||||||  || |||||||||||||||||||||   | || ||| |||| |  ||  
cattttcttgcccacttttgtttgtaattctgattcatgttaagctttcttgattgaaaagtttata--agtattaatgaggtgctctgtggtaaaatgtagGTAGAAAGTAAAATTGTTCTGAATAGCAGGTTATCTGTTGAGGGACCACTTCGACTGAAAGAAGAATATGTTGAAGCGGTTCTAGAATCTCCTAAGGTTG

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|116394664|gb|EG437256.1|EG437256
EST:     CAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCG                         ATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
genomic: CAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCGgtaacacact ... aaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
EST: gi|116394673|gb|EG437265.1|EG437265
EST:     TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCG                         ATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
genomic: TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCGgtaacacact ... aaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
EST: gi|19877874|gb|AU238705.1|AU238705
EST:     TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCG                         ATANANNGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
genomic: TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCGgtaacacact ... aaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
EST: gi|116394674|gb|EG437266.1|EG437266
EST:     TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCG                         ATAGAAAGCAAAATCATTTTGTCATCAAAATTGACTGTTGAGGGACCACTG
genomic: TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCGgtaacacact ... aaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
EST: gi|116480998|gb|EG523590.1|EG523590
EST:     TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCG                         ATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
genomic: TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCGgtaacacact ... aaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
EST: gi|116480981|gb|EG523573.1|EG523573
EST:     TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCG                         ATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
genomic: TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCGgtaacacact ... aaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
EST: gi|116394672|gb|EG437264.1|EG437264
EST:     TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCG                         ATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
genomic: TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCGgtaacacact ... aaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
EST: gi|116394269|gb|EG436861.1|EG436861
EST:     TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCG                         ATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG
genomic: TCAAGGATGCTAACGCAAAGGCGACTGCAAATATCAAACTTTTGAACTCGgtaacacact ... aaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgtttactcagaatcacaaaggaggtttctcacagtggcagaaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTGAGATTGAAAGAAGAATATGTTGAAGGTATGCTTGAAACTCCAACAGTCA
                              ttctcac  putative branch site (score: 2)
                                           agaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacacactcaaaccctttttccaaagtttgattatttgtttactcagaatcacaaaggaggtttctcacagtggcagaaaaatgcagATAGAAAGCAAAATCATTCTGTCATCAAAATTGACTGTTGAGGGACCACTGAGATTGAAAGAAGAATATGTTGAAGGTATGCTTGAAACTCCAACAGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG