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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggacatactagtatccaaagcatatggggaattttaaagttgttttcttatatgtttgattggtttgaatttgatagttttactctgtcttttgtgcagTTTGGTGTAGAAGAACTGATGAACTTGTGGATGGGCCAAATGCTTCACATATAACTCCCATGGCTTTAGATAGATGGGAAGCAAGGTTAGAAGATCTTTT

Basic information

species Arabidopsis thaliana
transcript AT5G17230.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G17230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G40720.1 (Glycine max), 3'ss of exon 3
aggacata-ctagtatccaaagcatatggggaattttaaagttgtttt---cttatatgtttgattggtttgaatttgatagttttactctgtcttttgtgcagTTTGGTGTAGAAGAACTGATGAACTTGTGGATGGGCCAAATGCTTCACATATAACTCCCATGGCTTTAGATAGATGGGAAGCAAGGTTAGAAGATCTTTT
   ||||| ||  | ||  | |  | ||    | |   |  |    |    |  || | | ||||   ||   | |||    | |  | ||  || || | |||| |||||||| ||||| ||||||||||| ||||| || ||||||||||| || || || |  ||||| ||||| |||||| |||| || ||||| |||||
---acatatcttttgtcagatgactgtgcaagagtgctatatgaagtaagaccaatttatctgatcaattctcaattgcct-tatagcgctccctgttattcagTGTGGTGTAGGAGAACGGATGAACTTGTTGATGGCCCTAATGCTTCACAAATTACACCAACTGCTTTGGATAGGTGGGAATCAAGATTGGAAGAACTTTT

upper sequence: AT5G17230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G39050.1 (Glycine max), 3'ss of exon 3
aggacata-ctagtatccaaagcatatg---gggaattttaaagttgttttcttatatgtttgattggtt-tgaatttgatagttttactctgtcttttgtgcagTTTGGTGTAGAAGAACTGATGAACTTGTGGATGGGCCAAATGCTTCACATATAACTCCCATGGCTTT-AGATAGATGGGAAGCAAGGTTAGAAGATCTTTT
   ||||| ||  | ||  | |  | ||   | |   | ||          |  || | | ||||   || | ||||   |  | || |||  | ||||   |||| |||||||| ||||| ||||||||||| ||||| || ||||||||||| || || || |  ||||  | |||| |||||| |||| || ||||| |||| 
---acatatcttttgtcagatgattgtgcaagagtgctatatgaagcaagaccaatttatctgatcaattctcaattgccttatgttgctccctgttttt--cagTGTGGTGTAGGAGAACGGATGAACTTGTTGATGGTCCTAATGCTTCACAAATTACGCCAACTGCTTAGAAATAGGTGGGAATCAAGATTGGAAGAACTTT-

upper sequence: AT5G17230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 3
aggacatactagtatccaaagcatatgggg--aattttaaagttgttttcttatatgtttgattggtttgaatttgatagttttactctgtcttt-tgtgcagTTTGGTGTAGAAGAACTGATGAACTTGTGGATGGGCCAAATGCTTCACATATAACTCCCATGGCTTTAGATAGATGGGAAGCAAGGTTAGAAGATCTTTT
      |   | ||| || |  | |   |   |||  | ||           |    ||  |||   ||   |||  ||   | | ||| |||   ||  |||| |||||| | ||||| ||||| ||||| |||||||| ||||| ||||| ||||| || |  || || ||||| |||||  ||||||| |||||||||||
gaattttgtaaatatgcacaatacacaagttcaatactgaaacaaagacgagaggatttatattctcttttgtttctta---tgattctctctccatgaacagTGTGGTGTCGGAGAACAGATGAGCTTGTTGATGGGCCTAATGCATCACACATAACCCCAACAGCCTTGGATAGGTGGGAGTCAAGGTTGGAAGATCTTTT

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|164107416|gb|EL968193.1|EL968193
EST:     AACTTTGCTTATGACACCCGAAAGGCGAA-GGCGATTTGGGCTATCTACG                         TTTGGTGTAGAAGAACTGATGAAC
genomic: AACTTTGCTTATGACACCCGAAAGGCGAAAGGCGATTTGGGCAATCTACGgtaagttact ... ttttgtgcagTTTGGTGTAGAAGAACTGATGAAC
EST: gi|116476475|gb|EG519067.1|EG519067
EST:     AACTTTGCTTATGACACCCGAAAGGCGAAAGGCGATTTGGGCAATCTACG                         CTTGGTGTAGAAGAACTGATGAACTTGTGGATGGGCCAAATGCTTCACATA
genomic: AACTTTGCTTATGACACCCGAAAGGCGAAAGGCGATTTGGGCAATCTACGgtaagttact ... ttttgtgcagTTTGGTGTAGAAGAACTGATGAACTTGTGGATGGGCCAAATGCTTCACATA
EST: gi|116476476|gb|EG519068.1|EG519068
EST:     AACTTTGCTTATGACACCCGAAAGGCGAAAGGCGATTTGGGCAATCTACG                         CTTGGTGTAGAAGAACTGATGAACTTGTGGATGGGCCAAATGCTTCACATA
genomic: AACTTTGCTTATGACACCCGAAAGGCGAAAGGCGATTTGGGCAATCTACGgtaagttact ... ttttgtgcagTTTGGTGTAGAAGAACTGATGAACTTGTGGATGGGCCAAATGCTTCACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttatatgtttgattggtttgaatttgatagttttactctgtcttttgtgcagTTTGGTGTAGAAGAACTGATGAACTTGTGGATGGGCCAAATGCTTCACATATAACTCCCATGGCTTTAGATAGATGGGAAGCAAGGTTAGAAGATCTTTT
                        atttgat  putative branch site (score: 5)
                                 ttttactctgtctttt  putative PPT
                       aatttgatagtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggacatactagtatccaaagcatatggggaattttaaagttgttttcttatatgtttgattggtttgaatttgatagttttactctgtcttttgtgcagTTTGGTGTAGAAGAACTGATGAACTTGTGGATGGGCCAAATGCTTCACATATAACTCCCATGGCTTTAGATAGATGGGAAGCAAGGTTAGAAGATCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - -atccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttga