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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgatatgttctgttctctgctttgattaaaaaaagtgattgcttgttttcatttactgatatgaattgtttttgttacgcttgttattgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA

Basic information

species Arabidopsis thaliana
transcript AT3G52560.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
atatgatatgttctgttctctgctttgattaaaaaaagtgattgcttgttttcatttactgatatgaattgtttttgttac--gcttgttattgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA
 ||     |||| |  |      |   ||| ||  |   || | || ||    ||| | ||  || |  || || ||| ||   |   | ||   |||  ||||||  | || ||  || | || |||||||| || ||||| ||||| || ||||| |||||||| ||||||||||||||||||||||  |||||||||||
ttagttcctgtttttgtaaaatataatattgaattagtagagtactagtaga-attcattg-cattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA

upper sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G027378_T02 (Zea mays), 3'ss of exon 1
atatgatatgttctgttctctgctttgattaaaaaaagtgattgcttgttttcatttactgatatgaattgtttttgttac--gcttgttattgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA
 ||     |||| |  |  |   |  |||| |   |   || | || ||    ||| | ||  || |  || ||  || ||   |   |  |   |||  ||||||  | || ||  || | || |||||||| || ||||| ||||| || ||||| ||||| || ||||||||||||||||||||||  |||||||||||
gtagttcctgtttttgtaacatataagattcatttagtagagtactagtaga-attcattg-cattacctgcttgcgtaactgacaaatgttaaaaatgcagTTCCTCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATCTA

upper sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G35790.1 (Glycine max), 3'ss of exon 1
-atatgatatgttctgttctctgctttgattaaaaaaagtgattgcttgttttcatttactgatatgaat-tgtttttgttacgcttgttattgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA
 || || | ||     ||   |  | |    |       |  ||  |     |    |  |   |||| | |||  ||       ||  || |  |||  |||||| ||||| ||  | ||| |||||||||||||    || || ||||| || || |||||||| || |||||||||||||||||||| || ||||| ||
aatttggt-tgaaggattacata-tgtagccattcttgatatttattgaagatacaatgttagcatgagtatgtagttaaaggcatttgtactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATCGGAGATGGAACAGTTAGCTATGGAATGGATGATGGTGACGACATTTA

upper sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 1
---------atatgatatgttctgttctctgctttgattaaaaaaagtgattgcttgttttcatttact-gatatgaattgtttttgttacgcttgttattgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA
          |  || ||| |  ||    ||  |  | | |||  |     |  | | |   | ||||  | ||||  | ||||||||    |||  | ||    |  ||| ||  | || ||  | ||| ||||||| ||||||||||||||||| |||||||| ||||| |||||||| |||||||||||||||||||||||||| ||
acaactggagttggaaatgcttggtatcttgtctcaagtgaaacta-----tcttagatggaagttacaaggtatgtgt-gtttttgt----ctttatgttatcttgcagTCCCTCGCAACTTCAGATTGCTGGAGGAACTTGAACGTGGGGAGAAGGGTATTGGAGATGGTACTGTGAGTTATGGAATGGATGATGGAGATGACATATA

upper sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 2
atatgatatgttctgttctctgctttgattaaaaaaa-gtgattgcttgttttcatttactgatatgaattgtttttgttacgcttgttattgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA
  |   |   |    |  |    | |   ||     | |     | ||| ||     | | | | |||  | ||    ||  | || |  |   |   ||||||| ||||| |||||  |  | || || |||||  | || |||||||||||||| ||||| || || |||||||| ||||| ||||| |||||| | | 
gaagagttcatagaatgttgacatgtagctagtcgtatgctgaggtttgattctcgctccagttctgatgtattaac-ttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT

upper sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
-------atatgatatgttctgttctctgctttgattaaaaaaagtgattgcttgttttcatttactgatatgaattgtttttgttacgcttgttattgcaa-tatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA
       | ||| |      |  | | || ||| ||     |   | | | | |  |||  |||  |        || ||||   || |    ||  | ||| ||||||||| ||||| |||||  |  | |||||||||||  | || ||||||||||| || ||||| || ||||||||||| |||||||| || || ||  | | 
ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttcttttttttctt--------ttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT

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|86062376|gb|DR358133.1|DR358133
EST:     TTGGCTCAGGAGGATCTAGCGTTGTTGGTATAAAATTTCGATTCTTTCGG                         TTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTA
genomic: TTGGCTCAGGAGGATCTAGCGTTGTTGGTATAAAATTTCGATTCTTTCGGgtttgttctc ... tgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTA
EST: gi|86087082|gb|DR382841.1|DR382841
EST:     TTGGCTCAGGAGGATCTAGCGTTGTTGGTATAAAATTTCGATTCTTTCGG                         TTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTA
genomic: TTGGCTCAGGAGGATCTAGCGTTGTTGGTATAAAATTTCGATTCTTTCGGgtttgttctc ... tgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttcatttactgatatgaattgtttttgttacgcttgttattgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA
           tactgat  putative branch site (score: 2)
                atatgaattgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgatatgttctgttctctgctttgattaaaaaaagtgattgcttgttttcatttactgatatgaattgtttttgttacgcttgttattgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG