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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctaatcatcttcaaaattagaatcatctcgctcgttgtggtcattgtatatgttagttttgcttgccatatgtaagctaaaacgtcattagGTTCCAGGTATTGTATTTGCACGAGGACCAGCTGTAGCTGTGCTTATTCTCTTGGAGTCAGATGGTGAGACTTATGCGGTTCTCACTGAACAG

Basic information

species Arabidopsis thaliana
transcript AT4G11980.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g03910.1 (Oryza sativa), 3'ss of exon 2
-gtatctaatcatcttcaaaattagaatcatctcgctcgttgtggtcattgtatatgttagttttgcttgccatatgt-aagct---aaaacgtcattagGTTCCAGGTATTGTATTTGCACGAGGACCAGCTGTAGCTGTGCTTATTCTCTTGGAGTCAGATGGTGAGACTTATGCGGTTCTCACTGAACAG
  |  ||  |    |    |||||||             | |   |||  |||   |    || ||  |   |||| |  || |   | ||  |    || ||||||| |||||||||||| |||| || ||||| |||||| | ||||| ||||||||  | ||  | ||||| || ||||| || ||||||
tattccttgtagcatgttgaattagatgtggtcgttgtataggattcaaagtaagcggattttgtgtgtattatattttgagttttgacaatatatccagATTCCAGGAATTGTATTTGCAAGAGGGCCTGCTGTTGCTGTGTTGATTCTTTTGGAGTCTAAAGGGCAAACTTACGCTGTTCTTACAGAACAG

upper sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G04160.1 (Glycine max), 3'ss of exon 3
-------gtatctaatcatcttcaaaattagaatcatctcgctcgttgtggtcattgtatatgttagttttgct-tgccatatgtaagctaaaacgtcattagGTTCCAGGTATTGTATTTGCACGAGGACCAGCTGTAGCTGTGCTTATTCTCTTGGAGTCAGATGGTGAGACTTATGCGGTTCTCACTGAACAG
       || |  ||     ||||  | |  ||| ||||  |   | ||| |  |  || ||| |  |||   | |   |||| |||  |||  ||| ||||| ||||||| |||||||||||| |||||||||||||||||||||| || ||| |||| ||||| |||||||||||||| ||||| |||||||||
tcggattgtgtacaaaatatttcattagttcaattatct-acatttagtgctgctccta-atgctgatttgattattttatat-taaagtaagccgtgattagATTCCAGGCATTGTATTTGCAAGAGGACCAGCTGTAGCTGTGCTGATACTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAG

upper sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G04150.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------gtatc--taatcatcttcaaaattagaatcatctcg-ctcgttgtggtcattgtata-----tgttagttttgct-tgccatatgtaagctaaaacgtcattagGTTCCAGGTATTGTATTTGCACGAGGACCAGCTGTAGCTGTGCTTATTCTCTTGGAGTCAGATGGTGAGACTTATGCGGTTCTCACTGAACAG
                                                        |||     | | | || | ||     |  ||| | | ||  || | | | | ||| |     || |  |||   | |   |||| ||| ||||| | | ||||||||||||||||||| |||||| ||||||||||||| |||||| | || ||| |||| ||||| |||||||||||||| ||||| |||||||||
gtatgagatggtttacatacaagtataaatctatgttggcatgttttcctgtgttagtaatggcagtgagctgcgaaccagtatgcatattgtctacttttagacttagtacacctaatgctgatttcattcttttatat-taaactaaagcattattagGTTCCAGGTATTGTGTTTGCAAGAGGACCAGCTGTGGCTGTGTTGATGCTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAG

upper sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g04840.t01 (Vitis vinifera), 3'ss of exon 3
--------------gtatctaatcatcttcaaaattagaatcatctcgctcgttgtggtcattgtatatgttagttttgcttgccatatgtaagctaaaacgtcattagGTTCCAGGTATTGTATTTGCACGAGGACCAGCTGTAGCTGTGCTTATTCTCTTGGAGTCAGATGGTGAGACTTATGCGGTTCTCACTGAACAG
              || | | ||  |||  |   | | ||  || |  | | ||      ||  |||   ||   ||    |   | |  |    |||||| |  ||||||||| || ||||| |||||| |||||||||||||||||||||| || || ||||| ||||| || || | |||  | ||||| || ||||||
gaaattacatatacgtgttttattttctctaccttgaaaagtatataccccatt------atcatat-catt--cttcatgtagtagacatggattaaaaccttcttagGTTCCTGGCATTGTGTTTGCAAGAGGACCAGCTGTAGCTGTGCTGATCCTTTTGGACTCAGAGGGCGAAATTTACACTGTTCTTACAGAACAG

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|86055093|gb|DR350850.1|DR350850
EST:     GATTTCTCAAATTCAAAGCGGATATTTTCGACAAGGAAACTGGTCAAAAG                         GTTCCAGGTATTGTATTTGCACGAGGACCAGCTGTAGCTGTGCTTATTCTC
genomic: GATTTCTCAAATTCAAAGCGGATATTTTCGACAAGGAAACTGGTCAAAAGgtatctaatc ... acgtcattagGTTCCAGGTATTGTATTTGCACGAGGACCAGCTGTAGCTGTGCTTATTCTC
EST: gi|86055095|gb|DR350852.1|DR350852
EST:     GATTTCTCAAATTCAAAGCGGATATTTTCGACAAGGAAACTGGTCAAAAG                         GTTCCAGGTATTGTATTTGCACGAGGACCAGCTG
genomic: GATTTCTCAAATTCAAAGCGGATATTTTCGACAAGGAAACTGGTCAAAAGgtatctaatc ... acgtcattagGTTCCAGGTATTGTATTTGCACGAGGACCAGCTG
EST: gi|86055094|gb|DR350851.1|DR350851
EST:     GATTTCTCAAATTCANAGCGGATATTTTCGACAAGGAAACTGGTCAAAAG                         GT-CCAGGTATTGTATTTGCACGAGGACCAGCTGTAGCTGTGCTTATTCTC
genomic: GATTTCTCAAATTCAAAGCGGATATTTTCGACAAGGAAACTGGTCAAAAGgtatctaatc ... acgtcattagGTTCCAGGTATTGTATTTGCACGAGGACCAGCTGTAGCTGTGCTTATTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtcattgtatatgttagttttgcttgccatatgtaagctaaaacgtcattagGTTCCAGGTATTGTATTTGCACGAGGACCAGCTGTAGCTGTGCTTATTCTCTTGGAGTCAGATGGTGAGACTTATGCGGTTCTCACTGAACAG
                                      agctaaa  putative branch site (score: 3)
          tatatgttagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctaatcatcttcaaaattagaatcatctcgctcgttgtggtcattgtatatgttagttttgcttgccatatgtaagctaaaacgtcattagGTTCCAGGTATTGTATTTGCACGAGGACCAGCTGTAGCTGTGCTTATTCTCTTGGAGTCAGATGGTGAGACTTATGCGGTTCTCACTGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG