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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgaactactcaaaacaatctctatatcttcatggcattcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT

Basic information

species Arabidopsis thaliana
transcript AT1G31880.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G17590.1 (Glycine max), 3'ss of exon 1
-gtatttgaactactcaaaacaatc----tctatatcttcatggcattcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
  |||    | ||  |||| ||       | | ||  ||    | | | ||   |     | |||  ||| ||| |||||   | |  | |   |||||| |||||||||||||| |||| |||||||||||| | |||||||||||||| || ||||  ||| | || |||||||| || |||||||||||    ||||||
aatataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggag-caaagactgacaatacttagcatttgaatttgaa-gCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT

upper sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G08070.1 (Glycine max), 3'ss of exon 3
-gtatttgaactactcaaaacaatc----tctatatcttcatggcattcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
  |||    | ||  |||| ||       | | ||  ||    | | | ||   |     | |||  ||| ||| |||||   | |  | |   |||||| |||||||||||||| |||| |||||||||||| | |||||||||||||| || ||||  ||| | || |||||||| || |||||||||||    ||||||
catataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggag-caaagactgacaatacttagcatttgaatttgaa-gCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT

upper sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G35180.1 (Glycine max), 3'ss of exon 1
---gtatttgaactact--caaaacaatctctatatcttcatggcattcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
    ||||   || | |   | |      | |   |  |      | | ||   |  |  | |||  ||| ||| |||||     |  | |   |||||| |||||||||| ||||| |||||||||||||||   |||||||||||||| |||||||  ||| | || |||||||| || |||||||| || || ||||||
tctttattcagaccattagtatataggaattttagttgttgaaaaagttaattgtccagtaggag-caaagactgacaatactaagcatttaaatttgaa-gCCGAGAGATTTTTGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT

upper sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G34600.1 (Glycine max), 3'ss of exon 3
---gtatttgaactactc--aaaacaatctctatatcttcatggcattcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
    ||||   || | |   | |  |   | |   |  |      | | ||   |  |  | |||  ||| ||| | |||   | |  | |   |||||| |||||||||| || || |||||||||||||||   |||||||||||||| |||||||  ||| | || |||||||| || |||||||| || || ||||||
tctttattgagaccatttgtatatgagaattttagttgttgaaaaagttaattatccagtaggag-caaagacttataatagttagcatttacatttgaa-gCCGAGAGATTTTCGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT

upper sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 2
--gtatttgaactact-caaaacaatctctatatcttcatggcattcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
    ||   ||||    |        ||| || |  |      ||     | |      |     |||    |  |  |  | |  |      ||  |||||| ||||||||| |||| ||||||||||| || |||||||| ||||| ||||||  |||| | ||||| |||||||| |||||||| ||||||||||||
tttcatagaaactgggactttggggcctcaatttgcttgaaatatcttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT

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|116385343|gb|EG427935.1|EG427935
EST:     TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAG                         CCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA
genomic: TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAGgtatttgaac ... gttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA
EST: gi|116385353|gb|EG427945.1|EG427945
EST:     TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAG                         CCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA
genomic: TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAGgtatttgaac ... gttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA
EST: gi|116385350|gb|EG427942.1|EG427942
EST:     TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAG                         CCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA
genomic: TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAGgtatttgaac ... gttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA
EST: gi|116385355|gb|EG427947.1|EG427947
EST:     TTTGCTTCTCTTCC-ACTGGAGGAA-TGATCTCAAACGGATCCGTTTCAG                         CCGAGAGATGTCTGATAAGTGGCAAAGCTCA
genomic: TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAGgtatttgaac ... gttttgaaagCCGAGAGATGTTTGATAAGTGGCAA-GCTCA
EST: gi|116385354|gb|EG427946.1|EG427946
EST:     TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAG                         CCGAGAGATGTCTGATAAGTGGCGAAGCTCAACGGTGGTGGGGTGAGAACT
genomic: TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAGgtatttgaac ... gttttgaaagCCGAGAGATGTTTGATAAGTGGC-AAGCTCAACGGTGGTGGGGTGAGAACT
EST: gi|116385340|gb|EG427932.1|EG427932
EST:     TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAG                         CCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA
genomic: TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAGgtatttgaac ... gttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA
EST: gi|116385341|gb|EG427933.1|EG427933
EST:     TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAG                         CCGAGGGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA
genomic: TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAGgtatttgaac ... gttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA
EST: gi|116385352|gb|EG427944.1|EG427944
EST:     TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAG                         CCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGA
genomic: TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAGgtatttgaac ... gttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGA
EST: gi|116385342|gb|EG427934.1|EG427934
EST:     TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAG                         CCGAGGGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGGTGAGAACT
genomic: TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAGgtatttgaac ... gttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGG-TGAGAACT
EST: gi|116385359|gb|EG427951.1|EG427951
EST:     TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAG                         CCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA
genomic: TTTGCTTCTCTTCCCACTGGAGGAAATGATCTCAAACGGATCCGTTTCAGgtatttgaac ... gttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
                       aactaac  putative branch site (score: 1)
                                         tcttgtttt  putative PPT
                  ataaaaactaacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgaactactcaaaacaatctctatatcttcatggcattcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT