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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaaagaatgtttatctattttgcacaagagctcaagtttttttttttttttggtttctgatgtgagcaatttgttgcagCGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCATGATGACAATTGTTGATGACCTTGTGTCTGTGGACAACCTCATTGAAGACCATCT

Basic information

species Arabidopsis thaliana
transcript AT5G12110.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G12110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G44460.1 (Glycine max), 3'ss of exon 5
gtaagtcaaagaatgttta----tctattttgcacaa-----gagctcaagttttttt----ttttttttggtttctgatgt----gagcaatttgttgcagCGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCATGATGACAATTGTTGATGACCTTGTGTCTGTGGACAACCTCATTGAAGACCATCT
||| ||  ||   |    |    | | | ||||| |      |   | || || |||     ||    ||  | |   ||||    |    | ||| |  ||| ||| |||| ||||| || || ||||| |||||  |    ||||||||||| ||||||||||||||||| || ||||||| |||  |||| || |   |
gtatgttgaaattttcacaaacttttctcttgcatatttgatgcatttaatttctttcaaaattaccatttatctaaaatgttcttgtttcaattggtaaagCCAAACTGGTTCCTGTGGGATATGGGATCAAGAAGTTGCAGATCATGATGACTATTGTTGATGACCTTGTATCCGTGGACACCCTTGTTGAGGAACGCTT

upper sequence: AT5G12110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G44460.2 (Glycine max), 3'ss of exon 5
----gtaagtcaaagaatgtttatctattttgcacaagagctcaagttttttt-----ttttttttggtttctgatgt----gagcaatttgttgcagCGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCATGATGACAATTGTTGATGACCTTGTGTCTGTGGACAACCTCATTGAAGACCATCT
      |  |  |  ||  ||| |||    |     |    |  | ||| |||     ||    ||  | |   ||||    |    | ||| |  ||| ||| |||| ||||| || || ||||| |||||  |    ||||||||||| ||||||||||||||||| || ||||||| |||  |||| || |   |
gttgaaattttcacaaacttttctcttgcatatttgatgcatttaatttctttcaaaattaccatttatctaaaatgttcttgtttcaattggtaaagCCAAACTGGTTCCTGTGGGATATGGGATCAAGAAGTTGCAGATCATGATGACTATTGTTGATGACCTTGTATCCGTGGACACCCTTGTTGAGGAACGCTT

upper sequence: AT5G12110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G04350.1 (Glycine max), 3'ss of exon 5
-----gtaagtcaaagaatgtttatctattttgcacaagagctcaagttttttt----ttttttttggtttctgatgtgagca--atttgttgcagCGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCATGATGACAATTGTTGATGACCTTGTGTCTGTGGACAACCTCATTGAAGACCATCT
       |  |  |  ||  |||   |||||    ||     | || || |||     || | |||  | |   ||||  |    | ||| | |||| ||| | || || || || || || || |||||  |    ||||||||||| ||||||||||||||||| || |||||||  ||  |||| || |   |
gtatgaaattttcataaacttttgcatatttgatgca----tttaacttctttcaaaattatattttatctaaaatgtttgtttcaattggtacagCCAAACTAGTTCCCGTGGGATATGGTATCAAGAAGTTGCAGATCATGATGACTATTGTTGATGACCTTGTATCAGTGGACACTCTTGTTGAGGAACGCTT

upper sequence: AT5G12110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0009g02410.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------gtaagtcaaa---gaatgtttatctattttgcacaagagctcaagtttttttttttttttggtttctgatgtgagcaatttgttgcagCGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCATGATGACAATTGTTGATGACCTTGTGTCTGTGGACAACCTCATTGAAGACCATCT
                                           ||  | ||   ||   ||  | |||| |      || ||  |    |   |  ||  |   |  |  ||  |   |||||||||||| |||||||  || |||||||| |||||||||||| |    ||||||||||| ||||| ||||||||||| ||||||||   | | || ||||| |||||
gtatggtttgattattaatttaaacaccctttttccccccttcaaaccgaaattgaccattcttatattcttatgctgaccttgacaactgaatgcttggttaatagttgtgctatggatttgttgcagCAAAATTGGCTCCAGTTGGTTATGGGATAAAGAAATTGCAGATCATGATGACCATTGTGGATGACCTTGTCTCTGTGGATTCCGTTATAGAAGAGCATCT

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|124878255|gb|EH957692.1|EH957692
EST:     GCTGTTCGTAGTGTTCAGATGCCAGGTCTTACATGGGGAGCTT                         CGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCATGATGA
genomic: GCTGTTCGTAGTGTTCAGATGCCAGGTCTTACATGGGGAGCTTgtaagtcaaa ... tttgttgcagCGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCATGATGA
EST: gi|124776342|gb|EH866469.1|EH866469
EST:     ACATGGGGAGCTT                         CGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCAT
genomic: ACATGGGGAGCTTgtaagtcaaa ... tttgttgcagCGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCAT
EST: gi|19742318|gb|AU227671.1|AU227671
EST:     ATAAGAAGCTGTTCGTAGTGTTCAGATGCCAGGTCTTACATGGGGAGCTT                         CGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCATGATGA
genomic: AGAAGAAGCTGTTCGTAGTGTTCAGATGCCAGGTCTTACATGGGGAGCTTgtaagtcaaa ... tttgttgcagCGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCATGATGA
EST: gi|164047457|gb|ES067806.1|ES067806
EST:     AGAAGAAGCTGTTCGTAGTGTTCAGATGCCAGGTCTTACATGGGGAGCTT                         CGAAATTGGTACCTGTTGGTTACGGGATAAAGAAAC
genomic: AGAAGAAGCTGTTCGTAGTGTTCAGATGCCAGGTCTTACATGGGGAGCTTgtaagtcaaa ... tttgttgcagCGAAATTGGTACCTGTTGGTTACGGGATAAAGAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagagctcaagtttttttttttttttggtttctgatgtgagcaatttgttgcagCGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCATGATGACAATTGTTGATGACCTTGTGTCTGTGGACAACCTCATTGAAGACCATCT
                              ttctgat  putative branch site (score: 3)
         aagttttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaaagaatgtttatctattttgcacaagagctcaagtttttttttttttttggtttctgatgtgagcaatttgttgcagCGAAATTGGTACCTGTTGGTTACGGGATAAAGAAACTCACAATCATGATGACAATTGTTGATGACCTTGTGTCTGTGGACAACCTCATTGAAGACCATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA