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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtactctatccatttattggcttttttgtttctctgtttttggttttgacttggtcaatcttgatttgtcttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG

Basic information

species Arabidopsis thaliana
transcript AT3G51240.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G51240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g56700.1 (Oryza sativa), 3'ss of exon 2
gttagtactctatccatttattggcttttttgtttctctgtttttggttttgacttggtcaatcttgatttgtcttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG
|| ||||||    |||   | ||  |  || ||   | |||||| | |  ||  |   | |  |   || ||   |  || ||| | |||||||||||||||||||||| || ||||| ||||| |||||||||||  |||   || |  | || || || |||||||||||||| |||||||
gtgagtactacggccac--actgtatccttggtgattttgttttagatcatgcatctcttaggc--aatgtgaact--tgcagTATCTGAGCAATGGGAGGTTCAAGAACGCGGATCACCAGGCGGTGGTGAACTCCGACTGCTGCCGGCTGTCGATCGCGACGTTCCAGAACCCGGCGCCGG

upper sequence: AT3G51240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G23880.1 (Glycine max), 3'ss of exon 2
--------gttagtactctatccatttattggctttt--ttgt-ttctctgtttttggttttgacttggtcaa-tcttgatt-----tgtcttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG
          |  || | |   ||   |  |||||||    || | || ||||||   |  | | ||  |||| | |||  |     ||  |  ||| ||| | |||||||||| |||||||||| |||||||||||| || ||||||||||| |||   ||| | || |||||||||||||| || ||||| |  ||  
attaattttattttatttttatcaagcaagggcttttgaccgtgtactttgttttccataataatttattcaaattttgggtgtgggtgcatccatgcagTATCTGAGCAATGGAAGGTTCAAGAGTGCTGATCATCAAGCGGTGGTGAACTCAAACCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCTGTACCAA

upper sequence: AT3G51240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G37120.1 (Glycine max), 3'ss of exon 2
gttagtactctatccatttat------tggcttttttg-tttctctgtttttggttttga-----cttggtcaatct-------tgatttgtct-tgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG
   | || |   |||||||||      |  |||||||  |||||   | | |  |  |||      |   | ||| |       | |  | | | ||||| ||| | |||| ||||| |||||||||||||||||||| || || ||||||||||| | ||  ||| |  ||||||||||||| ||||| ||||| || |  |
---aatatttcttccatttatgatatttaactttttttctttctacctatctattactgagagaattcaattaatttatgcgggtaacatatttgtgatgcagTATCTGAGTAATGGAAGGTTCAAGAATGCTGATCACCAAGCAGTGGTGAACTCAAGCTGCAGCCGTGTATCCATAGCCACATTCCAAAACCCAGCACAAG

upper sequence: AT3G51240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G05450.2 (Glycine max), 3'ss of exon 2
-----gttagtactctatccatttattggcttttttgttt-ctctgtttt---tggttttgacttggtcaatctt--------gatttgtcttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG
      |||  |  |      | |||||| ||    || | || ||||||   |  |||  | ||| ||| | ||        | |     |  ||| ||| | |||||||||| |||||||||||||||||||| || || ||||||||||| |||   ||| | || ||||||||||| || || ||||| || ||  
ttatttttatgaagcagcaagtctattggtttgaccgtgtactttgtttttcataatttaaatttgttcatttttttgtggtgggtgcacatgaatgcagTATCTGAGCAATGGAAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCAAACCATAGCCGTTTGTCCATAGCCACTTTTCAAAACCCAGCACCAA

upper sequence: AT3G51240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G05470.1 (Glycine max), 3'ss of exon 2
----------gttagtactctatccattta-ttggcttttttgtttctctgtttttggttttgacttggtcaatcttgatt------tgtcttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG
             || |     || ||||  || |    | |  ||   | ||  |  |||  | ||| ||| | ||   |      ||  |  ||| ||| | ||| |||||| |||||||||||||||||||| || || ||||||||||| ||    ||| | || |||||||||||||| || ||||| || ||  
tttatttttatgaagcagcaagtctatttggtttgaccgtgtactttgtttttcataatttaaatttgttcatttttttgtggtgggtgcatgaatgcagTATCTGACCAATGGAAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCAAATCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCAGCACCAA

upper sequence: AT3G51240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g14310.t01 (Vitis vinifera), 3'ss of exon 2
gttagtact--ctatccatttattggcttttttgtttctctgtttttggttttgact--------tggtcaatcttgatttgtcttgatga----agTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG
|| |||| |   | ||   |||||    |||| | ||| |  |    ||    || |        |  | ||   ||  ||   |||| |     ||| | ||||||||||||||||||| ||||| || || || || |||||||||||  |||  ||  | || || || ||||||||||||||||| || || |
gtgagtagtgattctctgcttattcctcttttggattccccatcgaaggggcagaataatataattaattaactctgcattcgattgacgtgggcagTATCTGAGCAATGGGAGGTTCAAAAATGCGGACCACCAAGCTGTGGTGAACTCCGACTGCAGTCGGTTGTCGATTGCCACGTTCCAGAACCCAGCCCCAG

upper sequence: AT3G51240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0023g03370.t01 (Vitis vinifera), 3'ss of exon 2
---------------gttagtactctatccatttattggcttttttgtttctctgtttttggttttgacttg---gtcaatcttgatttgtcttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG
                  | || ||  |||   ||| ||  ||    ||  |               |   |   || | | ||| ||||   || || ||| | ||||||||||||||||||||||||||||||| || || ||||||||||| ||    |||||| | |||||||| || ||||| |||||||| ||||
tatgtggtcaacatccacaatagtccttcctgatat-ggtattcaaattcatgctacccgaacccgaaagagagagtgattattggtttggtatggtgcagTATCTGAGCAATGGGAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCCAATCATAGCAGACTGTCCATAGCAACATTCCAAAACCCCGCACCGG

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|116450515|gb|EG493107.1|EG493107
EST:     TTCAGCCTGTTGAAGGAGCGTTTGTCGTCAATCTCGGCGACCACGGCCAT                         TTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAAC
genomic: TTCAGCCTGTTGAAGGAGCGTTTGTCGTCAATCTCGGCGACCACGGCCATgttagtactc ... cttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAAC
EST: gi|86080026|gb|DR375783.1|DR375783
EST:     TTCAGCCTGTTGAAGGAGCGTTTGTCGTCAATCTCGGCGACCACGGTCAT                         TTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAAC
genomic: TTCAGCCTGTTGAAGGAGCGTTTGTCGTCAATCTCGGCGACCACGGCCATgttagtactc ... cttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttctctgtttttggttttgacttggtcaatcttgatttgtcttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG
                                        tttgtctt  CT-rich tract
          tgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtactctatccatttattggcttttttgtttctctgtttttggttttgacttggtcaatcttgatttgtcttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT