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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaccctaatttcattgagaaaaagctattttttaaaactctatgagcttttctagtgaaacttgtgagtaaattgaagaaaatttgggctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA

Basic information

species Arabidopsis thaliana
transcript AT5G51940.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G51940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 1
agaaaccctaatttcattgagaaaaag-ctattttttaaaactctatgagcttttctagt--gaaacttgtgagtaaattgaagaaaatttgggctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
   |||  ||   |   |||   |  |  | || | |   | | ||   | || | | ||  || | |  |     ||| | |    ||||   |   ||||| ||||||||||||||| |||| ||||||||||| 
-acaactatatgattgctgaagcactgattgttatatgtcattttaaaggattgttttgttggatattgattttggaatggcattgtatttt--cctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG

upper sequence: AT5G51940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv12s0028g01210.t01 (Vitis vinifera), 3'ss of exon 1
---agaaaccctaatttcattgagaaaaagctattttttaaaactctatgagcttttctagtgaaacttgtgagtaaattgaagaaaatttgggctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
          | | ||      |  ||    || |   |    || | | | |  ||  || |   ||| | | | |||  || ||| ||||   |  ||||||||||||||||| ||  |||||||||||||||||
tgtgtgtgtgcgagttggtaccaataactattaataaattttgctttgttatccatttaag-gtgccttattatttaatgaaacaaattttga--tgctgcagATATGAGGATGAACCTCCAGAGCCTGAGATTGAA

upper sequence: AT5G51940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0100g00530.t01 (Vitis vinifera), 3'ss of exon 3
agaaaccctaatttcattgagaaaaagct--attttttaaaactctatgagcttttctagtgaaacttgtgagtaaattgaagaaaatttgggctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
    |     ||| ||    | |  |  |  || |   |   || | ||   | || |||   |         |||||    ||  | ||  | |  ||||||||||||||||||||  |||||||||||||||||
--tcatgtagattacagaatgtaccatatgaatgtacaatggctatctgtaatattatagcatagtggaattttaaatatttgatgaattttgttgatgcagATATGAGGATGAGCCGCCAGAGCCTGAGATTGAA

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|86024724|gb|DR320477.1|DR320477
EST:     AAATCGACATTAATGGCTGRGGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCRGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86075593|gb|DR371350.1|DR371350
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024725|gb|DR320478.1|DR320478
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024718|gb|DR320471.1|DR320471
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024719|gb|DR320472.1|DR320472
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024716|gb|DR320469.1|DR320469
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024723|gb|DR320476.1|DR320476
EST:     AAATCGACATTAATGGCTGACGAAGATTACNACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024715|gb|DR320468.1|DR320468
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024714|gb|DR320467.1|DR320467
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024721|gb|DR320474.1|DR320474
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024722|gb|DR320475.1|DR320475
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024720|gb|DR320473.1|DR320473
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024726|gb|DR320479.1|DR320479
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024730|gb|DR320483.1|DR320483
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024729|gb|DR320482.1|DR320482
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024713|gb|DR320466.1|DR320466
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024728|gb|DR320481.1|DR320481
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024717|gb|DR320470.1|DR320470
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
EST: gi|86024727|gb|DR320480.1|DR320480
EST:     AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGG                         ATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
genomic: AAATCGACATTAATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGgttattctct ... gctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagcttttctagtgaaacttgtgagtaaattgaagaaaatttgggctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA
                          taaattgaagaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaaccctaatttcattgagaaaaagctattttttaaaactctatgagcttttctagtgaaacttgtgagtaaattgaagaaaatttgggctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
-gaaaccc
- - - - - - - - - -agaaaaa
- - - - - - - - - - - - - - - - - - aaaactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa