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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaagaacaaaacatgaaagtctatagataacgaaatagtcaaagaagaagactcactagagtttcttcatgcagGCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGCTTCGTGGTGGGTTATGGAGACAAATACCCACAATTTGTGCATCATAGAGGAGCTTCGATCC

Basic information

species Arabidopsis thaliana
transcript AT1G75680.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G75680.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G02760.1 (Glycine max), 3'ss of exon 5
-------gtaacaagaacaaaacatg-aaagtctatagataacgaaata-gtcaaagaagaagactcactagagtttcttcatgcagGCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGCTTCGTGGTGGGTTATGGAGACAAATACCCACAATTTGTGCATCATAGAGGAGCTTCGATCC
        | |  |  |     |    ||  ||||     |  ||     ||  ||   ||| |   | |  | |   ||||    |||||||||| |  |||| ||||||||  ||   | ||| ||  ||||||| |||||||| |||||||||||||||||||||||||| || ||||| || |
gtgtgcattcattattattttgctcacaatatctacttggagtgatccgtgtttaaattgaaaatcta-tgtaatactttca----gGCTGATTACGTATTGGGCAAGAATCCTATGCATATGAGTTTTCTGGTGGGCTATGGAGATAAATACCCACAATTTGTGCATCATAGGGGTGCTTCAATTC

upper sequence: AT1G75680.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G02740.1 (Glycine max), 3'ss of exon 5
--------gtaacaagaacaaaacatgaaagtctatagataacgaaata-gtcaaagaagaagactcactagagtttcttcatgcagGCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGCTTCGTGGTGGGTTATGGAGACAAATACCCACAATTTGTGCATCATAGAGGAGCTTCGATCC
          |  |  |     |||    | |||      |  ||     ||  ||   ||| |   | |  | |   ||||    |||||||||| |  |||| ||||||||  ||   | ||| ||  ||||||| |||||||| |||||||| ||||||||||||||||| || ||||| || |
gtatgcatccattattatttgcacacatta-tctgcttggagtgatccgtgtttaaattgaaaatcta-tgtaatactttca----gGCTGATTACGTATTGGGCAAGAATCCTATGCATATGAGTTTTCTGGTGGGCTATGGAGATAAATACCCTCAATTTGTGCATCATAGGGGTGCTTCAATTC
















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|164156513|gb|ES149783.1|ES149783
EST:     ACGGG-AAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAG                         GCTGATTACATGCTGGGGAAGAATCCGCTGGGAACGAGC
genomic: ACGGGAAAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAGgtaacaagaa ... cttcatgcagGCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGC
EST: gi|47831716|gb|CK121400.1|CK121400
EST:     ACGGGAAAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAG                         GCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGCTTCGTGGTGGGT
genomic: ACGGGAAAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAGgtaacaagaa ... cttcatgcagGCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGCTTCGTGGTGGGT
EST: gi|86085998|gb|DR381757.1|DR381757
EST:     ACGGGAAAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAG                         GCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGCTTCGTGGTGGGT
genomic: ACGGGAAAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAGgtaacaagaa ... cttcatgcagGCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGCTTCGTGGTGGGT
EST: gi|164223078|gb|ES159305.1|ES159305
EST:     ACGGGAAAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAG                         GCTGATTACATGCTGGGGAAGAATCC
genomic: ACGGGAAAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAGgtaacaagaa ... cttcatgcagGCTGATTACATGCTGGGGAAGAATCC
EST: gi|164138745|gb|ES089403.1|ES089403
EST:     ACGGGAAAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAG                         GCTGATTACATGCTGGGGAAGAATCCGCTGGGAACGAGCTTCG
genomic: ACGGGAAAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAGgtaacaagaa ... cttcatgcagGCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGCTTCG
EST: gi|164184371|gb|ES036966.1|ES036966
EST:     ACGGGAAAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAG                         GCTGATTACATGCTGGGGAANAATCCGCTGGGAACGAGCTTCGTGGTGGGT
genomic: ACGGGAAAATCTTCAAAGCAACAGAGCTTAGAGATTTCGCCAAATCGCAGgtaacaagaa ... cttcatgcagGCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGCTTCGTGGTGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatagataacgaaatagtcaaagaagaagactcactagagtttcttcatgcagGCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGCTTCGTGGTGGGTTATGGAGACAAATACCCACAATTTGTGCATCATAGAGGAGCTTCGATCC
                              gactcac  putative branch site (score: 2)
                                          tttcttcat  putative PPT
             aaatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaagaacaaaacatgaaagtctatagataacgaaatagtcaaagaagaagactcactagagtttcttcatgcagGCTGATTACATGCTGGGGAAGAATCCGTTGGGAACGAGCTTCGTGGTGGGTTATGGAGACAAATACCCACAATTTGTGCATCATAGAGGAGCTTCGATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT