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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaccctcaagttttgaatttcacgatttctgaaactgttcgaacgaaaatcagaagaaaaaaaattgggttgaaattggtttctcaaattgcgggggggatgggaataaaaagctagggttttgttagagaagggttgaagatttatcatgattttaactgaagtgctgtgtgtgtttgtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGTACTACGACTCTTGCTTTTATATTTAAGGAGGGTGTTATGGTAGCTGCTG

Basic information

species Glycine max
transcript GLYMA06G17960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17960.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagtaccctcaagttttgaatttcacgatttctgaaactgttcgaacgaaaatcagaagaaaaaaaattgggttgaaattggtttctcaaattgcgggggggatgggaataaaaagctagggttttgttaga----gaagggttgaagatttatcatgattttaac-tgaagtgctgtgtgtgtttgtggtga------tagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGTACTACGACTCTTGCTTTTATATTTAAGGAGGGTGTTATGGTAGCTGCTG
                                                                                                   | | | |     ||  ||  ||| ||| | |  ||     |     |     |||    | |||| |   |||  || ||  | ||||||| ||        ||||| |||||||||  |||| ||||| |  ||||||||||||| || |||||||| || || ||||| ||||| |||||||| |||||||||||||||||||
---------------------------------------------------------------------------------------------------gtgagttttagttacgaaattagagttctttcggattccaatatactttgattttgcttttatttgattgtgatatgttgcttttgtttgttgttggttttttagTTTGATGGGTTTCAGAAAAAAGCTGTGGAGATGGTGAAGCCTGCAAAGGGTACAACTACACTTGCGTTTATCTTTAAGGAAGGTGTTATGGTAGCTGCTG

upper sequence: GLYMA06G17960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtaccctcaagttttgaatttcacgatttctgaaactgttcgaacgaaaatcagaagaaaaaaaattgggttgaaattggtttctcaaattgcgggggg----gatgggaataaaaagctagggttttgttagagaagggttgaagatttatcatgattttaactgaagtgctgtgtgtgtttgtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGTACTACGACTCTTGCTTTTATATTTAAGGAGGGTGTTATGGTAGCTGCTG
                                                      | ||     | | | |||  ||  |||     | ||||         ||      | |||||   | |  |   |||  ||    |    ||  ||| | |  | |      ||||||        ||| ||     |   |||| |||||||||  |||||| |||||||| ||||||||||| || ||||| || || |||||||| || || |||||||||||||| ||||| |||||||
-----------------------------------------------------gtgagttctgatacatttgatttagaatcttcctatcaatgaaaaaaaggctcaatttggaatgtgatgtcacactttcctttagtagaaatt--agaatcagtaggg-----actgaaa------atgttttccctttttcagTTTGATGGGTTTCAGAAAGATGCTATTCAAATGGTGAAGCCAGCAAAGGGAACAACAACTCTTGCCTTCATTTTTAAGGAGGGTGTAATGGTTGCTGCTG
















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|57574193|gb|CX547168.1|CX547168
EST:     CGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: CGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|192326892|gb|FK015134.1|FK015134
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|192317518|gb|FK008970.1|FK008970
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|209696468|gb|BW664017.1|BW664017
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|151396982|gb|EV266855.1|EV266855
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCACATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|208141894|gb|GD939582.1|GD939582
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCGGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|6502012|gb|AW203385.1|AW203385
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|209722634|gb|BW682710.1|BW682710
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|57574361|gb|CX547336.1|CX547336
EST:     GACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: GACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|207685792|gb|GD669124.1|GD669124
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|9440180|gb|BE440690.1|BE440690
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|17023638|gb|BM094672.1|BM094672
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|120532998|gb|EH261131.1|EH261131
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|298182845|gb|HO031580.1|HO031580
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|254332573|gb|GR846511.1|GR846511
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|120533057|gb|EH261190.1|EH261190
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|209710868|gb|BW653629.1|BW653629
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|193585349|gb|FK539028.1|FK539028
EST:     CTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: CTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|298181007|gb|HO022446.1|HO022446
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTACCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|4314044|gb|AI461163.1|AI461163
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|213599779|gb|DB968429.1|DB968429
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
EST: gi|19345836|gb|BM890716.1|BM890716
EST:     TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGAT                         TTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT
genomic: TTGGAGAACTCTCCGCCGCTCCATCCTTCGACCTTCCGAATTCCAACGATgtgagtaccc ... gtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgaagatttatcatgattttaactgaagtgctgtgtgtgtttgtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGTACTACGACTCTTGCTTTTATATTTAAGGAGGGTGTTATGGTAGCTGCTG
                   ttttaac  putative branch site (score: 2)
        atttatcatgatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaccctcaagttttgaatttcacgatttctgaaactgttcgaacgaaaatcagaagaaaaaaaattgggttgaaattggtttctcaaattgcgggggggatgggaataaaaagctagggttttgttagagaagggttgaagatttatcatgattttaactgaagtgctgtgtgtgtttgtggtgatagTTCGATGGGTTTGTGAAAGAAGCTATTCAGATGGTGAAGCCCGCGAAGGGTACTACGACTCTTGCTTTTATATTTAAGGAGGGTGTTATGGTAGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT