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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactggaagtctgaaacaatttgcgccttatttctccccttcaatttgattgttttcctcctgcttttgcttttattccaatttctcacatttttgtttcaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT

Basic information

species Glycine max
transcript GLYMA08G02940.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 3
gtaactggaagtctgaaacaatttgcgccttatttctccccttcaatttgattgttttcctcctgc--ttttgcttttattccaatttctcacattt-ttgtttcaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
                        |    | ||  |    | |  || || ||  ||  |||  ||  |  | || |     | ||| ||||| | |  | |||||  |   |||| ||||||||||| || ||||||||||| ||||||||||| |||||||||||||| || ||||||||||| || ||||| || || ||||| ||||| ||
------------------------gttagtaatgacaagacattcatgtgcttagttaactcaagcggtgattctgtggaagccattgctcacttctgctctttcatgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTGCTGGCCTGAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 3
gtaactggaagtctgaaacaatttgcgccttatttctccccttcaatttgattgttttcctcctgcttttgcttttattccaatttctcacatttttgtttcaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
     | | |  ||||| || | |||   |||  |||     |   | ||       |     ||   | ||||       | || || |  ||||  |||        |||| |||||||||||||| ||||||||||| ||||||||||||||||||||||| || |||||||||||||| || ||||| || || ||||| ||||| ||
---gttagtaa-ctgaaccattctgctggttacctctagtagttgttatg-------taaaaatgtggtggctt-------acttccttatgttttgttttt-----tgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 3
gtaactggaagtctgaaacaatttgcgccttatttctccccttcaatttgattgttttcctcctgcttttgcttttattccaatttctcacatttttgtttcaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
     | | |  |||||  | | |||   |||  |||           |  ||||| |       | |      | | | |  | | |    ||||| |          |||| |||||||||||||| ||||||||||| ||||||||||||||||||||||| || |||||||||||||| || ||||| || || ||||| ||||| ||
---gttagtaa-ctgaacaattctgctggttacctctag---------tagttgttatgtaaaaacgtggcggctcacttccttgtgttgtgttttttt---------gcagCGTACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaactggaagtctgaaacaatttgcgccttatttctccccttcaatttgattgttttcctcctgcttttgcttttattccaatttctcacatttttgtttcaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
                   | ||||    |||| | |    |  |     ||  || |  ||    ||| |   ||  |    | | |    ||||||  |    |||  ||||||||||||||||||||| ||||| || || |||||||||||||| |||||||| ||||||||||||||||| || || ||||| ||||| ||||| ||
----------------gttagtttgt-tgttatatatgtggtggagaggtatctttattatctgtatttggtgattgattgtttatttggtgtttttgactt---tgcgtagCTTACTTCAATGATGCTCAAAGGCAAGCTACTAAGGATGCTGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATTAATGAACCTACTGCTGCTGCTAT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaactggaagtctgaaac-aatttgcgccttatttctccccttcaatttgattgttttcctcctgcttttgcttttattccaatttctcacatttttgtttcaa-atgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
      |  ||| ||     |||| | |  || | |      |  | |       |     || |   | |  |  |  |   |||  | |  ||  ||||| |  |||| |||||||||||||||||||||| ||||| || ||||||||||| ||||| |||||||| ||||||||||||||||| ||||||||||| ||||| ||||| ||
------gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgatt-gattgtttat-ttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtaactggaa-gtctgaaacaatttgcgccttatttctccccttcaatttgattgttttcctcctgcttttgcttttattccaatttctcacatttttgtttca---aatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
                ||  |  || || |||     |   |  |    ||   | ||||  ||  | |||       |   || | | ||        || |||| |||    || ||   ||  | ||||||||||||||||||| ||||||||||| || ||||||||||| || |||||||| || ||||||||  ||||||| || || || ||||| || || ||
gtgagtatcactcttctagatataacgtgtgaggttttgaactgcccgcttacactcttc--ttgaaatgtgaattagcattttgttcattaggatgttttactcatattagctttccatgcaacccgcagCTTACTTCAATGATGCCCAGAGGCAGGCTACAAAGGATGCTGGCGTTATTGCTGGCCTGAATGTTGCACGAATTATTAATGAGCCAACTGCTGCAGCTAT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
gtaactggaagtctgaaacaatttgcgccttatttctccccttcaatttgattgttttcctcctgcttttgcttttattccaatttctcacatttttgtttcaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
       | | | | ||||| ||||    ||  |        | ||||    |||||| ||  ||   |  ||| | || | ||| || |||  ||            |||||||||||||||||||| ||||||||||||||||||||||| ||  | |||||||| || |||||||| ||||| ||||| ||||| || || || |||||
-------gtaatgtaaaacagtttga--tttgatggatgaagtaaatt--gctgtttttctgttgagatgacttatgtttctatt-cttacaacttc----------tacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ17607 (Selaginella moellendorffii), 3'ss of exon 3
gtaactggaagtctgaaacaatttgcgccttatttctccccttcaatttgattgttttcctc-ctgcttttgcttttattccaatttctcacatttttgtttcaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
                                                |  |  ||   ||   || || |  |   | ||  | || | ||  |  | ||    |||  |||| ||||||||||| || ||||||||||| || |||||||| |||| ||| || || || ||||| ||| | ||||||||||| |||||||| || || ||
-----------------------------------------------gtactcattcatctagttgtttgttttccaaatcatagtttttac--tgatcttctcgatg-gcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCGCCGGACTGAATGTGGCTCGTATTATCAACGAGCCCACTGCGGCAGCAAT

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 3
gtaactggaagtctgaaacaatttgcgccttatttctccccttcaatttgattgttttcctc-ctgcttttgcttttattccaatttctcacatttttgtttcaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
                                                |  |  ||   ||   || || |  |   | ||  | || | ||  |  | ||    |||  |||| ||||||||||| || ||||||||||| || |||||||| |||| ||| || || || ||||| ||| | ||||||||||| |||||||| || || ||
-----------------------------------------------gtactcattcatctagttgtttgttttccaaatcatagtttttac--tgatcttctcgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCGCCGGACTGAATGTGGCTCGTATTATCAACGAGCCCACTGCGGCAGCAAT

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|16284366|gb|BI946046.1|BI946046
EST:     GGAAGCATTCCTCGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAG                         CTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
genomic: GGAAGCATTCCTCGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaa ... aaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
EST: gi|254343099|gb|GR859261.1|GR859261
EST:     GGAAGCATTCCTCGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAG                         CTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
genomic: GGAAGCATTCCTCGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaa ... aaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
EST: gi|254341733|gb|GR852870.1|GR852870
EST:     GGAAGCATTCCTCGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAG                         CTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
genomic: GGAAGCATTCCTCGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaa ... aaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
EST: gi|16284523|gb|BI946135.1|BI946135
EST:     GGAAGCATTCCTCGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAG                         CTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
genomic: GGAAGCATTCCTCGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaa ... aaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
EST: gi|298177863|gb|HO027416.1|HO027416
EST:     GGAAGCATTCCTCGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAG                         CTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
genomic: GGAAGCATTCCTCGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaa ... aaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcctgcttttgcttttattccaatttctcacatttttgtttcaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
                           ttctcac  putative branch site (score: 2)
                                  atttttgtttcaaat  TA-rich tract