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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccccttcccacccaaatgaagtgttagcgaagtatttttctttaagatattctatgtacaagttttgcttgaaactcgttaacatatgttctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGATCCAACGATCCAAGTTCTTTCTTAGTGGGAGTTCCAGATATTGAACTATG

Basic information

species Glycine max
transcript GLYMA11G01340.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G01340.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G128080_T02 (Zea mays), 3'ss of exon 6
ccccttcccacccaaatgaagtgttagcgaagtatttttctttaagatattctatgtacaagttttg---cttgaaactcgttaacatatgttctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGATC--CAAC-GATCCAAGTTCTTTCTTAGTGGGAGTTCCAGATATTGAACTATG
 |  |||        || | ||   |  |  |   |||| || || | ||  |   |||| | |  |   | |  ||||  ||  |||||| |  |  |  |||||||||  |||||||||||||||| |||||||| ||||| || || | |||  || | |||||| | | ||  |   | || |  || ||  |||| |    
tctattcttgatttgatta-gttcaattgctggcatttttttaaacagatagtcattacatgctgagaaacatttaact--tttgcatatgcttgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAATCATCAGCAGATCCAGGCTATTCTTATTTTGGTGCCCCGGACTTTGATCA---

upper sequence: GLYMA11G01340.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G03780.1 (Arabidopsis thaliana), 3'ss of exon 6
ccccttcccacccaaatgaagtgttagcgaagtatttttctttaagatattctatgtacaagttttgcttgaaactcgttaacatatgttctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGATCCAACGATCCAAGTTCTTTCTTAGTGGGAGTTCCAGATATTGAACTATG
          | |||||    | |  ||  | ||||        |||||  | |   | | ||||   ||| ||||| ||    | ||||  ||   ||||||||||| | ||||| |||||||| | ||||||||||||||| ||||||   || |  ||||  || | | || |||||| | | ||| | |||  || 
-----gtatgcacaaatctcatatccgcacactatt--------agatac-caaccaatacgttt---ttgtaactcttttttgtttgtttgtttattagCTTGCTTTAGCGTTCACGTGAGAGGATTAGAGTATATTCCACTGCTTGGAGATAATGCACCAACATCATACCTATTGGGAGCTGCTGATGTCGAATGATT

upper sequence: GLYMA11G01340.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0010g00580.t01 (Vitis vinifera), 3'ss of exon 6
-ccccttcccacccaaat-gaagtgttagcgaagtatttt-tctttaagatattctatgtacaagttttgcttgaaactcgttaacatatgttctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGATCCAACGATCCAAGTTCTTTCTTAGTGGGAGTTCCAGATATTGAACTATG
  |  ||   ||    || |  |   |   | ||||     | ||    ||| | | |  ||  ||  ||  |    || ||| | ||||||| || |||||||||||||| |||| |||||||| || ||||||||| ||| ||| |  |||||||  ||||| ||||   | ||| ||||  | || ||    ||| ||||
ttcttttttgacatgcattgctgctctcatgcagtagacagtgttctgaataatttctaaacttgtactgaatc--ccttgttta-atatgttgttaatgtagCTTGCTTTAGTGTCCATGTGAGGGGATCAGAGTATGTTCAACTGCCCGGATCCAGTGATCCCAGTTACCTTTTATTGGGGATGCCTGACCACGAAATATG

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|51343237|gb|CO983970.1|CO983970
EST:     GAAAACAAAGATGGATGTAATGCTCCAAAGTGTCATGAAAATAGAGAATG                         CTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGAT
genomic: GAAAACAAAGATGGATGTAATGCTCCAAAGTGTCATGAAAATAGAGAATGgtaatgcatt ... ctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGAT
EST: gi|192294418|gb|FG987347.1|FG987347
EST:     GAAAACAAAGATGGATGTA-TGCTCCAAAGTGTCATGAAAATAGAGA-TG                         CTTGCTTTGGTGT-CATGTGAGAGGGTCAGAGTATATTC
genomic: GAAAACAAAGATGGATGTAATGCTCCAAAGTGTCATGAAAATAGAGAATGgtaatgcatt ... ctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTC
EST: gi|192326479|gb|FK017256.1|FK017256
EST:     GAAAACAAAGATGGATGTAATGCTCCAAAGTGTCATGAAAATAGAGAATG                         CTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGAT
genomic: GAAAACAAAGATGGATGTAATGCTCCAAAGTGTCATGAAAATAGAGAATGgtaatgcatt ... ctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGAT
EST: gi|151394898|gb|EV264769.1|EV264769
EST:     GAAAACAAAGATGGATGTAATGCTCCAAAGTGTCATGAAA-TAGAGA-TG                         CTTGCTTTGGTGTTCATGTGAGAGGGTCA
genomic: GAAAACAAAGATGGATGTAATGCTCCAAAGTGTCATGAAAATAGAGAATGgtaatgcatt ... ctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattctatgtacaagttttgcttgaaactcgttaacatatgttctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGATCCAACGATCCAAGTTCTTTCTTAGTGGGAGTTCCAGATATTGAACTATG
                               cgttaac  putative branch site (score: 3)
                                         tgttcttt  putative PPT
                                 ttaacatat  TA-rich tract