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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccccttcccacccaaatgaagtgttagcgaagtatttttctttaagatattctatgtacaagttttgcttgaaactcgttaacatatgttctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGATCCAACGATCCAAGTTCTTTCTTAGTGGGAGTTCCAGATATTGAACTATG

Basic information

species Glycine max
transcript GLYMA11G01340.1
intron # 6
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|192326479|gb|FK017256.1|FK017256
EST:     GAAAACAAAGATGGATGTAATGCTCCAAAGTGTCATGAAAATAGAGAATG                         CTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGAT
genomic: GAAAACAAAGATGGATGTAATGCTCCAAAGTGTCATGAAAATAGAGAATGgtaatgcatt ... ctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGAT
EST: gi|51343237|gb|CO983970.1|CO983970
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
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccccttcccacccaaatgaagtgttagcgaagtatttttctttaagatattctatgtacaagttttgcttgaaactcgttaacatatgttctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGATCCAACGATCCAAGTTCTTTCTTAGTGGGAGTTCCAGATATTGAACTATG

- - - cccaccc
- - - - - - - - tgaagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - tatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catatgt