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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtaagattatgctttgtgttagtggtttattactgggatttcttattttgatgaaaattgtgaaatgagatggaacagatttttgtttcttatatttattggcttgtcaggcaagtcttctcagcttgccgtccatagttttattgtgctgacaggggtgtttcatccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAGCTTGGCTGAAAAATTGAACACAGCTGCTCAGATTCTGTGATTCTTCCGC

Basic information

species Glycine max
transcript GLYMA18G03340.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G03340.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 5
ggtaagattatgctttgtgttagtggtttattactgggatttcttattttgatgaaaattgtgaaatgagatggaacagatttttgtttcttatatttattg-gcttgtcaggcaagtcttctcagcttgcc--gtccatagttttattgtgctgacaggggtgtttcatccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAGCTTGGCTGAAAAATTGAACACAGCTGCTCAGATTCTGTGATTCTTCCGC-
                                                                                 | ||| ||||     || ||| | |||       |     | ||  ||||   ||  ||       |     |||      | |    |   ||  |||| ||||| ||  | ||||| || || || |||||||| || ||||| ||||| || ||||| ||||||||||||||||| || | || |  | |   | 
-------------------------------------------------------------------------------tctgttgcttctgtccattgttgtgtttgatcattgaaaacccacaatttgcatggtttatctcaccgtaaaaatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA
















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|192333945|gb|FK024758.1|FK024758
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|254317274|gb|GR826219.1|GR826219
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|208339064|gb|GE139288.1|GE139288
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCT
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCT
EST: gi|193516845|gb|FK472973.1|FK472973
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|214003981|gb|DB985250.1|DB985250
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|209700663|gb|BW670452.1|BW670452
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|21675436|gb|BQ627787.1|BQ627787
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|193699661|gb|FK640354.1|FK640354
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|209728076|gb|BW655309.1|BW655309
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|254317273|gb|GR826218.1|GR826218
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|193404924|gb|FK375451.1|FK375451
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|193645433|gb|FK590835.1|FK590835
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|193318580|gb|FK287152.1|FK287152
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|31466038|gb|CD408066.1|CD408066
EST:     CCCGAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACTAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|209713286|gb|BW684373.1|BW684373
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|209718437|gb|BW666249.1|BW666249
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|209705150|gb|BW667782.1|BW667782
EST:     CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCA                         GGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAG
EST: gi|151393162|gb|EV263037.1|EV263037
EST:     CCCAAATTGTCCCCATCAGTTTT-GATAAGCTTGTGAATGACAGTTTGCA                         G-ATCACTTGCTTTTGCTG
genomic: CCCAAATTGTCCCCATCAGTTTTTGATAAGCTTGTGAATGACAGTTTGCAggtaagatta ... atccatttcaGGATCACTTGCTTTTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcagcttgccgtccatagttttattgtgctgacaggggtgtttcatccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAGCTTGGCTGAAAAATTGAACACAGCTGCTCAGATTCTGTGATTCTTCCGC
                           tgctgac  putative branch site (score: 2)
                                         tttcatcc  putative PPT
               atagttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaagattatgctttgtgttagtggtttattactgggatttcttattttgatgaaaattgtgaaatgagatggaacagatttttgtttcttatatttattggcttgtcaggcaagtcttctcagcttgccgtccatagttttattgtgctgacaggggtgtttcatccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAGCTTGGCTGAAAAATTGAACACAGCTGCTCAGATTCTGTGATTCTTCCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT