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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatccttatttaccgtcttttaagttttatttccatcatttttcttattctacaatgataatattaaggaaagtataaatatatatgatttttttgccagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAGACAACATTGGTTGCACTTCAAGACATCACTCTGGAAAAGATTTTTGATG

Basic information

species Glycine max
transcript GLYMA04G09000.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G09000.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G32880.1 (Arabidopsis thaliana), 3'ss of exon 16
tatccttatttaccgtcttttaagt-tttatttccatcatttttcttattctacaatgataatattaaggaaagtataaatatatatgatttttttgccagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAGACAACATTGGTTGCACTTCAAGACATCACTCTGGAAAAGATTTTTGATG
     | |||| |   ||| ||     | |    ||||  || |  |  |  | |||    |||  |||||||||  || |   | ||||  |||        ||  || || ||||| ||||| || ||||||||  | |||||||| ||||| || ||||| ||||||||||| |||||||| || ||||| || |   
----gtaattttcttacttctactcactcaagaacatcgattatgctcatacataat--ctataacaaggaaagtg-aactggttttgatcatttcagGCCTTATCTCCGGTATTCACATTTGCGAACCAAGCTGGTTTAGACATGCTGGAGACGACGTTGGTGGCACTTCAAGATATCACTCTCGACAAGATCTTCG---

upper sequence: GLYMA04G09000.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv04s0008g03250.t01 (Vitis vinifera), 3'ss of exon 16
tatccttatttaccgtcttttaagttttatttccatcatttttcttattctacaatgataatatt-aaggaaagtataaata--tatatgatttttttgc-cagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAGACAACATTGGTTGCACTTCAAGACATCACTCTGGAAAAGATTTTTGATG
   | | |  ||  ||||||  |  | |  || | | || |||  | || |  |    ||||||| || || | | |||      ||  ||| | | |   |||||| | || ||||| || ||||||||||| || || |||||||||||||||||||| || || || ||||| || || |||||||| ||||  |||||||
--acttcaacta--gtctttgcatctctcattactttatatttgcttttgttaatgtttaatatttaaagacattctaacccatcatgcgatatctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAGACAACCTTAGTAGCCCTTCAGGATATAACTCTGGAGAAGACCTTTGATG
















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|15287384|gb|BI471275.1|BI471275
EST:     TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAG                         GCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAG
genomic: TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAGgttatttctt ... tttttgccagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAG
EST: gi|208186467|gb|GD983050.1|GD983050
EST:     CAAGTCCCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTACTTTAAAG                         GCATTACCCGTTTTCACG
genomic: CAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCT-CTTTAAAGgttatttctt ... tttttgccagGCATTACCCGTTTTCACG
EST: gi|208197450|gb|GD997173.1|GD997173
EST:     TCAAGTCCCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAG                         GCATTACCCGTTTTCA
genomic: TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAGgttatttctt ... tttttgccagGCATTACCCGTTTTCA
EST: gi|193362602|gb|FK325356.1|FK325356
EST:     TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAG                         GCATTAACCCGTTTTCACGTTTGCAA
genomic: TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAGgttatttctt ... tttttgccagGCATTA-CCCGTTTTCACGTTTGCAA
EST: gi|207773170|gb|GD743636.1|GD743636
EST:     TCAGATGCTAGTTTTTGTTGCTGCTCTTTAAAG                         GCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAG
genomic: TCAGATGC-AG-TTTTG-TGCTGCTCTTTAAAGgttatttctt ... tttttgccagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAG
EST: gi|208060371|gb|GD856223.1|GD856223
EST:     TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAG                         GCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTT
genomic: TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAGgttatttctt ... tttttgccagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTT
EST: gi|193356332|gb|FK323045.1|FK323045
EST:     TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAG                         GCATTACCCGTTTTCACGTTTGCAA
genomic: TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAGgttatttctt ... tttttgccagGCATTACCCGTTTTCACGTTTGCAA
EST: gi|26057413|gb|CA800327.1|CA800327
EST:     TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAG                         GCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAG
genomic: TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAGgttatttctt ... tttttgccagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAG
EST: gi|193356289|gb|FK320552.1|FK320552
EST:     TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAG                         GCATTACCCGTTTTCACGTTTGCAA
genomic: TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAGgttatttctt ... tttttgccagGCATTACCCGTTTTCACGTTTGCAA
EST: gi|193518039|gb|FK476968.1|FK476968
EST:     TCAAGTCTCTTTGGCATCACNCAGATGCAGTTTTGTGCTGCTCTTTAAAG                         GCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAG
genomic: TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAGgttatttctt ... tttttgccagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAG
EST: gi|208144355|gb|GD942106.1|GD942106
EST:     TCAAGTCCCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAG                         GCATTACCCGTTTTCACG
genomic: TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAGgttatttctt ... tttttgccagGCATTACCCGTTTTCACG
EST: gi|208269640|gb|GE071698.1|GE071698
EST:     TCAAGTCTCTTTGGCATCACTCGGATGCAGTTTTGTGCTGCTCTTTAAAG                         GCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAG
genomic: TCAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAGgttatttctt ... tttttgccagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAG
EST: gi|208314940|gb|GE115270.1|GE115270
EST:     CAAGTCCCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAAAG                         GCATTACCCGTTTTCACG
genomic: CAAGTCTCTTTGGCATCACTCAGATGCAGTTTTGTGCTGCTCTTTAAA-Ggttatttctt ... tttttgccagGCATTACCCGTTTTCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctacaatgataatattaaggaaagtataaatatatatgatttttttgccagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAGACAACATTGGTTGCACTTCAAGACATCACTCTGGAAAAGATTTTTGATG
                                           tttttttgcc  CT-rich tract
            ataatattaaggaaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatccttatttaccgtcttttaagttttatttccatcatttttcttattctacaatgataatattaaggaaagtataaatatatatgatttttttgccagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAGACAACATTGGTTGCACTTCAAGACATCACTCTGGAAAAGATTTTTGATG

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