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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacatttggaatcctaaagggaggtcaatgtaatttattatttgcattatctttaaatgtataaggaaagaaacatgaatccaatagtttcaatttccagGTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCTCGCCATCTTGCTCAACGATATAGTCGGATGAGACAAGAAGCAGAGGCAC

Basic information

species Glycine max
transcript GLYMA05G29700.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G29700.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G18060.1 (Arabidopsis thaliana), 3'ss of exon 4
gacatttggaatcctaaagggaggtcaatgtaat-ttattatttgcat-tatctttaaatgtataaggaaagaaacatgaatccaatagtttcaatt--tccagGTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCTCGCCATCTTGCTCAACGATATAGTCGGATGAGACAAGAAGCAGAGGCAC
    || ||    ||      |  |   | |||| ||| ||| |  |  ||   |||||| ||  ||  || ||     || |   | |||  |     |  |||| ||||||||| | |||   ||| |    |||  |||| | || |||||||| |||||||||||||| || || || |||||||||||||||||| |||
---gttcgg----cttggattatctgtgtttaatcttagtatgtttacgtagaattaaatctagtagataacaagagaaaacctttttgttaaatgccgttaagGTTTTGGATCCTCTAAGAGCTATGGTTGCCGGTTCTCCTCTTGAAGATGCTCGTCATCTTGCTCAACGTTACAGCCGCATGAGACAAGAAGCAGAGACAC

upper sequence: GLYMA05G29700.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0003g02590.t01 (Vitis vinifera), 3'ss of exon 4
gacatttggaatcctaaagggaggtcaatgtaatttattatttgcattatctt-taaatgtataaggaaaga-------aacatgaatccaatagtttca---atttccagGTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCTCGCCATCTTGCTCAACGATATAGTCGGATGAGACAAGAAGCAGAGGCAC
           | ||||||| |  |   | |  |||   ||||   ||| ||  | ||  || ||| |  ||       |||||   |    |  ||| |   |||| ||| | || ||||||||||||  |||| ||| ||||| ||||||||| ||||| || ||||| |||||||| ||||| || |||||||| ||||| ||| |||
-----------ttctaaaggaacctttttctgttttccaatttttgttaactaattaagatagaagcattgattcctcaaacattttttttttgtttttatatattttcagATTTTAGATCCTTTGAGAGCAATGGTCACTGGTGCTCCTTTGGAAGATGCCCGTCATCTAGCTCAACGTTATAGCCGAATGAGACATGAAGCTGAGACAC
















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|193730742|gb|FK663112.1|FK663112
EST:     AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTGAGAC
genomic: AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGAC
EST: gi|193513257|gb|FK470021.1|FK470021
EST:     AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTGAGAC
genomic: AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGAC
EST: gi|193396156|gb|FK361911.1|FK361911
EST:     AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTGAGACAAA
genomic: AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGACAAA
EST: gi|151393188|gb|EV263063.1|EV263063
EST:     AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCT
genomic: AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCT
EST: gi|209698264|gb|BW667553.1|BW667553
EST:     AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCT
genomic: AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCT
EST: gi|151413137|gb|EV282945.1|EV282945
EST:     AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTTGAGACAAATGATCAATGGTGTTCCTTTTGGAGGATG
genomic: AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTT-GAGACAAATGATCAATGGTGTTCCTTT-GGAGGATG
EST: gi|193443747|gb|FK405671.1|FK405671
EST:     AAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCT
genomic: AAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCT
EST: gi|208048537|gb|GD847496.1|GD847496
EST:     AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTGAGACAAATGATCAATGG
genomic: AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGACAAATGATCAATGG
EST: gi|193686261|gb|FK625948.1|FK625948
EST:     GCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTTATCTACACAG                         GTATTGGATCCTTTGAGACAAA
genomic: GCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTT-ATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGACAAA
EST: gi|193515808|gb|FK475148.1|FK475148
EST:     AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTGAGACAAA
genomic: AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGACAAA
EST: gi|193700820|gb|FK636807.1|FK636807
EST:     AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTGAGAC
genomic: AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGAC
EST: gi|193721240|gb|FK659922.1|FK659922
EST:     AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTGAGACAAA
genomic: AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGACAAA
EST: gi|208203101|gb|GD997533.1|GD997533
EST:     AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAG                         GTATTGGATCCTTTGAGACAAA
genomic: AGCATGTGGAAAAGGAGCACGAAGAATTAAATCGGCTTTTATCTACACAGgtggactttt ... caatttccagGTATTGGATCCTTTGAGACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatctttaaatgtataaggaaagaaacatgaatccaatagtttcaatttccagGTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCTCGCCATCTTGCTCAACGATATAGTCGGATGAGACAAGAAGCAGAGGCAC
                                                tttcc  CT-rich tract
      tttaaatgtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacatttggaatcctaaagggaggtcaatgtaatttattatttgcattatctttaaatgtataaggaaagaaacatgaatccaatagtttcaatttccagGTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCTCGCCATCTTGCTCAACGATATAGTCGGATGAGACAAGAAGCAGAGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC