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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaacatttttgttactgagggaaggttattattttttcaaacgaactctcttgattcatacttaagtcagttaagtgcatgatgggaatgcatattaccaccctattcatatattttaacagaaattcatcagttgatttactgaaagtgacctattccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTAGCAAAGGATCCAGACCAAGCTGCACTTCTAAAGGTGAAGGAAATTAAGA

Basic information

species Glycine max
transcript GLYMA20G35530.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35530.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0089g01170.t01 (Vitis vinifera), 3'ss of exon 6
gtatgtaacatttttgttactgagggaaggttattattttttcaaacgaactctcttgattcatacttaagtcagttaagtgcatgatgggaatgcatattaccaccctattcatatattttaacagaaattcatcagttgatttactgaaagtgacctattccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTAGCAAAGGATCCAGACCAAGCTGCACTTCTAAAGGTGAAGGAAATTAAGA
| || || | ||||| | | || |||| | | || | || | | || | | ||| |||| | | | || || || | ||||||||||| ||||||||||| ||||||||||| ||||| || |||| || ||||| || |||||||| |||||||| || ||||||||||| |||||||
---------------------------------------------------------------aaacgaattcttaatattgcattaagtcaacattcattagta---tgcccaaagatgt-agcatca-ctggtcatatgatctcattat--tggtctttttgctgtagGATTTGGAGGACAAGCTTCACCCAGGTGGTCCTTTTGATCCTCTGGGGCTTGCAAATGACCCAGACCAGGCTGCACTGCTTAAGGTGAAGGAGATTAAGA
















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|209727197|gb|BW655235.1|BW655235
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|22933515|gb|BU550654.1|BU550654
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|24135389|gb|BU925899.1|BU925899
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|31305455|gb|CD390658.1|CD390658
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|31464590|gb|CD406618.1|CD406618
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|20814435|gb|BQ298913.1|BQ298913
EST:     GAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: GAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|31305180|gb|CD390383.1|CD390383
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|31312504|gb|CD397707.1|CD397707
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|9898921|gb|BE607889.1|BE607889
EST:     GATAGTTCTTGGGGGTGGTGCTGAGTACTACAGAATTAAT-AATGGCCTG                         GATTTTGAAGACAAGCTTCATCCA
genomic: GATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAAT-AATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCA
EST: gi|209697501|gb|BW670002.1|BW670002
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|31470972|gb|CD413000.1|CD413000
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|209715031|gb|BW650882.1|BW650882
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|214005601|gb|DB984609.1|DB984609
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|31475874|gb|CD417902.1|CD417902
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|209727225|gb|BW655236.1|BW655236
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|8670142|gb|BE191249.1|BE191249
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         AATTTGGGAGACAAGCTTCATCCAGGTGGTCCATTTGACCCCATTGG-CCT
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCC-ATTGGGCCT
EST: gi|192293843|gb|FG986052.1|FG986052
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|209717865|gb|BW669004.1|BW669004
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|213606035|gb|DB980187.1|DB980187
EST:     GATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCTCT-                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCT
genomic: GATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGC-CTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCT
EST: gi|209715030|gb|BW650881.1|BW650881
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATC
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATC
EST: gi|31309414|gb|CD394617.1|CD394617
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACCGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|213606013|gb|DB980165.1|DB980165
EST:     AGGTAGTTCTTGTGGGTTGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|20813004|gb|BQ297482.1|BQ297482
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|31474651|gb|CD416679.1|CD416679
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTTATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|13480449|gb|BG509792.1|BG509792
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|31460969|gb|CD402997.1|CD402997
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|31470087|gb|CD412115.1|CD412115
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTTATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
EST: gi|213595532|gb|DB962430.1|DB962430
EST:     AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTG                         GATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA
genomic: AGATAGTTCTTGTGGGTGGTGCTGAGTACTACAGAATAATTAATGGCCTGgtatgtaaca ... ttccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattttaacagaaattcatcagttgatttactgaaagtgacctattccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTAGCAAAGGATCCAGACCAAGCTGCACTTCTAAAGGTGAAGGAAATTAAGA
                                         cctattcctt  CT-rich tract
 aaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaacatttttgttactgagggaaggttattattttttcaaacgaactctcttgattcatacttaagtcagttaagtgcatgatgggaatgcatattaccaccctattcatatattttaacagaaattcatcagttgatttactgaaagtgacctattccttatagGATTTGGAAGACAAGCTTCATCCAGGTGGTCCATTTGACCCATTGGGCCTAGCAAAGGATCCAGACCAAGCTGCACTTCTAAAGGTGAAGGAAATTAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA