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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagctttgagtcctaagattttctgtttttcatttttaacctgttgtgtgtgtggcaataaatcatgttttgtgtatgtgcatgcaacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATGTACAGTGAGCTCTCAAGAACTGATACTTCTCAGAAAACGTTGTGAAAAT

Basic information

species Glycine max
transcript GLYMA20G28200.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 22
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 22
gcaagctttgagtcctaagattttctgtttttcatttttaacctgttgtgtg------tgtggcaataaatcatgttttgtgtatgtgcatgcaacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATGTACAGTGAGCTCTCAAGAACTGATACTTCT-CAGAAAACGTTGTGAAAAT
  ||  |  |      |||  | ||||  ||  || |   |    | |          ||||  |||  ||   |     || || || ||  ||  || ||| ||||||| || ||||| ||||||||||||||| |||||||| |  | |||||||  |||||        ||||| | ||| |  | |  | | ||  |  
--aaaatcggtaaaaaaagcatatctggattggatgtgggataattagcaaaaccaattgtgaaaatggattgaggcaaatggatttg-attgaatattgcagATTAAGAGACCACAAGCAAAGGAATATTTCGCAGAAGCAATAACAAACATGTACAAGGAGCTTGGTGCTTCTGATCCCTCTGCTAATAGAGGTTTGTGAT-
















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|10231873|gb|BE800761.1|BE800761
EST:     TGCTCGAACCATNTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAA                         GTTAAGAAGCCTCAAGCGAAGGAAATATT-CGCAAAA
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAA-TATTTCGCAAAA
EST: gi|9984323|gb|BE658431.1|BE658431
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|6482302|gb|AW201571.1|AW201571
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|6724335|gb|AW308734.1|AW308734
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|8286445|gb|BE024013.1|BE024013
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|12691086|gb|BG157422.1|BG157422
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGC-AAAGCAATATCTGATATG
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|21479843|gb|BQ576526.1|BQ576526
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|22928570|gb|BU545709.1|BU545709
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|21676461|gb|BQ628812.1|BQ628812
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|5761162|gb|AI966525.1|AI966525
EST:     GCTCGTAACCATTTACGTGGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: GCTCG-AACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|21594959|gb|BQ610322.1|BQ610322
EST:     GAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: GAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|208299583|gb|GE097122.1|GE097122
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|208296976|gb|GE096572.1|GE096572
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|21993972|gb|BQ785500.1|BQ785500
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATG
EST: gi|213596223|gb|DB981811.1|DB981811
EST:     GCCTGTTGACTCCGACATTCAAG                         GTTTGGAGGCAACAAGCGAAGGAATATTTCGCAAAAGCAACGA-ATGATAT
genomic: GCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAA-TATCTGATAT
EST: gi|6481851|gb|AW201122.1|AW201122
EST:     TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAG                         GTTAAGAGGCCTCAAGCGAAGGAA
genomic: TGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttg ... aacttttcagGTTAAGAGGCCTCAAGCGAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgtgtgtgtggcaataaatcatgttttgtgtatgtgcatgcaacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATGTACAGTGAGCTCTCAAGAACTGATACTTCTCAGAAAACGTTGTGAAAAT
                                               cttttc  CT-rich tract
                aataaatcatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagctttgagtcctaagattttctgtttttcatttttaacctgttgtgtgtgtggcaataaatcatgttttgtgtatgtgcatgcaacttttcagGTTAAGAGGCCTCAAGCGAAGGAATATTTCGCAAAAGCAATATCTGATATGTACAGTGAGCTCTCAAGAACTGATACTTCTCAGAAAACGTTGTGAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC