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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatttatttgatatggagagaatacaagtttcttggatgttgtgatatttttgttttgggtgctgggaaatgcttctgactgttgctttcaactcaactcctagcgtggtcatgacttcaaaattgtgtttaattgttgcag

Basic information

species Glycine max
transcript GLYMA15G40110.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 11
TGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcat--ttatttgatatggagagaatacaagtttcttggatgttgtgatatttttgttttgggtgctgggaaatgcttctgactgttgctttcaactcaactcctagcgtggtcat---gacttcaaaattgtgtttaattg--ttgcag-----------------------
||| ||||| |||||||| |||||||| || ||||||||||||||||| ||| | |  || ||| | |||||||| | ||| || ||||||||  | || ||     |   | || |  | |    |   |    ||| |  |  |  | | |   |  | | |     | |  |   |  || || ||| | || |  |      |   |   ||  |||   || ||     |  | | ||||||  |||  |                       
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTCTGAGACTGGCAGCTAGAGTTGACGCCATCAAGGACAACCTGGAGAATGATGAGCAGAAGgtttacaaccatgatctactttattcattgtttttgtt-cgagtgttctataaacctcatctctcaaaagttctg---tttttgtgcctgctactatgtatatgggttagaa-atgaccatctcgaatttgttgtcctttctaattgacttgttgtatgtattgcttgaactttttag

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 10
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
TGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatttatttgatatggagagaatacaagtttcttggatgttgtgatatttttgttttgggtgctgggaaatgcttctgactgttgctttcaactcaactcctagcgtggtcatgacttcaaaattgtgtttaattgttgcag
||| ||||| |||||||| |||||||||||||||||||| ||  | |||||||||||||| ||  | |||||||||| |||||| |||||||||||||| |||| |          | ||  |||   |  || ||| ||| |  |||   |  | ||  |    |   |   || |  |||  |    |                                                          
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggc------aaaatcaagaattttgaaattttttgcaaattgct-tgctcttact----gcattttcaactatttcccatctctag--------------------------------------------------------

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 10
lower sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 11
TGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatttatttgatatggagagaatacaagtttcttggatgttgtgatatttttgttttgggtgctgggaaatgcttctgactgttgctttcaactcaactcctagcgtggtcatgacttcaaaattgtgtttaattgttgcag
||| ||||| |||||||| |||||||||||||||||||| ||  | ||||| || ||||| ||  | || || |  |  |||||||||||||||||||| || | ||| | |  |  |      ||| |  ||   || || |  ||  | | | | |   ||   |||||   | | | | |                                                                 
TGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAGAAAAGgtaaatcaatcaagtcttc-----agattttaa--ctcatgaacctt-cggtttctctaactt---tgctgatgattccctttag---------------------------------------------------------------

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
TGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtga-----gtcatt-tatttgatatggagagaatacaagtttcttggatgttgtgatatttttgttttgggtgctgggaaatgcttctgactgttgctttcaactcaactcc--tagcgtggtcatgacttcaaaattgtgtttaattg-ttgcag
||| ||||| || ||||| || |||||||| |||||||| ||||||||||| |||||||||||  | |||||||| |  |||||||||||||| ||||| ||||     ||   | | ||  ||||||      | |||     |  | | | ||  |     |  ||||  |  ||   ||||  |   |    ||     |  |   |     ||  ||| | ||    | ||| | |  || ||||| ||||||
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag

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|16278868|gb|BI943136.1|BI943136
EST:     CATCANAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCCTTTGAA-TTAAT
genomic: CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCC-TTTGAAATTAAT
EST: gi|16278211|gb|BI942785.1|BI942785
EST:     CATCANAGGTGGACACAATCAAAGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGGTACCCTTTGGAATTAATT
genomic: CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|16995951|gb|BM085323.1|BM085323
EST:     CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
genomic: CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|31475719|gb|CD417747.1|CD417747
EST:     CATCAAAGGTGGACACCATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
genomic: CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|207828846|gb|GD798493.1|GD798493
EST:     CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
genomic: CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|208148111|gb|GD949727.1|GD949727
EST:     TAATGATGAAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAAT
genomic: TAATGATG-AAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAAT
EST: gi|26046015|gb|CA783382.1|CA783382
EST:     CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTG
genomic: CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTG
EST: gi|16276840|gb|BI942072.1|BI942072
EST:     CATCANAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAANAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAA
genomic: CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAA
EST: gi|298170123|gb|HO018747.1|HO018747
EST:     CATCAAAGGTGGACACAATCAAGGATAGCCTTGACAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
genomic: CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|15589717|gb|BI674333.1|BI674333
EST:     CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
genomic: CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|31309826|gb|CD395029.1|CD395029
EST:     CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
genomic: CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|193403060|gb|FK369006.1|FK369006
EST:     CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAG
genomic: CATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... attgttgcagGTTGGAGCTGATATTGTGAAAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatttatttgatatggagagaatacaagtttcttggatgttgtgatatttttgttttgggtgctgggaaatgcttctgactgttgctttcaactcaactcctagcgtggtcatgacttcaaaattgtgtttaattgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA