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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggtttacctttaatgcttcttcttttgacctgtgatcttgttccttgaaaaatattgcattcactcctacattgctttaactttctgatatttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCGAGAGGCCATTGCCGCAGCTGGTGGAGTTCAGGCCTTG

Basic information

species Glycine max
transcript GLYMA09G37720.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g41360.1 (Oryza sativa), 3'ss of exon 5
----aggtttacctttaatgcttcttc---ttttgacctgtgatcttgttccttgaaaaatattgcattcactccta---cattgctttaactttctgatatttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCGAGAGGCCATTGCCGCAGCTGGTGGAGTTCAGGCCTTG
    |  | || ||    ||||  ||    ||   ||   |||| |||  | || ||  ||| |  ||    |||||    | |  | | | |       ||||| | || ||||| ||||||||||| || |||||| |||||||||| |||||||| || || | |||||| || || ||||| ||| | || |||
gtatacttctagctgatgtgctgttttaagttgcaacgcctgattttgc-cattaaattatactttatattatcctaatttaatattgtgattcctgtgcatttaattagACAAGAAGCTGCTGGTGCTCTGTGGAATCTGTCATTTGATGATAGAAACCGTGAAGGCATTGCTGCTGCGGGTGGCGTTGAAGCTTTG

upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0021g01810.t01 (Vitis vinifera), 3'ss of exon 6
-----aggtttacctttaatgcttcttcttttgacctgtgatcttgttccttgaaaaatattgcattcactcctacattgctttaactttctgatatttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCGAGAGGCCATTGCCGCAGCTGGTGGAGTTCAGGCCTTG
     |     ||||  |      |      | || |  ||     |   ||  | |  ||   |     |  |    | | |  |  |||| ||    |  ||||||||| |||||||||||| | |||||||| |||||||| || ||||| || || || ||||| || |||||||| ||| ||||| ||
atccaaaaacaacctagaccaagcccatagattacataggaaagaatgttttagatagcatcttacctgat--tgttatccatgtatgttctcat---caaacagGCAAGAAGCTGCTGGTGCATTGTGGAATTTATCATTTGATGACAGAAACCGCGAAGCAATTGCAGCTGCTGGTGGCGTTGAGGCCCTG

upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S13_130V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------aggtttacctttaatgcttcttctt-ttgacctgtgatcttgttccttgaaaaatattgcattcactcct-acattgctttaacttt--ctgatatttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCGAGAGGCCATTGCCGCAGCTGGTGGAGTTCAGGCCTTG
                |||      |       |     |  |||  |  |||  |||      |   ||  | |    |   ||| ||| |  |||    |   ||   |  | | ||| ||||| || ||||| ||||| |||||| |||| ||||| |||||||| ||||| || ||||| ||||||||||| ||  ||||  ||
gtacgtgtgatctctgaggcgagtgtgcggcattgaaattggttggtcaatgagattggataaggtccaaactcggtgacttacctgacagtattttggtatcggctttcacatgtgcagACAAGAAGCAGCTGGAGCACTGTGGAATCTGTCTTTTGATGATAGAAACCGAGAAGCTATTGCAGCAGCTGGTGGCGTGGAGGCACTG

upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ24586 (Selaginella moellendorffii), 3'ss of exon 5
aggtttacctttaatgcttcttcttttgacctgtgatcttgttccttgaaaaatattgcattcactcctacattgctttaactttctgatatttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCGAGAGGCCATTGCCGCAGCTGGTGGAGTTCAGGCCTTG
                                              |||      ||   ||||   |||   ||  || | ||| || |  || |  |||||||| |||||||| || || ||||| |||||||||||||| |||||||| ||||| ||||| ||||||||||| ||| |||| |||
---------------------------------------------gtgaggtcgtttcgtttcaagtctatcatggatttagtttgtgtttcttct--agGCAAGAAGCTGCTGGCGCCCTGTGGAACTTGTCATTTGACGACAGAAATCGGGAGGCAATTGCTGCAGCTGGTGGTGTTGAGGCATTG

upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ24022 (Selaginella moellendorffii), 3'ss of exon 5
aggtttacctttaatgcttcttcttttgacctgtgatcttgttccttgaaaaatattgcattcactccta-cattgctttaactttctgatatttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCGAGAGGCCATTGCCGCAGCTGGTGGAGTTCAGGCCTTG
                                              |||      ||   ||||   ||| ||| | ||||  || |   | | | |  |||||||| |||||||| || |||||||| |||||||||||||| |||||||| ||||| ||||| ||||||||||| ||| |||| |||
---------------------------------------------gtgaggtcgtttcatttcaagtctatcatggatttagtttgc--gtctct-tctagGCAAGAAGCTGCTGGCGCCCTTTGGAACTTGTCATTTGACGACAGAAATCGGGAGGCAATTGCTGCAGCTGGTGGTGTTGAGGCATTG

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|26058330|gb|CA801244.1|CA801244
EST:     GCCCTTGAGGCTCTTGTTCAACTTACTTGCTCTCCCCACGAGGGTGTCAG                         GCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCG
genomic: GCCCTTGAGGCTCTTGTTCAACTTACTTGCTCTCCCCACGAGGGTGTCAGgtaatcttta ... atttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCG
EST: gi|209716858|gb|BW679610.1|BW679610
EST:     GCCCTTGAGGCTCTTGTTCAACTTACTTGCTCTCCCCACGAGGGTGTCAG                         GCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCG
genomic: GCCCTTGAGGCTCTTGTTCAACTTACTTGCTCTCCCCACGAGGGTGTCAGgtaatcttta ... atttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCG
EST: gi|6719933|gb|AW307580.1|AW307580
EST:     GCCCTTGAGGCTCTTGTTCAACTTACTTGCTCTCCCCACGAGGGTGTCAG                         GCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCG
genomic: GCCCTTGAGGCTCTTGTTCAACTTACTTGCTCTCCCCACGAGGGTGTCAGgtaatcttta ... atttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCG
EST: gi|7041810|gb|AW471704.1|AW471704
EST:     GCCCTTGAGGCTCTTGTTCAACTTACTTGCTCTCCCCACGAGGGTGTCAG                         GCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCG
genomic: GCCCTTGAGGCTCTTGTTCAACTTACTTGCTCTCCCCACGAGGGTGTCAGgtaatcttta ... atttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaaaatattgcattcactcctacattgctttaactttctgatatttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCGAGAGGCCATTGCCGCAGCTGGTGGAGTTCAGGCCTTG
                                      ttctgat  putative branch site (score: 3)
                                              tttattc  CT-rich tract
                               tttaactttctgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggtttacctttaatgcttcttcttttgacctgtgatcttgttccttgaaaaatattgcattcactcctacattgctttaactttctgatatttattcagGCAAGAGGCTGCTGGTGCACTTTGGAATTTGTCATTTGACGATAGAAATCGAGAGGCCATTGCCGCAGCTGGTGGAGTTCAGGCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - tgcttct
- - - - - - - - - - - - - - -cctgtga
- - - - - - - - - - - - - - - - - - - - -ttccttg
- - - - - - - - - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttctg