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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacctggaaaaaaaaatgccacattcccatctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

Basic information

species Glycine max
transcript GLYMA14G37520.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
tacctggaaaaaaaaatgccacattcccatctgta-gttcatctaatttagtaaaat--aaaata--tttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
        |  || ||||    ||| |  ||  |  ||| |  || |||| ||   |  ||| ||  |||| |  |      |  |  | ||          |||||  | ||||||||||| || ||||| |  || || ||||| || ||||| || |||||||||||||||||| | || ||||||||||||||||| |||
-----catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
tacctggaaaaaaaaatgcc--acattcccatctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttcctt------agGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
    | | | || || |       ||| |    |    ||||| |   | | |        || ||  |||    ||  | |   ||      | | |||      ||||  |  | |||||||| || || ||||  || |||||||| || ||||| || ||||| |||||||||||| | |||| ||| ||||||||||| |||
----tagtataataattatttgttattgcatcttaagattcatttgtatcactgctt----attttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
tacctggaaaaaaaaatgccacattccc-atctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttctt-ttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
 | ||||||  |     |  |        |  |||  ||| |    | |   | |  |  ||   || |  |   |  ||| || |  | ||  |    |||||  |  | ||||||||||| ||||| |  || ||||||||||| ||||||||||| ||||||||||||||| | || ||||||||||||||||| |||
-agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttt-tttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
-tacctggaaaaaaaaatgccacattcccatctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
  | ||   |  || |       | | |||| ||| |  | |  || ||  |  |  ||  |  || |||||||||  ||  |  |  || | |   | ||||  | |||||||||||||| || ||||  |||||||||||||| |||||||||||||| ||||| |||||| | |||||||||||||||||||| |||
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaatt-tatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
tacctggaaaaaaaaatgccacattcccatctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttc-----cttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
        ||  ||  |   ||||| | | ||  |||||  ||  || |  | |  | |   | |  ||     | |  |  | |  || |  |       | ||||  |  | || |||||||| |||||||  || |||||||| || || ||||||||  | ||| | || ||| |||||||||||||||||||||| |||
-----tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagcttcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 3'ss of exon 7
----tacctggaaaaaaaaatgccacattcccatctgtagttcatctaatttagtaaaataaaatat--ttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
    | ||| | |    |      |   |   || ||    |   | |||| |      |||  ||   | | |  ||||| | |       | |  |    | ||||  | || || ||||| || ||||| | ||||||||||||||| || |||||| | || |||||||||||| | ||||| |||||||||||||| |||
tgctttcctagtagtgtattgttgagcgtataatgtgattgtggccaaattcacgctgttaagctacgctgggagttgaatgagtc------tctgatggtttcagGTTGGGTTACCGGCTCGTGGAAAGACATTCACTGCAGCTAAACTGACCAGATATTTGCGGTGGTTAGGTCATGACACCAAGCACTTCAATGTTGGCAAG

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 7
-------tacctggaaaaaaaaatgc-cacattcccat-ctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
       | ||    |  |    ||   | |||  | | ||||||   |  |   | | ||  |    || || | |  |||| || |||  ||||  ||       ||||  | ||||| || || || ||||||| |||||||||||| || ||  ||||| | |||||| |||||||| ||||||| ||||| ||||| || |||
atcggggtgcccattattatggttggatatattatcttgctgtagccaagtt--ctcaatatcaagctatgttgggagttgaacaagttc--tagtgactac-----agGTTGGGTTGCCGGCGCGTGGAAAGACTTTCACTGCAGCTAAGCTGACCCGATATTTGCGATGGCTAGGTCATGATACCAAGCACTTTAATGTCGGCAAG

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
tacctggaaaaaaaaatgccacattcccatctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
                                                 ||| | |    |  ||     | | |  | || ||   |    |||   ||||| | || |||||  | || || |||| |||||| |  || ||||||||||||||||| ||| | |||||| | || ||||||||||| ||||| || 
-------------------------------------------------gtagattgtcgtcattct---taactcttatctttgaatcgggttctacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
                                tttcattagtttcttt  CT-rich tract
     taaaataaaatatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacctggaaaaaaaaatgccacattcccatctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

- - - -aaaaaaa
- - - - - - - aatgcca
- - - - - - - - - - -cattccc
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatgaa