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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattagattctctgtttatacatcttgtttaatagagtcatagtcggactggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC

Basic information

species Glycine max
transcript GLYMA04G38480.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 3
tattagattctctgtttatacatcttgtttaatagagtcatagtcggactggaaactaattcattaagtgagagatat--aatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC
  ||   ||   |    ||| | |||| ||          |||||    |   | | ||   | | | ||     | |  ||  ||    |  |  |  |||||||||| ||||||||||| || |||||||||||||| || ||||| |||||||| ||| | ||||||||||| ||||| ||||| ||  |||| |  ||
-tttcactttgttacacatagaccttggttggctagaaattagtccctttttca-caaacatactgactgtagtttctttaaaatgttcatacatattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC

upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g06930.1 (Oryza sativa), 3'ss of exon 3
tattagattctctgtttatacatcttgtttaatagagt--catagtcggactggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC
 ||  | |  ||  |  |    | || | || |       | || ||  | |     |   ||| |    | |||| ||  ||   ||  |     |  |||| ||||| || |||||||| || |||||||||||||| || ||||||||||| || ||| | |||||||| |||||||| ||||| ||  |||| |  ||
-atgggctcatcattccaattgttttatatactgtctctccgtattccaagtatgttcattttcctctccttagagctaatatgaaacactcacgttt-tagGAAAATTTAGGCACCTCCCAGTGGTGGAAAATGGTGAGGTTATTGCCATGCTAGACATTGCAAAATGCCTCTATGATGCAATATCAAGACTGGAAAAGGC

upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g73040.1 (Oryza sativa), 3'ss of exon 3
-----tattagattctctgtt-tatacatcttgtttaatagagtcatagtcggactggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC
        |||||||| | || | | | |||   | |||    |     |     | |   || | |  |    || |      ||  || | ||   | | | ||| || |||||||| || ||||| |||||| | ||||| || |||||||||||||| |||||||| | |||||||||||| || || || ||||| |  ||
aagttagatagattctttcttatgttcttctgagtgaattattttccttttctttttgggtctgaatgctctcttgtgg----caacatggcattc--attaacagGAAAGTTCAGACATCTTCCTGTAGTGGAACACGGTGAGGTAATTGCCATGCTGGACATTACCAAGTTCCTTTATGATGCAATTTCAAGAATGGAAAAGGC

upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G052277_T01 (Zea mays), 3'ss of exon 3
---tattagattctctgtttatacatcttgtttaatagagtcatagtcggactggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC
   ||    |  |    | | |  || ||  || | | |  | || |  || |  |  ||| |    |   |||     ||  | |   ||||| | || |||||||||| |||||||| || || || ||||||||||| || ||||| ||| |||| ||||| |||||||| |||||||| ||||| ||  |||| |  ||
gcataggctaaccctcatgtttttatgttacttga-ataaacttacttcga-tatatgctattcatctttctgaatttaatgttgtagatttttta-tgttagGTAAATTTAGACACCTTCCAGTTGTAGAAAATGGTGAGGTTATTGCGATGTTGGACATTACAAAATGCCTCTATGATGCAATATCAAGACTGGAAAAGGC

upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G126656_T01 (Zea mays), 3'ss of exon 3
--------tattagattctctgtttatacatcttgtttaatagagtcatagtcggac-tggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC
        |  |    ||  || ||| | | | ||   | |  |||| |||| |||  ||   |||||  ||| |  |      || ||| ||   | | |  |  |||| ||||| |||||||| || || || ||||||||||| || ||||| |||||||| ||| | |||||||||||||| || ||| | ||  |||| |  ||
gctgtttgttctcatgtccttgcttagaaaccctg---agtcaagtcttagttggatatgttcactaa--catcagcttt----tacaatatgttctctcatattttagGGAAATTTAGACACCTTCCCGTTGTAGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCAAAATGCCTTTATGAAGCAATAGCAAGACTGGAAAAGGC

upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G131118_T01 (Zea mays), 3'ss of exon 1
------tattagattctctgtttatacatcttgtttaatagagtcatagtcggactggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC
         || |     |  ||  |    |  || |||| | | |   |  ||  || |  | ||||  |   |  ||  | |||| ||  ||||    | ||||| ||||| |||||||| || || || ||||||||||| || ||||| |||||||| ||| | ||||| || |||||||| ||||| ||  |||| |  ||
tgcataggctaaacctcattatttcaatgttccttgaataaacttac--tttga--ggtatgttattc-ctgtctctgaagt-taatatgttttttcttattatagGGAAATTTAGACACCTTCCGGTTGTTGAAAATGGTGAGGTTATTGCGATGCTGGACATTGCAAAATGTCTCTATGATGCAATATCAAGACTGGAAAAGGC

upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G031609_T02 (Zea mays), 3'ss of exon 3
----tattagattctctgtttatacatcttgtttaatagagtcatagtcggactggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC
       || |     |  ||  |    |  || |||| | |  || |  ||  || |  | |||| ||       || ||  ||     ||||    | ||||| ||||| |||||||| || || || ||||||||||| || ||||| |||||||| ||| | ||||| || |||||||| ||||| ||  |||| |  ||
cataggctaaacctcattatttcaatgttccttgaataaact--taatttga--ggtatgttattcctttctctgaagttaatatggtttttttcttattatagGGAAATTTAGACACCTTCCAGTTGTTGAAAATGGTGAGGTTATTGCGATGCTGGACATTGCAAAATGTCTGTATGATGCAATATCAAGACTGGAAAAGGC

upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0031g02750.t01 (Vitis vinifera), 3'ss of exon 3
tattagattc--tctgtttatacatcttgttt-aatagagtcatagtcggactggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC
||||   |||  |   | ||| ||  |  ||| |||  | || |  |        |  |||||   |    |  |  || |   |||   | ||     | ||| || || || ||||||||||| || |||||||||||||| ||||||||  |||||||||| || ||||| |||||||| |||||| | |||||||  ||
tatttatttcatttcatatatgcacttcatttgaatgaattctttattacttattagcctaatatttgttttatggcatcttgcttg---tgttggtcaacagGCAAGTTTAGGCACCTCCCTGTTGTAGAAAATGGTGAAGTTATTGCCATATTGGATATTACAAAGTGCCTCTATGATGCTATATCTCGAATGGAGAAGGC

upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ12244 (Selaginella moellendorffii), 3'ss of exon 3
tattagattctctgtttatacatcttgtttaatagagtcatagtcggactggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC
                                          ||        |   | ||    |  ||||||     ||     | |||        ||| ||||| |||||||| || |||||||| ||||| |||||||||||  |||||||||| || |||||| | |||||||| ||  | || |||||||  ||
------------------------------------------gtattctacaactttgatagccttcgtgagattcccaaacctccatttc--tctgcagGGAAATTTAGACACCTTCCAGTCGTGGAGAATGGCGAAGTCATTGCACTGCTGGATATAACAAAATGCTTGTATGATGCGATTGCGAGAATGGAGAAAGC

upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ25849 (Selaginella moellendorffii), 3'ss of exon 3
tattagattctctgtttatacatcttgtttaatagagtcatagtcggactggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC
                                       ||  |   |||   ||    |||     ||||||     ||     | |||        ||| ||||| |||||||| || |||||||| ||||| |||||||||||  |||||||||| || |||||| | |||||||| ||  | || |||||||  ||
-------------------------------------gtattctacaactttgaaagccttc-----gtgagattcccaaacctccatttc--tctgcagGGAAATTTAGACACCTTCCAGTCGTGGAGAATGGCGAAGTCATTGCACTGCTGGATATAACAAAATGCTTGTATGATGCGATTGCGAGAATGGAGAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggactggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC
                                          ttttaac  putative branch site (score: 2)
                                        cttttt  CT-rich tract
                           agatataatttgactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattagattctctgtttatacatcttgtttaatagagtcatagtcggactggaaactaattcattaagtgagagatataatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -gaaactaa