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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgacaaaattattagaagttttatttcataatgtatatttatttctatattattttctcttaaaagattatctctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA

Basic information

species Glycine max
transcript GLYMA02G45000.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os07g46590.1 (Oryza sativa), 3'ss of exon 6
-actgacaaaattattag-aagttttatttcataatgtatatttatttctatattattttctcttaaaagattatctctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
 |  || || |  ||||  ||     |  |  |  || |     ||||  || |    || | |||||  ||| |  ||||  |  || |   | ||  ||||| || ||||||||||| || || || || || |||||||||||||| || || || |||||||||||||| ||||| |||||||| ||        || 
caaagaaaatagcattaacaaaacacagattcttctgcaggcacatttaaatgtctggttat-ttaaattattctagctaacttgattattgcatatg-cagGTCTCGCTTTTAAATATCGTTGTTGAGTTGAAAAAGTGCTGCAACCACCCATTTTTATTTGAAAGTGCTGATCATGGTTATGGTGGAGATAGCATTGGTG

upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 19
--------------------------------------------------------------------actgacaaaatta------ttagaagttttatttcataatgtatatttatttctat----------attatt-ttctcttaaaagattatctctaatctttttctgctaaatat-cagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
                                                                    | | | | |||||      || | |    |  ||| ||| | | ||  |  |||            |||| | | ||  ||  |  || | | | |     || |     | || ||||| || ||| | || ||||| || ||||| ||||| |||||||||||||| ||||||||||||||||| || ||||| |||||||| ||        || 
gtgagccaaatctgctctcccatgtgggcaaggattgattgtttataacttcatgtctgatctactaaattcaaataattagtgtgcttggtaacaattgttcttaaggcacatccaaatctgccctccaaaaaattagtgtcctgctatcatgttttatgtgactgacttgttaatgacatgcagGTATCACTTCTTAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTCTTGTTTGAAAGTGCCGATCATGGTTATGGTGGAGATAGCATCGGTG

upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 16
actgacaaaattattagaagttttatttcataatgtatatttatttctatattattttctcttaaaagattatc--tctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
  |    |  | | |     ||   |  || | || |   |     | |    |   |     |   |  || |   || |  |  |  ||  | ||  ||||| || ||||| || ||||| || ||||| ||||| |||||||||||||| || |||||||||||||| || || || |||||||| ||        |  
gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacacttggccattgg-ctaccaaactgacttgatcatggcatatg-cagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG

upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 17
lower sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 18
----------------------------------------------------------------actgacaaaatta-ttagaagttttatttcataatgtatatttatttctatattattttctcttaaaagattatctctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
                                                                 |   ||   | | ||||  |  |||||| |  ||| ||     ||  ||  ||  ||  | ||||     || |   ||||| |   |   ||  | |||||||| |||||||| || |||||||| || ||||| |||||||| ||||| ||||| ||||||||||| |||||||| ||||| || |||  |     ||
gtgagtgactttatgatgcacccaggttctcatatttattgttatgaataattattttctttgtccctgcactgtaagttaggtggattattttaatatgcatccgacttcttaagtttgttgatattaa---gctaac---aatctctgagttacaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA

upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S93_123V6.1 (Physcomitrella patens), 3'ss of exon 18
actgacaaaattattagaagttttatttcataatgtatatttatttc-tatattattttctcttaaaagattatctctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
|||  |      |   |   |||  |||  |  ||  | ||| | || |  ||| |         |||| ||  || |   |||||| |   |  |   |||||||| |  | || || || |||||  | || |||||||| || ||||| ||  ||||||||||||| ||||||||||||||||| ||  |    |  |
actaccggttaaaactgtgatttctttttctgctgcttgtttttctcctgcattttcaagaagctaaagttttactgtg-cctttttatctcatcttgtagGTTTCTTTGCTGAACATAGTTGTGGAGCTCAAAAAGTGCTGTAATCATCCATTTCTGTTTGAAAGTGCCGACCATGGCTATGGTGGAGATGCGAACATGA

upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S317_10V6.1 (Physcomitrella patens), 3'ss of exon 18
-actgacaaaattattagaagttttatttcataatg-tatatttatttctatattattttctcttaaaagattatctctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
 | |    ||||  | |    || | || ||   || | ||    | | | | |||    |||  |  |  | || |   |  | | | |   |     ||||||||  | || || || || |||||  | ||||||||||| || ||||| ||| ||||||||||||| ||| ||||||||||||| ||  ||   |  |
gatt--tgaaatcgtcatgtattctcttgcaacctgctttacccttgtgttttttacgagctcaaattaagtcatattgcagttgtgtgtttcattgcccagGTTTCCTTATTGAACATAGTCGTGGAGCTCAAGAAGTGCTGTAATCATCCATTCCTGTTTGAAAGTGCCGACTATGGCTATGGTGGAGATGCAAACACAA

upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 17
lower sequence: EFJ28029 (Selaginella moellendorffii), 3'ss of exon 16
actgacaaaattattagaagttttatttcataatgtatatttatttctatattattttctcttaaaagattatctctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
                                     ||||| |||   |  | |||  | |         || | | | ||  | |       |  ||||| |||||  | || || || |||||| |||||||||||||||||||||||||  | ||||| ||||| || ||||| || || |   |  ||   |  |
------------------------------------gtatttttttgcgtcctttttcttttcg------catttttgaactcctacc------ttgcagGTGTCTCTGCTGAACATAGTTGTGGAACTAAAGAAGTGCTGCAACCATCCCTTTCTTTTTGAGAGTGCGGATCATGGTTACGGAGCAAATGCAACTATGA

upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 17
lower sequence: EFJ29460 (Selaginella moellendorffii), 3'ss of exon 16
actgacaaaattattagaagttttatttcataatgtatatttatttctatattattttctcttaaaagattatctctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
                                     ||||| |||   |  | |||  | |         || | | | ||  | |       |  ||||| |||||  | || || || ||||||||||||||||||||||||||||||||  | ||||| ||||| || ||||| || || |   |  ||   |  |
------------------------------------gtatttttttgcgtcctttttcttttcg------catttttgaactcctacc------ttgcagGTGTCTCTCCTGAACATAGTTGTGGAATTAAAGAAGTGCTGCAACCATCCCTTTCTTTTTGAGAGTGCGGATCATGGTTACGGAGCAAATGCAACTATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatattattttctcttaaaagattatctctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
                                          tgctaaa  putative branch site (score: 2)
                                  tctttttctgct  CT-rich tract
     attattttctcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgacaaaattattagaagttttatttcataatgtatatttatttctatattattttctcttaaaagattatctctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
actgaca