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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataaaatagaaaagcaaaaggtgttaatttagtgtattcatgtgttcatgtattattattcttttagtaactctttcctttgtgttctatgatttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAG

Basic information

species Glycine max
transcript GLYMA15G29620.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G29620.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g45410.1 (Oryza sativa), 3'ss of exon 1
---------------------------------------------------------aataaaatagaaaagcaaaaggtgttaatttagtgtattcatgtgttcatg-tattattattcttttagtaactctttcctttgtgttctatgat---------------ttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAG
                                                          ||    |   |   |      | |||||| | |   |  |||| |||||| |   | | ||  |  | |     || | | | ||||  |||||               ||| |||||| ||||| || || |||||||||||||||||||| ||||| ||||| |||||||| || |||||||| ||||||
gtacgtagctacgctctatacatgactgatcttgatgctgagaatttgatttgattttatttggttcgagttcggttcttcttaattaattacttgtatgt-ttcatgatcaaactcttgatcaattgtaaattacttgtatgtttcatgatcaaactcttgatcaattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACACTTTACCATCTCAAGAGCCATCTTCAG

upper sequence: GLYMA15G29620.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g07770.1 (Oryza sativa), 3'ss of exon 1
--------aataaaatagaaaagcaaaaggtgttaatttagtgtattcatgtgttcatgtattattattcttttagtaactctttcctttgtgttctatgatttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAG
         || ||      || |||        ||   | |  |  || |  || || | || ||  ||||    | | |   |  |    ||  | |  |  |||||||| || || || || ||||||||||| |||||||||||||| |||||||| |||||||| |||||||| || |||
gtacgcatcatcaatctctcaatcaattctctccaaaaaaatcgaaacaagaattaatctcttctt--tcttacgatgaattgatgatc---gtcttgtcgtc-gcagAGGCGACGCCCAAGACGATCATGAGGGTGATGGGAGTGAAGGGCCTCACCCTCTACCACCTCAAGAGCCATCTCCAG

upper sequence: GLYMA15G29620.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G081671_T01 (Zea mays), 3'ss of exon 1
-----------------------------aataaaatagaaaagcaaaaggtgttaatttagtgtattcatgtgttcatgtattattattcttttagtaactctttcctttgtgttctatgatttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAG
                             | | |  |           |  ||    | | |  | ||  |   | | |  ||| |  ||  |||    |  ||| |||   |  |      |  | |||||| || || || || |||||||||||||||||||| ||||| |||||||| |||||||| ||||| |||||||||
gtacgtgatacatagagatgcatgctttcagttacgttacgtgttgctacttgccgctgtggaattttatttgatacgttaattttggttgatttgc--atccttccctaaattcttcgccgtacgtagAGGCAACGCCCAAGACCATCATGAGGGTTATGGGAGTCAAGGGCCTCACCCTCTACCACCTCAAGAGTCACCTTCAG

upper sequence: GLYMA15G29620.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G052544_T01 (Zea mays), 3'ss of exon 1
aataaaatagaaaagcaaaaggtgttaatttagtgtattcatgtgttcatgtattattattc-ttttagtaac--tctttcctttgtgttctatgatttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAG
    |  |  |  || |     |    |  |||    | |  |    |  |     |   || | || ||     || || | |    || | |     |||||||| ||||| || || ||||||||||| |||||||| ||||| || ||||| |||||||| |||||||| ||||||
--gtacgtgtagtagtagctactagctagctagctgctgctagctccctggcccggtcgctcgtcttggttctgatcgtttcctccctttttctctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG

upper sequence: GLYMA15G29620.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S25_131V6.1 (Physcomitrella patens), 3'ss of exon 1
aataaaatagaaaagcaaaaggtgttaatttagtgtattcatgtgttcatgtattattattcttttag---taactctttcct--ttgtgttctatgatttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAG
      ||      |   ||| || || |  | |||||   |  ||     || |||||     | |    |||||| |   |  ||||  |  |  ||   ||||||| || || ||| |  | ||||| || ||||||||||||||||| || ||||||||  | |||||||| ||||||
-----gatgttgctgactaagttggtagtaaaatgtatgtcttcgtgggattagtattaggtcatcaaaactaactcgtctgtcattgttgttcacaatggacagAGGCTACACCGAAATCTGTAATGAGAGTCATGGGAGTGAAGGGTCTTACTCTTTACCATTTGAAGAGCCATCTTCAG

upper sequence: GLYMA15G29620.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S201_75V6.1 (Physcomitrella patens), 3'ss of exon 1
aataaaatagaaaagcaaaa-ggtgttaatttagtgtattcatgtgttcatgtattattattcttttagtaactctttcctttgtgttcta--tgatttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAG
  |    |      |  | | | |   | | |||   ||  |   | |   ||| |       |   | |  ||| ||  | |||| |  |    | |  ||||||| || || ||  |  | |||||||||||||||||||||||||| || || |||||  | |||||||| || |||
--tgggcttctgctgagagatgatcggagtgtaggtgatctaaacgatt-cgtagtgacgaagtccaactctctcgtttgtctgtggtgaaatcaactgacagAGGCTACACCGAAGTCTGTGATGAGGGTTATGGGAGTGAAGGGTCTTACGCTCTACCATTTGAAGAGCCATCTCCAG

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|4292903|gb|AI441971.1|AI441971
EST:     ACTACATGAACGCTTTGTTGATGCTGTTGCTCAGCTTGGAGGACCTGATA                         AGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCC
genomic: ACTACATGAACGCTTTGTTGATGCTGTTGCTCAGCTTGGAGGACCTGATAgtactattct ... tgatttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCC
EST: gi|21676951|gb|BQ629302.1|BQ629302
EST:     ACTACATGAACGCTTTGTTGATGCTGTTGCTCAGCTTGGAGGACCTGATA                         AGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCC
genomic: ACTACATGAACGCTTTGTTGATGCTGTTGCTCAGCTTGGAGGACCTGATAgtactattct ... tgatttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgtattattattcttttagtaactctttcctttgtgttctatgatttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAG
                    tagtaac  putative branch site (score: 1)
      tattattattctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataaaatagaaaagcaaaaggtgttaatttagtgtattcatgtgttcatgtattattattcttttagtaactctttcctttgtgttctatgatttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAG

aataaaa
- - - - -gaaaagc
- - - - - - - - - - ggtgtta
- - - - - - - - - - - - - - - - - - - tcatgtg
- - - - - - - - - - - - - - - - - - - - - - - -catgtat