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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaaagtttagctctgcttcattgtcttgtcccatgcttttatttcctcttcctgtaatactattttcatttgactgtggttgtctccacaaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGATGAACTTGTTGTCCCCATAATTGAGAACACGGCCTACGAGTATCAGCTCA

Basic information

species Glycine max
transcript GLYMA12G35390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G574782_T01 (Zea mays), 3'ss of exon 3
--tagaaagtttagctctgcttcattgtcttgtcccatgcttttatttcctcttcctgtaatactattttcatttgactg--tggttgt-ctccacaaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGATGAACTTGTTGTCCCCATAATTGAGAACACGGCCTACGAGTATCAGCTCA
  || ||    ||| |    |  ||||| |  |   |||||   ||      ||   |||| |  ||  | ||||||||   |  |  | ||   |  || |||| | || |||||||||||||| ||||||||||| || ||||||||  |||||||| | ||  | || || |||||||| ||  | || |||||| ||||||
cctaaaattcatag-tggattctattgtatatttgtatgctagaataa----ttgtggtaagaaaatccttatttgactagatactgatgctgatcttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCA

upper sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G53850.3 (Arabidopsis thaliana), 3'ss of exon 4
tagaaagtttagctctgcttcattgtcttgtcccatgcttttatttcctcttcctgtaatactatttt-catttgactgtggttgtct---ccacaaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGATGAACTTGTTGTCCCCATAATTGAGAACACGGCCTACGAGTATCAGCTCA
        | |||| |  | | || | | ||   |   ||  |  | | |     |   ||  | ||| ||||| | |||   |  ||   | |||  |   |||| ||||||||||| ||||||||||| ||  | || || || || |||||||||||||||||||| || || |||||||| || || ||| || | || |
-------gtaagctgtaatgc-ttatttggtag-acaattccaggttccccagtagagttaggactttgcattttaatgtttcttcctgtccgacatttcatagATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGATGAACTTGTTGTCCCAATCATAGAGAACACAGCATATGAGAATGAACTAA

upper sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 3
tagaaagtttagctctgcttc-attgtcttgtc-ccatgcttttatttcctcttcctgtaatactattttcatttgactgtggttgtctccacaaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGATGAACTTGTTGTCCCCATAATTGAGAACACGGCCTACGAGTATCAGCTCA
 | ||  |||  | ||   |  | ||| |  |     || |||  ||  ||  |    |   | |   || | ||   | || || | | || ||||  ||||||||||| ||||||||||||||||||||  | || ||||| ||||||||||| ||||| ||||| || || |||||||| ||| ||||     ||||||
-ataattttttacactttctagaatgtataataattctgttttggttctctgatatcttttaatttgcttgaattttttatgtttttgtgca-aaattacagATCACTCATATGGAAATGATAAAAGGAATTCAAGGACATGGTTATTATGATGAGCTTGTGGTCCCAATCATAGAGAACACTGCCCACGAAAGGGAGCTCA

upper sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ34464 (Selaginella moellendorffii), 3'ss of exon 3
tagaaagtttagctctgcttcattgtcttgtcccatgcttttatttcctcttcctgtaatactattttcatttgactgtggttgtctccacaaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGATGAACTTGTTGTCCCCATAATTGAGAACACGGCCTACGAGTATCAGCTCA
                             ||   |   || | ||||   ||    | ||   |  | ||| |   ||||| ||            | |||||||||||||||| ||||| ||||||||||| |||||||| || || || || ||||| ||||| || ||||| ||| | || || || ||  ||||||
-----------------------------gtaatacttttctttttctctttttattcatttgagctccatctcg-tgtggctgct----------gtagATCACTCACATGGAGATGATCAAAGGAATCAAAGGGCATGGTTACTACGACGAGCTTGTAGTCCCGATCATTGAAAACTCTGCGTATGAATACGAGCTCA

upper sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ05817 (Selaginella moellendorffii), 3'ss of exon 3
tagaaagtttagctctgcttcattgtcttgtcccatgcttttatttcctcttcctgtaatactattttcatttgactgtggttgtctccacaaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGATGAACTTGTTGTCCCCATAATTGAGAACACGGCCTACGAGTATCAGCTCA
                                                |  | || |  |  | || || ||| ||| |  |   |||||      | |||||||||||||||| ||||| ||||||||||| |||||||| || || || || || || ||||| || ||||| ||| | || || || ||  ||||||
-----------------------------------------------gtaatacttt--tctttttctctttttactcttttgagctccatctgctgtagATCACTCACATGGAGATGATCAAAGGAATCAAAGGGCATGGTTACTACGACGAGCTCGTAGTCCCGATCATTGAAAACTCTGCGTATGAATACGAGCTCA

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|8670347|gb|BE191454.1|BE191454
EST:     TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGA                         ATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT
genomic: TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGAgtaagtattt ... caaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT
EST: gi|209709958|gb|BW657304.1|BW657304
EST:     TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGA                         ATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT
genomic: TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGAgtaagtattt ... caaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT
EST: gi|6341560|gb|AW164384.1|AW164384
EST:     TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGA                         ATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT
genomic: TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGAgtaagtattt ... caaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT
EST: gi|16995954|gb|BM085326.1|BM085326
EST:     TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGA                         ATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT
genomic: TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGAgtaagtattt ... caaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT
EST: gi|9986611|gb|BE660719.1|BE660719
EST:     TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGA                         ATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT
genomic: TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGAgtaagtattt ... caaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT
EST: gi|254313702|gb|GR831331.1|GR831331
EST:     TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGA                         ATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT
genomic: TAGAGTCTTGTCTCGTAACAATGATCAATCCTTTATCAAAGGAGTTTCGAgtaagtattt ... caaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcttcctgtaatactattttcatttgactgtggttgtctccacaaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGATGAACTTGTTGTCCCCATAATTGAGAACACGGCCTACGAGTATCAGCTCA
                        atttgac  putative branch site (score: 4)
                                       tctccac  putative PPT
           taatactattttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaaagtttagctctgcttcattgtcttgtcccatgcttttatttcctcttcctgtaatactattttcatttgactgtggttgtctccacaaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGATGAACTTGTTGTCCCCATAATTGAGAACACGGCCTACGAGTATCAGCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - ctctgct
- - - - - - - - - - - -tgtcttg
- - - - - - - - - - - - - - - - ccatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg