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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttgttaattttcacttgctagacttttttcttttctttctttctttctttcattcttgttttttgttaactcacctatatgatttgtcttaactagAGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAG

Basic information

species Glycine max
transcript GLYMA15G41690.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv19s0085g00880.t01 (Vitis vinifera), 3'ss of exon 16
tttgttgttaattttcacttgctagacttttttcttttctttctttctttctttcattcttgttttttgt--taactcacc-tatatga-tttgtcttaactagAGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAG
   | ||   | |||  | |  |  |  ||  ||| |   || |||     | ||||  ||||||| |||  |||  ||   ||| | | | |||||| || ||  | ||||  |||||||||||||||||||| ||| | || ||||| || ||||| |||||| | ||||| || ||||| ||||| |
--agctg--gactttttccttttgaagcttactctgtgtgttatttgggcttgtcatgtttgttttatgtgctaatacatggtatttaaatctgtcttcaccagGAATGAAGTGTTTGGACCTGTTGCACCCCTCTTGCGCTTTAAAACCGAGGAGGAAGCTATCCGCATTGCAAATGACACCAATGCTG

upper sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ27974 (Selaginella moellendorffii), 3'ss of exon 15
tttgttgttaattttcacttgctagacttttttcttttctttctttctttctttcattcttgttttttgttaactcacctatatgatttgtcttaact--agAGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAG
                                               || ||  |  |   ||   |     ||||   | | |  | | |  |  ||  ||||||||||  ||||| ||||||||||||||  | ||||||||||| || ||||| || ||||| ||||| |||  |||  | || |
-----------------------------------------gtaagtttgctgccggtgaagtggatcagggactccgtttttttttcttttctttctgcagAGAGGAAGTTTTTGGGCCTGTTGCACCCCTGATCAGATTCAAAACAGACGAGGACGCAATCAGGATTGCCAACAGCACCGAAGCTG

upper sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ36701 (Selaginella moellendorffii), 3'ss of exon 15
tttgttgttaattttcacttgctagacttttttcttttctttctttctttctttcattcttgttttttgttaactcacctatatgatttgtcttaact--agAGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAG
                                               || ||  |  |   ||   |     ||||   | | |  | | |  |  ||  ||||||||||  ||||| ||||||||||||||  | ||||||||||| || ||||| || ||||| ||||| |||  |||  | || |
-----------------------------------------gtacgtttgctgccggtgaagtggatcagggactccgtttttttttcttttctttctgcagAGAGGAAGTTTTTGGGCCTGTTGCACCCCTGATTAGATTCAAAACAGACGAGGACGCAATCAGGATTGCCAACAGCACCGAAGCTG

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|48574885|gb|CO036126.1|CO036126
EST:     TATGAACCCACGGTCATCAGTGATGTCAACAGTGATATGCGCATATCAAG                         AGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGA
genomic: TATGAACCCACGGTCATCAGTGATGTCAACAGTGATATGCGCATATCAAGgtaaaccttt ... tcttaactagAGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGA
EST: gi|151400125|gb|EV269939.1|EV269939
EST:     TATGAACCCACGGTCATCAGTGATGTCAACAGTGATATGCGCATATCAAG                         AGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGA
genomic: TATGAACCCACGGTCATCAGTGATGTCAACAGTGATATGCGCATATCAAGgtaaaccttt ... tcttaactagAGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGA
EST: gi|7146475|gb|AW508397.1|AW508397
EST:     TATGAACCCACGGTCATCAGTGATGTCAACAGTGATATGCGCATATCAAG                         AGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGA
genomic: TATGAACCCACGGTCATCAGTGATGTCAACAGTGATATGCGCATATCAAGgtaaaccttt ... tcttaactagAGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGA
EST: gi|151404401|gb|EV274211.1|EV274211
EST:     TATGAACCCACGGTCATCAGTGATGTCAACAGTGATATGCGCATATCAAG                         AGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGA
genomic: TATGAACCCACGGTCATCAGTGATGTCAACAGTGATATGCGCATATCAAGgtaaaccttt ... tcttaactagAGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGA
EST: gi|298198520|gb|HO040059.1|HO040059
EST:     TATGAACCCACGGTCATCAGTGATGTCAACAGTGATATGCGCATATCAAG                         AGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGA
genomic: TATGAACCCACGGTCATCAGTGATGTCAACAGTGATATGCGCATATCAAGgtaaaccttt ... tcttaactagAGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttctttcattcttgttttttgttaactcacctatatgatttgtcttaactagAGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAG
                          aactcac  putative branch site (score: 2)
                                         tttgtctt  putative PPT
              ttgttttttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttgttaattttcacttgctagacttttttcttttctttctttctttctttcattcttgttttttgttaactcacctatatgatttgtcttaactagAGAGGAAGCATTTGGACCTGTTGCACCCCTTTTGAGATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- tgttgtt
- - - - - - - -cacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg