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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcttgttttggaaatgggaatgatttatcatagaagttgaggatgttattcaagttgtagttagagtttagatactgatgctatttgtgtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGATATGGAATTTGCCGCTTACAACTTGCTTTGTGTCATAATGCATTCAAATA

Basic information

species Glycine max
transcript GLYMA20G38620.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38620.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0067g03720.t01 (Vitis vinifera), 3'ss of exon 4
ttgcttgttttggaaatgggaatgatttat-catagaagttgaggatgttattca-agttgtagttagagtttagatactgatgctatttgtgtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGATATGGAATTTGCCGCTTACAACTTGCTTTGTGTCATAATGCATTCAAATA
|| ||  |||    | ||    | ||   |   ||  | |||  |||   | | | | ||  |  |   || |   ||    |  | |||||| |  | ||||||||||| |||||| |||| |||||||| ||||| |||||||| | ||||||||||||||| ||||||||| ||||||||| |||  |||| || | ||
ttcctcttttgcttagtgccttttataggtatctattatttgccgattaaaataataattagacgtgttgtctgactatct-tattctttgtg-gtctacagTGCCAATCACAGTTGAAAACCCTTTATGCAGAAGGAATTGAGGGATGTGATATGGAATTTGCTGCTTACAACCTGCTTTGTGCCATCTTGCACTCTAGTA
















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|208220922|gb|GE018058.1|GE018058
EST:     TTTGGGGTACTTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGACAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGA
genomic: TTTGGGG-ACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTG-CAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGA
EST: gi|193396881|gb|FK365015.1|FK365015
EST:     AATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
genomic: AATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
EST: gi|193563810|gb|FK517933.1|FK517933
EST:     CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
genomic: CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
EST: gi|208207228|gb|GE008451.1|GE008451
EST:     CCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGGTCTGA
genomic: CCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGA-GGGGTCTGA
EST: gi|193682710|gb|FK621764.1|FK621764
EST:     CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTANGCCGAAGGCATTGAGGGGTCTGAT
genomic: CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
EST: gi|193690224|gb|FK627997.1|FK627997
EST:     CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
genomic: CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
EST: gi|207822545|gb|GD795208.1|GD795208
EST:     CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
genomic: CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
EST: gi|208301196|gb|GE100779.1|GE100779
EST:     TGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
genomic: TGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
EST: gi|193532296|gb|FK491976.1|FK491976
EST:     CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
genomic: CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
EST: gi|193694976|gb|FK634348.1|FK634348
EST:     CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
genomic: CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
EST: gi|208319804|gb|GE110829.1|GE110829
EST:     CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
genomic: CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
EST: gi|193454256|gb|FK420823.1|FK420823
EST:     CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
genomic: CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
EST: gi|207814153|gb|GD786382.1|GD786382
EST:     GAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
genomic: GAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
EST: gi|208284795|gb|GE085609.1|GE085609
EST:     CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAG                         TGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT
genomic: CACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAGTATAATCAGgtttgttctg ... gtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttattcaagttgtagttagagtttagatactgatgctatttgtgtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGATATGGAATTTGCCGCTTACAACTTGCTTTGTGTCATAATGCATTCAAATA
                             tactgat  putative branch site (score: 2)
                       tttagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcttgttttggaaatgggaatgatttatcatagaagttgaggatgttattcaagttgtagttagagtttagatactgatgctatttgtgtgaatgcagTGCCAATCTCAGTTGCAAACTCTTTATGCCGAAGGCATTGAGGGGTCTGATATGGAATTTGCCGCTTACAACTTGCTTTGTGTCATAATGCATTCAAATA

-tgcttgt
- - - - - - - - - ggaatga
- - - - - - - - - - - - - - - - - - - - gaggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgc