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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctgatttatttgattgctttcttccttgcttgctctggcccctcttttgtatatgttgaaatttgtggaatgtttattcaaaggaaacaaagtgtttgagtggcttgacttgtggtattaggcatttaccattttgtctggccatttaaagctcttataaacttcttgttgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG

Basic information

species Glycine max
transcript GLYMA17G34990.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34990.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g00650.t01 (Vitis vinifera), 3'ss of exon 3
gtctctgatttatttgattgctttcttccttgcttgctctggcccctcttttgtatatgttgaaatttgtggaatgtttattcaaaggaaacaaagtgtttgagtggcttgacttgtggtattaggcatttaccattttgtctggccatttaaagctcttataaacttcttgttgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
                                                                                               || | | | ||  || | ||      ||  |||| |  ||     |    |  | |     ||||  || ||| ||||| |||  ||||||||||| ||||| |||||||||||| || |||| || ||||||||||| 
-----------------------------------------------------------------------------------------------gtctctaattgattttatttac----ttctgcatgt--cagcacat---acattgtggcagtctttgaatcttattgttattttgtagGCATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA
















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|209713753|gb|BW681879.1|BW681879
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTGTACTTTCAGTTTGGCGTCAAGTTAAACAACGTAGTGGATACCCAG
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|193336183|gb|FK298083.1|FK298083
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTATTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCA
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGT-ACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCA
EST: gi|15663150|gb|BI700521.1|BI700521
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTGTACTTTCAGTTTGGCATCAAGTTAAACAACGTAGTGGATACCCAG
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|254339165|gb|GR847882.1|GR847882
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|20498112|gb|BQ273042.1|BQ273042
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTGTACTTTCAGTTTGGCGTCAAGTTAAACAACGTAGTGGATACCCAG
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|33390324|gb|CA853519.1|CA853519
EST:     AAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
genomic: AAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|208077136|gb|GD877815.1|GD877815
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTATACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|18040715|gb|BM309009.1|BM309009
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|5760980|gb|AI966343.1|AI966343
EST:     CGGGACAGTGAG                         GCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
genomic: CGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|298193107|gb|HO033541.1|HO033541
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTGTACTTTCAGTTTGGCATCAAGTTAAACAACGTAGTGGATACCCAG
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|192296230|gb|FG991556.1|FG991556
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|209709559|gb|BW661886.1|BW661886
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTGTACTTTCAGTTTGGCGTCAAGTTAAACAACGTAGTGGATACCCAG
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|298194665|gb|HO043137.1|HO043137
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACGGTGAG                         GCATTGTACTTTCAGTTTGGCATCAAGTTAAACAACGTAGTGGATACCCAG
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
EST: gi|254336075|gb|GR841400.1|GR841400
EST:     AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAG                         GCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
genomic: AGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatt ... tgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaccattttgtctggccatttaaagctcttataaacttcttgttgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG
                                     cttcttgtt  CT-rich tract
                              ttataaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctgatttatttgattgctttcttccttgcttgctctggcccctcttttgtatatgttgaaatttgtggaatgtttattcaaaggaaacaaagtgtttgagtggcttgacttgtggtattaggcatttaccattttgtctggccatttaaagctcttataaacttcttgttgtttactagGCATTGTACTTTCAGTTTGGCATCAAGTTGAACAACGTAGTGGATACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA