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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGAAATGCTTGTTAATTTGGGAATTCCTTGGGTTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtgttcaattggccttgctttatattctcttgttaaaaaattctactttgtgaagttgcttgtaatggcaaaaacataacatttactaaatattttactgtctatcag

Basic information

species Glycine max
transcript GLYMA13G41120.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G41120.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0004g04800.t01 (Vitis vinifera), 5'ss of exon 4
TGCTGAAATGCTTGTTAATTTGGGAATTCCTTGGGTTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtgttcaattggccttgctttatattctcttgttaaaaaattctactttgtgaagttgcttgtaatggcaaaaacataacatttac-taaatat-tttactgtctatcag-----------
|||||| |||||||| |||||||| ||||||||||||||| ||||||| |||||| | ||    |||||   |||||||||||||||| |   || |  | || |     |  |  ||   |  ||  |    || ||||| ||     |||| || ||   |  |  |  ||| | | |   | | | |  | | ||| |            
TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatggtgcagtgacacatatgcagctttaatctttgcacg--tcaactttttgcttaggcttttattgttgatgatgtgtcatctgcctttgtgtatctgttctttataattgtgaatgcag
















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|207829294|gb|GD798942.1|GD798942
EST:     AACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: AACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|6071447|gb|AW100834.1|AW100834
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|18040397|gb|BM308691.1|BM308691
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|207707167|gb|GD687645.1|GD687645
EST:     GAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: GAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|193513329|gb|FK470093.1|FK470093
EST:     GCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: GCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|207830106|gb|GD801462.1|GD801462
EST:     AACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: AACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|6915528|gb|AW397058.1|AW397058
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|208279834|gb|GE078464.1|GE078464
EST:     GAATGAATACAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTAT
genomic: GAATGAAT-CAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTAT
EST: gi|10843979|gb|BF067325.1|BF067325
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|207698002|gb|GD681067.1|GD681067
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|193651612|gb|FK598213.1|FK598213
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|192308239|gb|FK002751.1|FK002751
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|193406346|gb|FK372995.1|FK372995
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|15662424|gb|BI699795.1|BI699795
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|192300263|gb|FG987840.1|FG987840
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|193308287|gb|FK277292.1|FK277292
EST:     GAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: GAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|207840806|gb|GD810999.1|GD810999
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|37997347|gb|CF808936.1|CF808936
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|207791068|gb|GD762429.1|GD762429
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|9986087|gb|BE660195.1|BE660195
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|151409950|gb|EV279758.1|EV279758
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|207745235|gb|GD715939.1|GD715939
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
EST: gi|207765423|gb|GD738622.1|GD738622
EST:     TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG                         TTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA
genomic: TTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtg ... tgtctatcagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGAAATGCTTGTTAATTTGGGAATTCCTTGGGTTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAGgtacaaagtgttcaattggccttgctttatattctcttgttaaaaaattctactttgtgaagttgcttgtaatggcaaaaacataacatttactaaatattttactgtctatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT