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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAAAACCACCAAGAAAATTGTGTTGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatcactttccgtcgtcgttttgtattgttattgtgcatgtttggtttacagtcgaaaatgctgctgtgcacgaaccaatgcaaatccaatgaa...

Basic information

species Glycine max
transcript GLYMA05G24930.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G24930.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g33898.1 (Oryza sativa), 5'ss of exon 3
GCGAAAACCACCAAGAAAATTGTGTTGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatcactttccgtcgtcgttttgtattgttattgtgcat-gtttggtttacagtcgaaaatgctgctgtgcacgaaccaatgcaaatccaatgaa
|| |||||||||||||| |||||| ||| ||| || |||||| | |||||||||  ||| |||||| | |||||||||     ||| | ||     ||    || |   || |  || ||   |  || |    |   |  || ||      |     || |   | ||     | 
GCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAGgtattatttcattgtcaagactcaagctgaaa-attgtcatgaatcaatcagtatctttttagatgtgttgggtgctatcttacattattattctttacag

upper sequence: GLYMA05G24930.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 5'ss of exon 3
GCGAAAACCACCAAGAAAATTGTGTTGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatcactttccgtcgtcgttttgtattgttattgtgcatgtttggtttacagtcgaaaatgctgctgtgcacgaaccaatgcaaatccaatgaa-
|| |||||||||||||| |||||| ||| ||| || |||||| | |||||||||  ||| |||||| | |||||||||      || | |      ||    || |   || |  || ||     || |    |   |  || ||   ||| |      ||    || |  || | 
GCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAGgtatttttgcaatgtgaagattcaagctgaaa-attctcatgaat---cagtatctttttagatgtgttgg-atgctcacttacataattattctgtgcag

upper sequence: GLYMA05G24930.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv13s0064g00880.t01 (Vitis vinifera), 5'ss of exon 3
GCGAAAACCACCAAGAAAATTGTGTTGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgt-aaagcatcactttccgtcgtcgttttgtattgttattgtgcatgtttggtttacagtcgaaaatgctgctgtgcacgaaccaatgcaaatccaatgaa---------
|| || ||||||||||| |||||  |||||||||||||||| || ||||| || || || |||||| | |||||||| | ||  | |   ||   |  |  |||    | || |  ||| | ||||  |||||  |   | |  | |       |||    ||    | ||||            
GCTAAGACCACCAAGAAGATTGTTCTGAGGCTCCAGTGCCAGGGTTGCAAACACGTATCCCAGCACCCAATCAAGgtcagagtcttaacctcaagctacacttt----tcttttcctgcct-tttgtgttacaccccttacttttac-acaactgaatttttgttgttgcaattgggttttgcag

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|9902402|gb|BE611370.1|BE611370
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|17153656|gb|BM143589.1|BM143589
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|213617916|gb|DB967643.1|DB967643
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|207737990|gb|GD715670.1|GD715670
EST:     GCTCCAGTGACCAAAGGAATAGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: GCTCCAGTG-CC-AAGG-AT-GCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|192301868|gb|FG995486.1|FG995486
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|6095086|gb|AW119753.1|AW119753
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|14516449|gb|BI095121.1|BI095121
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|14258595|gb|BG881503.1|BG881503
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|151409954|gb|EV279762.1|EV279762
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATTTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|6747215|gb|AW317671.1|AW317671
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|8827682|gb|BE211412.1|BE211412
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|8826849|gb|BE210579.1|BE210579
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAA
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAA
EST: gi|8827235|gb|BE210965.1|BE210965
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|4314152|gb|AI461271.1|AI461271
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATC
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTT-GAGATCGGTGGTGACAAGAAGGGAAAAGGAACATC
EST: gi|193458986|gb|FK421723.1|FK421723
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
EST: gi|15287700|gb|BI471591.1|BI471591
EST:     TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG                         AGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT
genomic: TGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatc ... tgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAAAACCACCAAGAAAATTGTGTTGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAGgtaaagcatcactttccgtcgtcgttttgtattgttattgtgcatgtttggtttacagtcgaaaatgctgctgtgcacgaaccaatgcaaatccaatgaa

- - - - - - - - - - - - - - - - - - - -  AGGATG