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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttaggacactattatatgaatatcatctatttaatgtaaagtaaatatgtttgaatttgggatcatggactaagaatgatgatgattatgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCTAGCATTCAACATTGTTGCATGGATTGAAGATGTTCTTTATGTAGATAAA

Basic information

species Glycine max
transcript GLYMA18G46690.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46690.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G00460.1 (Arabidopsis thaliana), 3'ss of exon 6
attttaggacactattatatgaatatcatctatttaatgtaaagtaaatatgtttgaatttgggatcatggactaagaatgatgatgattatgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCTAGCATTCAACATTGTTGCATGGATTGAAGATGTTCTTTATGTAGATAAA-
   | |  ||   |  ||| || | ||    ||| ||| | |    | ||   |  | |     || |   |  || | || ||    || || |||||||||||| || ||||| ||  | ||||| || ||||||||  | |||||  |||| || ||||| ||||| |||||||| |||||||| |||||||| ||| 
--gtaaaaactgaagaata-gagtgtc--tcattgaatttgat---agtacactatagt----aattactta--aaaagtgttgtgctttttggtttgcagGATGTTGGAAAAGCTGTGTTGGAGAGCTACTCAAGAGTACTTGAAGGTTTAGCTTTTAACATAGTTGCTTGGATTGATGATGTTCTCTATGTAGACAAAA

upper sequence: GLYMA18G46690.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G01700.1 (Arabidopsis thaliana), 3'ss of exon 6
attttaggacactattatatgaatatcatctatttaatgtaaagtaaatatgtttgaatttgggatcatggacta--agaatgatg-atgatt-atgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCTAGCATTCAACATTGTTGCATGGATTGAAGATGTTCTTTATGTAGATAAA-
                              || ||||   | |   | |     |||||   |  | || || ||  | ||  ||  ||| ||  || |||||||||||| || ||||| ||  |||||||||||||||||||| | |||||  |||| || ||||| ||||| |||||||| ||||||||||||||||| ||| 
-----------------------------gtaattaagaaacaaacagtg-acctgaatcatgttttattgaatattataacaatttatggtttgtggtttgcagGATGTTGGAAAAGCTGTGTTAGAGAGTTATTCAAGAGTTCTTGAAGGTTTAGCTTTTAACATAGTTGCTTGGATTGATGATGTTCTTTATGTAGACAAAA

upper sequence: GLYMA18G46690.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0046g02530.t01 (Vitis vinifera), 3'ss of exon 6
attttaggacactattatatgaatatcatctatttaatgtaaagtaaatatgtttgaatttgggatcatggactaagaatgat-----gatgattatgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCTAGCATTCAACATTGTTGCATGGATTGAAGATGTTCTTTATGTAGATAAA-
               |     | |  |||| |  | |   ||||  || ||    | |      ||||||     | |||||      |   | ||| | ||||||||||| ||| | ||  | || ||||| || || ||||| |||||| | |||||||||| ||||||||| ||||||||||||||  |  ||| ||| | | 
--------------gtgagcaactg-catccaaattactaaaagctaaaattccagga----aaatcatgagtagaaaatgactgaaaggaaaatatttgttgcagGATGTCGGGCAGGCGATCCTGGAGAGCTACTCTAGAGTGTTGGAAAGTCTAGCATTCAGCATTGTTGCTTGGATTGAAGATGTATTACATGAAGACAGAA

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|193582959|gb|FK543171.1|FK543171
EST:     ATCCAATACAACCG                         GGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
genomic: ATCCAATACAACCGggtaagttta ... atgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
EST: gi|207810941|gb|GD782946.1|GD782946
EST:     CCTGAACTTTCACAAACTTCTTTGGACACATGCAAGATCCAATACAACCG                         GGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
genomic: CCTGAACTTTCACAAACTTCTTTGGACACATGCAAGATCCAATACAACCGggtaagttta ... atgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
EST: gi|207757857|gb|GD727679.1|GD727679
EST:     CCTGAACTTTCACAAACTTCTTTGGACACATGCAAGATCCAATACAACCG                         GGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
genomic: CCTGAACTTTCACAAACTTCTTTGGACACATGCAAGATCCAATACAACCGggtaagttta ... atgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
EST: gi|208172308|gb|GD966685.1|GD966685
EST:     ATCCAATACAACCG                         GGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
genomic: ATCCAATACAACCGggtaagttta ... atgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
EST: gi|208090889|gb|GD889186.1|GD889186
EST:     CCTGAACTTTCACAAACTTCTTTGGACACATGCAAGATCCAATACAACCG                         GGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
genomic: CCTGAACTTTCACAAACTTCTTTGGACACATGCAAGATCCAATACAACCGggtaagttta ... atgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
EST: gi|193658238|gb|FK605415.1|FK605415
EST:     CCTGAACTTTCACAAACTTCTTTGGACACATGCAAGATCCAATACAACCG                         GGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
genomic: CCTGAACTTTCACAAACTTCTTTGGACACATGCAAGATCCAATACAACCGggtaagttta ... atgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
EST: gi|208312137|gb|GE109905.1|GE109905
EST:     ATCCAATACAACCG                         GGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT
genomic: ATCCAATACAACCGggtaagttta ... atgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatgtttgaatttgggatcatggactaagaatgatgatgattatgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCTAGCATTCAACATTGTTGCATGGATTGAAGATGTTCTTTATGTAGATAAA
                                          attatgtttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttaggacactattatatgaatatcatctatttaatgtaaagtaaatatgtttgaatttgggatcatggactaagaatgatgatgattatgttttgcaGGATGTGGGGAAAGCAGTACTAGAGAGTTATTCAAGAGTTTTGGAAGGCCTAGCATTCAACATTGTTGCATGGATTGAAGATGTTCTTTATGTAGATAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - -atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgatg