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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgatatgttcttttctattattcaattaccattaacctctacatgttcttctctcaaagctcaatttaaccatatctttttcacttggattaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG

Basic information

species Glycine max
transcript GLYMA10G36210.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G34320.1 (Arabidopsis thaliana), 3'ss of exon 11
ttcgatatgttcttttctattattcaattaccattaacctctacatgttcttctctcaaagc---tcaatttaaccatatctttttcacttggattaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG
   ||| | ||  ||    | |   ||  |     ||   |   |  ||   || | ||||    |||   | |   |    | ||  |||   | ||   ||||| |||||||| ||||||||||||||||||||||| | | | ||
--tgatgtcttaattctgttaacaaaagcatgtaaaattcccttagttttaactattaaagtaagtcagacttattcttctgtcttttcttttctcaacc-agAGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGG

upper sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 10
ttcgatatgttcttttctattattcaattaccattaacctctacatgttcttctctcaaagctcaatttaaccatatctttttcacttggattaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG
 |   |||||| || ||| || || | |||  ||| |  | |   | || |   || ||    |    |   | | ||| |   | || |  |   | |||||||||||||||||||| |||||||| |||||||| ||||| ||
gtttttatgtttttgtctcttttttatttattatttatttatttttcttttatcctaaactaacctggtgtgcttgtctctgcaattttgtctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG

upper sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S54_228V6.1 (Physcomitrella patens), 3'ss of exon 10
ttcgatatgttcttttctattattcaattaccattaacctctacatgttcttctctcaaagctcaatttaaccatatctttttcacttggattaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG
|    | |  |  || ||  ||||   | |      | ||      ||| | |||  |      |   |  |  ||    ||| | |||| ||     ||    |||||||||||||||||||||||||| ||||| ||| | ||
tcttgtgttatagttactgctatttcgtgaatgagtatcttgtttggttatactcaaatcatggacgatctctttaatgctttgaattgggttgccacagGAAGCATCATGGCTTTGGATGGGTTGGAGAGTGGGCGAATGCTGG

upper sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ35129 (Selaginella moellendorffii), 3'ss of exon 9
ttcgatatgttcttttctattattcaattaccattaacctctacatgttcttctctcaaagctcaatttaaccatatctttttcacttggattaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG
                                 ||||    ||            |   | | | |   | ||   ||||||| |     ||   | |||||||||||| || |||||||||||||| |||||||| ||| | ||
--------------------------------gttaattcatatggtcaagctcgtgtgaacgctaaccagcctcctcttttttatc--aatc--tctagAGCTCATCACGGATTTGGATGGGTTGGCGAATGGGCAAATTCTGG

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|15662904|gb|BI700275.1|BI700275
EST:     ATGGAGAAAATATTGCAATGGCTTGTTCCTATTGCCGCCAATACAACAAA                         AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG
genomic: ATGGAGAAAATATTGCAATGGCTTGTTCCTATTGCCGCCAATACAACAAAgtatatttgc ... attaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG
EST: gi|120490977|gb|EH219144.1|EH219144
EST:     ATGGAGAAAATATTGCAATGGCTTGTTCCTATTGCCGCCAATACAACAAA                         AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG
genomic: ATGGAGAAAATATTGCAATGGCTTGTTCCTATTGCCGCCAATACAACAAAgtatatttgc ... attaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG
EST: gi|207759243|gb|GD734386.1|GD734386
EST:     ATGGAGAAAATATTGCAATGGCTTGTTCCTATTGCCGCCAATACAACAAA                         AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG
genomic: ATGGAGAAAATATTGCAATGGCTTGTTCCTATTGCCGCCAATACAACAAAgtatatttgc ... attaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcttctctcaaagctcaatttaaccatatctttttcacttggattaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG
                                            gattaat  putative branch site (score: 3)
                                             attaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcgatatgttcttttctattattcaattaccattaacctctacatgttcttctctcaaagctcaatttaaccatatctttttcacttggattaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - ccattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttgg