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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttaatgatggaaacgggtgctattgcttcatgctacaaagttatgtgtcttatgcattttgtctgatatatgattttctatatataatttaattgcagATCTCGGCTATTACTTGGATCATTGGTTCCCTCATCATGGGCATAAATATATACTATTTATTGACTAGCTTTGTCAAATTGCTTCTGCACGTCCACTTAA

Basic information

species Glycine max
transcript GLYMA08G23320.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23320.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 3'ss of exon 13
-----agttaatgatggaaacgggtgctattgcttcatgctacaaagttatgtgtcttatgcattttgtctgatatatgattttctatatataatttaattgc-agATCTCGGCTATTACTTGGATCATTGGTTCCCTCATCATGGGCATAAATATATACTATTTATTGACTAGCTTTGTCAAATTGCTTCTGCACGTCCACTTAA
     |  | || ||  |   |||||  |||     |||    || |  |||| | || |     ||  |   ||| ||| |   | | | |     |    | ||||  | || || ||||||||||| ||||||||  |||||| |||||||||||||||| |     | || ||  |||| |||||||| |||  ||| ||||
ctacaatgtgatcattaatgagggtggaatta----atgaagtaatgc-atgtatttttttagacttaacaattat-tgactcgatttttttccccaaccccccagATTACAGCCATCACTTGGATCATCGGTTCCCTTCTCATGGCCATAAATATATACTATCTTGCATCCAGTTTCATCAAGTTGCTTCTTCACAGCCATTTAA
















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|254317210|gb|GR826155.1|GR826155
EST:     AGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCACG                         ATCTCGGCTATTACTTGGATCATTGGTTCCCTCATCATGGGCATAAATATA
genomic: AGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCACGgtaatttttt ... ttaattgcagATCTCGGCTATTACTTGGATCATTGGTTCCCTCATCATGGGCATAAATATA
EST: gi|22523022|gb|BU081833.1|BU081833
EST:     AGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCACG                         ATCTCGGCTATTACTTGGATCATTGGTTCCCTCATCATGGGCATAAATATA
genomic: AGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCACGgtaatttttt ... ttaattgcagATCTCGGCTATTACTTGGATCATTGGTTCCCTCATCATGGGCATAAATATA
EST: gi|51344688|gb|CO985421.1|CO985421
EST:     AGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCACG                         ATCTCGGCTATTACTTGGATCATTGGTTCCCTCATCATGGGCATAAATATA
genomic: AGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCACGgtaatttttt ... ttaattgcagATCTCGGCTATTACTTGGATCATTGGTTCCCTCATCATGGGCATAAATATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtcttatgcattttgtctgatatatgattttctatatataatttaattgcagATCTCGGCTATTACTTGGATCATTGGTTCCCTCATCATGGGCATAAATATATACTATTTATTGACTAGCTTTGTCAAATTGCTTCTGCACGTCCACTTAA
                                           atttaat  putative branch site (score: 4)
            attttgtctgatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttaatgatggaaacgggtgctattgcttcatgctacaaagttatgtgtcttatgcattttgtctgatatatgattttctatatataatttaattgcagATCTCGGCTATTACTTGGATCATTGGTTCCCTCATCATGGGCATAAATATATACTATTTATTGACTAGCTTTGTCAAATTGCTTCTGCACGTCCACTTAA

- - -atgatgg
- - - - - - - -cgggtgc
- - - - - - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - - - - -tatgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - cttatgc