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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtctcaaagtaaaaaaaatttatattatggttttttaatcatgataccatagcaagatcttatttattagttactgattatacttttttattgcacagGTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCAACATTTACCCAGCAGCAATTCCGAGAATTTGATTATGAGAAGTTCACTC

Basic information

species Glycine max
transcript GLYMA02G46300.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46300.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0090g01020.t01 (Vitis vinifera), 3'ss of exon 9
ctgtctcaaagtaaaaaaaatttatattatggttttttaatcatgataccatagcaagatcttatttatt--agttactgattatacttttttattgcacagGTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCAACATTTACCCAGCAGCAATTCCGAGAATTTGATTATGAGAAGTTCACTC
||  ||     | |       | | || ||  |||||   ||  || |   |||  || |  |  ||||   | ||| |  ||| |   ||  |||||  ||||||| |||||||| ||||     || ||||||| ||||||||||||||||||||| ||||| ||| |||| | ||| ||||| ||||||||||||||||
ctaactagccttgattttgtctcaaatcat--tttttgtttctggagattgtagatagcttgttcttatggaaattaatctttaaagcattgcattgcttagGTCAAGATTAGAGGGAGGTTGTCCCAATGTGAAGTTTGTGGAGAAAATGCAACATTCACCCAACAGAAATTTCAAGATTTTGACTATGAGAAGTTCACTC
















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|26059118|gb|CA802032.1|CA802032
EST:     TCTCAGGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATT                         GTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCA
genomic: TCTCAGGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATTgtatgttaaa ... tattgcacagGTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCA
EST: gi|193330487|gb|FK295335.1|FK295335
EST:     CTGGACGGATTCGTATT                         GTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCA
genomic: CTGGACGGATTCGTATTgtatgttaaa ... tattgcacagGTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCA
EST: gi|208145588|gb|GD942709.1|GD942709
EST:     TCTCAGGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATT                         GTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAG
genomic: TCTCAGGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATTgtatgttaaa ... tattgcacagGTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAG
EST: gi|208232144|gb|GE033955.1|GE033955
EST:     TCTCAGGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATT                         GTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAG
genomic: TCTCAGGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATTgtatgttaaa ... tattgcacagGTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAG
EST: gi|31311697|gb|CD396900.1|CD396900
EST:     CAGGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATT                         GTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCA
genomic: CAGGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATTgtatgttaaa ... tattgcacagGTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCA
EST: gi|208250717|gb|GE043764.1|GE043764
EST:     TCTCAGGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATT                         GTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAG
genomic: TCTCAGGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATTgtatgttaaa ... tattgcacagGTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAG
EST: gi|9899477|gb|BE608445.1|BE608445
EST:     TCTCAAGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATT                         GTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCA
genomic: TCTCAGGAAGGATGCTTATCTTGGATGCATTGTCTGGACGGATTCGTATTgtatgttaaa ... tattgcacagGTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccatagcaagatcttatttattagttactgattatacttttttattgcacagGTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCAACATTTACCCAGCAGCAATTCCGAGAATTTGATTATGAGAAGTTCACTC
                            tactgat  putative branch site (score: 2)
                                       cttttttatt  putative PPT
             atcttatttattagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtctcaaagtaaaaaaaatttatattatggttttttaatcatgataccatagcaagatcttatttattagttactgattatacttttttattgcacagGTCAAAATTAGAGGAAGGTCTATGCAGTGTGAAGCTTGTGGAGAAAATGCAACATTTACCCAGCAGCAATTCCGAGAATTTGATTATGAGAAGTTCACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
ctgtctc
- - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - -tgatacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttactg