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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcggaactgtttgctatctactgagcacattcactgacttattgacatttttgtttagtataatggctaacagctgtgtgtttatgacttttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCAGTAAGCTGGAAATTTCTTTTTCCGAGGAGGAAATAAATGATCTTTTTGA

Basic information

species Glycine max
transcript GLYMA08G33830.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G33830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0015g01200.t01 (Vitis vinifera), 3'ss of exon 2
gtcggaactgtttgctatctactgagcacattcactgacttattgacatttttgtttagtataatggctaacagctgtgtgtttatgacttttctt-atagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCAGTAAGCTGGAAATTTCTTTTTCCGAGGAGGAAATAAATGATCTTTTTGA
 |  | |||| |      ||    | ||   |   ||   ||||  | | ||   |   |   ||| |     | ||    |   ||  ||||||| |||||||||||||| ||||| ||||||||||| || ||  ||||||  ||||||  ||| ||||| ||||||||||| ||||||||||| || |||||||||||
ttgagcactgctattatgctgtgtatcatccttcatgttgtatttgcttcttccctctctgacatg-ccggtggttgaaattcattgttttttcttcatagATGAGGATTCAAATGGTGCAATAGATCATGAAGAACTGAAAAGATGTTTCCTTAAACTGGAGATTTCTTTTTCAGAGGAGGAAATCAACGATCTTTTTGA
















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|151409948|gb|EV279756.1|EV279756
EST:     AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTG                         ATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
genomic: AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTGgtaggtttcc ... tttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
EST: gi|298193020|gb|HO033465.1|HO033465
EST:     AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTG                         ATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
genomic: AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTGgtaggtttcc ... tttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
EST: gi|298198185|gb|HO039724.1|HO039724
EST:     AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTG                         ATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
genomic: AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTGgtaggtttcc ... tttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
EST: gi|298170086|gb|HO018710.1|HO018710
EST:     AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTG                         ATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
genomic: AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTGgtaggtttcc ... tttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
EST: gi|298194650|gb|HO043122.1|HO043122
EST:     AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTG                         ATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
genomic: AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTGgtaggtttcc ... tttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
EST: gi|298163700|gb|HO012433.1|HO012433
EST:     AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTG                         ATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAG
genomic: AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTGgtaggtttcc ... tttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAG
EST: gi|192305727|gb|FG995697.1|FG995697
EST:     GAAAATGCAAAGCCATATTTGAGCAGTTTG                         ATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
genomic: GAAAATGCAAAGCCATATTTGAGCAGTTTGgtaggtttcc ... tttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
EST: gi|22523171|gb|BU081982.1|BU081982
EST:     AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTG                         ATGATGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
genomic: AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTGgtaggtttcc ... tttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
EST: gi|298169069|gb|HO020429.1|HO020429
EST:     AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTG                         ATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA
genomic: AAAGATTGATGAGAGCCTTAGAAAATGCAAAGCCATATTTGAGCAGTTTGgtaggtttcc ... tttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatttttgtttagtataatggctaacagctgtgtgtttatgacttttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCAGTAAGCTGGAAATTTCTTTTTCCGAGGAGGAAATAAATGATCTTTTTGA
                    ggctaac  putative branch site (score: 2)
                                           cttttcttat  putative PPT
     tttgtttagtataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggaactgtttgctatctactgagcacattcactgacttattgacatttttgtttagtataatggctaacagctgtgtgtttatgacttttcttatagATGAGGATTCTAATGGGGCAATAGATCAAGAGGAGTTGAAAAAGTGTTTCAGTAAGCTGGAAATTTCTTTTTCCGAGGAGGAAATAAATGATCTTTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - tgctatc
- - - - - - - - - -tactgag
- - - - - - - - - - - - - - cattcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagctgt