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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgatatgtgagttgtggcatcatatttttgctctacctgattttagctgtttctcaatgtgtacatttgcattgtttaattgatattttgacactgaagCTTCTACAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGTCAGCTGGGCCTGGACTTGAATCTCTTGTAGATC

Basic information

species Glycine max
transcript GLYMA15G40590.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40590.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0039g00240.t01 (Vitis vinifera), 3'ss of exon 1
--ctgatatgtgagttgtggcatcatatttttgctctacctg--attttagctgtttctcaatgtgtacatttgcattgtttaattgatat-tttgacactgaagCTT-----CTACAGGTGC----AAGGATAAGTGTGTGATCTATC---TATAAAC--GCAAGATGTCAGCTGGGCCTGGACTTGAATCTCTTGTAGATC
  |  |  ||||| |  ||   ||||  || |  | | |||   ||| |   ||||  ||  |||| | || |  |   |||  ||||| | |||  ||   ||  ||     | ||  || |    | || |  |  | | || ||||   ||  |||  |||| |||||| |||||||||||||||| ||||||||||   
cccaaagttgtgaataatgaattcattcttatagtgttcctacaattcttattgttattccgtgtgcaaatatttaagatttgcttgatttcttttgcagGAAAATTTGCTAGCAACCAGTTCTTCCAGGGGTTTGGCTATTATTTATCAGTTACCAACTTGCAACATGTCAACTGGGCCTGGACTTGAGTCTCTTGTAG---
















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|151399825|gb|EV269696.1|EV269696
EST:     CGACTTATCTCCGGAGACCCACAACTTTTCCGGCGACCAACCGT--GC-G                         ------CAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGT
genomic: CGACTTATCTCCGGAGACCCACAACTTTTCCGGCGACCAACCGTGCGCAGgttttttttc ... gacactgaagCTTCTACAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGT
EST: gi|213598025|gb|DB972213.1|DB972213
EST:     CGACTTATCTCCGGAGACCCACAACTTTTCCGGCGACCAACCGTGCGCAG                         CTTCTACAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGT
genomic: CGACTTATCTCCGGAGACCCACAACTTTTCCGGCGACCAACCGTGCGCAGgttttttttc ... gacactgaagCTTCTACAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGT
EST: gi|192300037|gb|FG992190.1|FG992190
EST:     CGACTTATCTCCGGAGACCCACAACTTTTCCGGCGACCAACCGT--GC-G                         ------CAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGT
genomic: CGACTTATCTCCGGAGACCCACAACTTTTCCGGCGACCAACCGTGCGCAGgttttttttc ... gacactgaagCTTCTACAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGT
EST: gi|151395293|gb|EV265164.1|EV265164
EST:     CGACTTATCTCCGGAGACCCACAACTTTTCCGGCGACCAACCGT--GC-G                         ------CAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGT
genomic: CGACTTATCTCCGGAGACCCACAACTTTTCCGGCGACCAACCGTGCGCAGgttttttttc ... gacactgaagCTTCTACAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGT
EST: gi|192310889|gb|FG998893.1|FG998893
EST:     CGACTTATCTCCGGAGACCCACAACTTTTCCGGCGACCAACCGT--GC-G                         ------CAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGT
genomic: CGACTTATCTCCGGAGACCCACAACTTTTCCGGCGACCAACCGTGCGCAGgttttttttc ... gacactgaagCTTCTACAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgtttctcaatgtgtacatttgcattgtttaattgatattttgacactgaagCTTCTACAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGTCAGCTGGGCCTGGACTTGAATCTCTTGTAGATC
                                         ttttgac  putative branch site (score: 3)
                          attgtttaattgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgatatgtgagttgtggcatcatatttttgctctacctgattttagctgtttctcaatgtgtacatttgcattgtttaattgatattttgacactgaagCTTCTACAGGTGCAAGGATAAGTGTGTGATCTATCTATAAACGCAAGATGTCAGCTGGGCCTGGACTTGAATCTCTTGTAGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
-tgatatg
- - - - - -gttgtgg
- - - - - - - - - - - - - - - -ctctacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcattg