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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttttttgccaacaggcgtccaaatataaaattaaatgatgtaatgacaaatagtaaccgggttgactaagatttacctttcctccttgactggcagTTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAAAAGTACAAGATGCATGCAGTTGTTGCAAATGAACTCTCAACTCGCAAGG

Basic information

species Glycine max
transcript GLYMA04G43390.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G43390.3 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0001g04420.t01 (Vitis vinifera), 3'ss of exon 9
ttgtttttttgccaacaggcgtccaaatataaaattaaatgatgtaatgacaaatagtaaccgggttgactaagatttacctttcctccttgactggcagTTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAAAAGTACAAGATGCATGCAGTTGTTGCAAATGAACTCTCAACTCGCAAGG
    |      | || |    |  ||   | ||||   |   | |  | |   | || |       |   |    || || ||  |   ||   |  ||| | |||||||||||||| || ||| || | || |||| |   |||||| | ||||||||||||||||| || || |||||||| || |||||||| || |
agagtaaaaaacaaaaaaatatgtaagattgaaatggcaatgtttgtttagttagaggagggcaaatttttcttgttaacattgtcaatttttttaacagCTGGAGACAGATTCAAATATCCTTTTACAAAAGGCTGATATGGCTCTTCAGAAGTACAAGATGCATGCTGTGGTAGCAAATGAGCTTTCAACTCGTAAAG
















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|254326215|gb|GR840807.1|GR840807
EST:     CAGTGC-TAGGAAAGA-TGGGCT-CTCTGGCTTTCTGCATATC-TTCAAG                         TTAGAGACAGA-TCAAACA-TC-TCTAAATAAAGCTGGTGCAGCTCTTGAA
genomic: CAGTGCTTAGGAAAGATTGGGCTCCTCTGGCTTTCTGCATATCTTTCAAGgtattgatat ... tgactggcagTTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAA
EST: gi|254340902|gb|GR854630.1|GR854630
EST:     CAGTGCTTAGGAAAGATTGGGCTCCTCTGGCTTTCTGCATATCTTTCAAG                         TTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAA
genomic: CAGTGCTTAGGAAAGATTGGGCTCCTCTGGCTTTCTGCATATCTTTCAAGgtattgatat ... tgactggcagTTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAA
EST: gi|254340903|gb|GR854631.1|GR854631
EST:     CAGTGCTTAGGAAAGATTGGGCTCCTCTGGCTTTCTGCATATCTTTCAAG                         TTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAA
genomic: CAGTGCTTAGGAAAGATTGGGCTCCTCTGGCTTTCTGCATATCTTTCAAGgtattgatat ... tgactggcagTTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAA
EST: gi|51344192|gb|CO984925.1|CO984925
EST:     CAGTGCTTAGGAAAGATTGGNNNNNNNTGGCTTTCTGCATATCTTTCAAG                         TTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAA
genomic: CAGTGCTTAGGAAAGATTGGGCTCCTCTGGCTTTCTGCATATCTTTCAAGgtattgatat ... tgactggcagTTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAA
EST: gi|31561978|gb|CD487816.1|CD487816
EST:     CAGTGCTTAGGAAAGATTGGGCTCCTCTGGCTTTCTGCATATCTTTCAAG                         TTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAA
genomic: CAGTGCTTAGGAAAGATTGGGCTCCTCTGGCTTTCTGCATATCTTTCAAGgtattgatat ... tgactggcagTTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAA
EST: gi|298163079|gb|HO011812.1|HO011812
EST:     CAGTGCTTAGGAAAGATTGGGCTCCTCTGGCTTTCTGCATATCTTTCAAG                         TTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAA
genomic: CAGTGCTTAGGAAAGATTGGGCTCCTCTGGCTTTCTGCATATCTTTCAAGgtattgatat ... tgactggcagTTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgacaaatagtaaccgggttgactaagatttacctttcctccttgactggcagTTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAAAAGTACAAGATGCATGCAGTTGTTGCAAATGAACTCTCAACTCGCAAGG
                              tttacctttcctcctt  CT-rich tract
      aaatagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttttttgccaacaggcgtccaaatataaaattaaatgatgtaatgacaaatagtaaccgggttgactaagatttacctttcctccttgactggcagTTAGAGACAGATTCAAACATTCTTCTAAATAAAGCTGGTGCAGCTCTTGAAAAGTACAAGATGCATGCAGTTGTTGCAAATGAACTCTCAACTCGCAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG