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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaattttaatatttaattgtgtcatagatgataattggataaaccaaacaaacaaattggttctcctttctaatttttttctactctgactgacacagGATAAGTCGAATGGGCTAAGTCGAGGAGGACCAAGACAAAGGGCTGAAGCCTTAGCAGCCTTAAACTCTGCATTTAATTCATCATCTGGAACCAAAGTTT

Basic information

species Glycine max
transcript GLYMA03G29280.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 20
lower sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 22
-taaaattttaat-----atttaattgtgtcatagatgataattggataaaccaaacaaacaaattggttctcctttctaatttttttctactctgactgacacagGATAAGTCGAATGGGCTAAGTCGAGGAGGACCAAGACAAAGGGCTGAAGCCTTAGCAGCCTTAAACTCTGCATTTAATTCATCATCTGGAACCAAAGTTT
  |||  ||| |      ||  |||  | ||  | || | |  |        |  |    |    |   |   |||      |  |||||       | ||  |  || |  || |||||   ||||| ||| || |||||||||||||||||||| ||||| |||||||  || ||||| ||||| ||| |    | ||||||  
gcaaacctttgagttgcaatcaaataatttctcaaatcacagctactagtgtcccatgttcttgatatgttgacttagacgctcatttctttaactgcagAGCCGAGACAGATCAAATGG---AAGTCAAGGGGGTCCAAGACAAAGGGCTGAAGCTTTAGCCGCCTTAACATCCGCATTCAATTCTTCA-CCATCATCAAAGT--
















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|7591265|gb|AW707001.1|AW707001
EST:     CTGCCTTAAATAATGCATTC-ATTCATCTCCTGAGGCAACATCCAGTGCG                         GATAAGTCGAATGGGCTAAGTCGAGGAGGACCAAGACAAAGGGCTGAAGCC
genomic: CTGCCTTAAATAATGCATTCAATTCATCTCCTGAGGCAACATCCAGTGCGgtacagcaac ... actgacacagGATAAGTCGAATGGGCTAAGTCGAGGAGGACCAAGACAAAGGGCTGAAGCC
EST: gi|193674835|gb|FK620433.1|FK620433
EST:     CTGCCTTAAATAATGCATTCAATTCATCTCCTGAGGCAACATCCAGTGCG                         GATAAGTCGAATGGGCTAAGTCGAGGAGGACCAAGACAAAGGGCTGAAGCC
genomic: CTGCCTTAAATAATGCATTCAATTCATCTCCTGAGGCAACATCCAGTGCGgtacagcaac ... actgacacagGATAAGTCGAATGGGCTAAGTCGAGGAGGACCAAGACAAAGGGCTGAAGCC
EST: gi|14126732|gb|BG791170.1|BG791170
EST:     CTGCCTTAAATAATGCATTCAATTCATCTCCTGAGGCAACATCCAGTGCG                         GATAAGTCGAATGGGCTAAGTCGAG
genomic: CTGCCTTAAATAATGCATTCAATTCATCTCCTGAGGCAACATCCAGTGCGgtacagcaac ... actgacacagGATAAGTCGAATGGGCTAAGTCGAG
EST: gi|207822164|gb|GD793525.1|GD793525
EST:     CTGCCTTAAATAATGCACTCAATTCATCTCCTGAGGCAACATCCAGTGCG                         GATAAGTCGAATGGGCTAAGTCGAGGAGGACCAAGACAAAGGGCTGAAGCC
genomic: CTGCCTTAAATAATGCATTCAATTCATCTCCTGAGGCAACATCCAGTGCGgtacagcaac ... actgacacagGATAAGTCGAATGGGCTAAGTCGAGGAGGACCAAGACAAAGGGCTGAAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaacaaacaaattggttctcctttctaatttttttctactctgactgacacagGATAAGTCGAATGGGCTAAGTCGAGGAGGACCAAGACAAAGGGCTGAAGCCTTAGCAGCCTTAAACTCTGCATTTAATTCATCATCTGGAACCAAAGTTT
                                            gactgac  putative branch site (score: 2)
                       tttctaatttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaattttaatatttaattgtgtcatagatgataattggataaaccaaacaaacaaattggttctcctttctaatttttttctactctgactgacacagGATAAGTCGAATGGGCTAAGTCGAGGAGGACCAAGACAAAGGGCTGAAGCCTTAGCAGCCTTAAACTCTGCATTTAATTCATCATCTGGAACCAAAGTTT

- - - - - - - - - - - - - - - - - - - - - - -ccaaaca