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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgctttgctttgttcagtaactgtcaactagtaatctgattcttagagaaaggtctaaagagtggttttattttgtttcattcatcaatgaagg

Basic information

species Glycine max
transcript GLYMA18G03480.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G439457_T01 (Zea mays), 5'ss of exon 6
----------------------------------TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgctttgctttgttcagtaactgtcaactagtaatctgattcttagagaaaggtctaaagagtggttt-tattttgtttcattcatcaatgaagg
                                  ||||||||| | ||||| ||||||||| | || ||||||||||| |||||||| || || |||  ||||     |    |      ||| || |   ||   | |||   || ||  || ||  | | || | |  ||| ||  || ||  |              
AGTCTAAATTTGATATTCTTTCTATTTGGACAGTTTCATTTCTGTGCCAAAAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattccagtac---tagtgacagatgacc--ttatcattttgttgaagcaatatgtcaacattactttgtaactttttgtag-------------

upper sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G439457_T02 (Zea mays), 5'ss of exon 7
-TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgctttgctttgttcagtaactgtcaactagtaatctgattcttagagaaaggtctaaagagtggttt-tattttgtttcattcatcaatgaagg
 ||||||||| | ||||| ||||||||| | || ||||||||||| |||||||| || || |||  ||||     |    |      ||| || |   ||   | |||   || ||  || ||  | | || | |  ||| ||  || ||  |              
TTTCATTTCTGTGCCAAAAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattccagtac---tagtgacagatgacc--ttatcattttgttgaagcaatatgtcaacattactttgtaactttttgtag-------------

upper sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 7
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 5'ss of exon 6
-TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgctttgctttgttcagtaactgtcaac-tagtaatctgattcttagagaaaggtctaaagagtggttttattttgtttcattcatcaatgaagg
 |||||||| || ||||| ||||||||||| || ||||| ||||| ||||||||||| |||||   ||| | ||||   |||     | | ||    |   |   ||| | |||  ||||| |||    | | | ||    |     | ||   || || ||| || 
GTTCATTTCGATTCCAAAAGACATGGGAACATTCAACTGCGGAGCGTTTGTTGCTGGCATAGTGAAGgtgagtgctcc-cttgacatattcacgaatagggttcaaatttaattggtagaggaaga---agataatgagcctgacacggtt---tcctctatgtag-

upper sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 6
-TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgctttgctt-tgttcagtaactgtcaactagtaatctgattcttagagaaaggtctaaagagtggttttattttgtttcattcatcaatgaagg
 || || || || || || ||||||||||| || |||||||| |||||||||||||| || ||| |||||  | |  || || | || | ||| | ||   || |  |||| |  ||   ||||| ||| |  |   |||||  ||| ||||  || |  | |    
ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGTTGCTGGCATTGTAAGGgtatgtaccatgtttgtttttactaattatctg-tact--tctggtcatt---gaaagctctgacaaacagtttttatttttttc--tctttgaag----

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|298197159|gb|HO041902.1|HO041902
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCT
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCT
EST: gi|192302735|gb|FG993755.1|FG993755
EST:     GGACATAGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|5606114|gb|AI900212.1|AI900212
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGN                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTCTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|6725080|gb|AW309479.1|AW309479
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|254342930|gb|GR859092.1|GR859092
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|254334110|gb|GR849028.1|GR849028
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|192304323|gb|FG996449.1|FG996449
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|207786390|gb|GD757075.1|GD757075
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GGCGTTT-GGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggG-CGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTC
EST: gi|208307666|gb|GE107610.1|GE107610
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGTTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|21676489|gb|BQ628840.1|BQ628840
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|151411324|gb|EV281135.1|EV281135
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|31309603|gb|CD394806.1|CD394806
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|192302734|gb|FG993754.1|FG993754
EST:     GGACATAGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|254342931|gb|GR859093.1|GR859093
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|192297468|gb|FG992696.1|FG992696
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|51334757|gb|CO978623.1|CO978623
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|254334109|gb|GR849027.1|GR849027
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|298176675|gb|HO026796.1|HO026796
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|208066461|gb|GD863124.1|GD863124
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCG-TTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|6567248|gb|AW234859.1|AW234859
EST:     GGACATGGGAACGTTTAACTGTGGAGCATNTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCNGGTTTCCAGCTGTTGTAACAGCTCAT
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCAT
EST: gi|192323071|gb|FK017012.1|FK017012
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
EST: gi|192304324|gb|FG996450.1|FG996450
EST:     GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGG                         GCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC
genomic: GGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgcttt ... tcaatgaaggGCGTTTTGGATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgctttgctttgttcagtaactgtcaactagtaatctgattcttagagaaaggtctaaagagtggttttattttgtttcattcatcaatgaagg

- - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA