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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCCATTTTCCAAGTTTTGCAAACTAGGGAGTTGCCACCTACCTATTTCCGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGGgtgagcatcatactgttttccttttcctcattttattcctttatttgtagttgtgtgtgtggaaagatgaggtttagttattgatattatgtgcagaata...

Basic information

species Glycine max
transcript GLYMA11G12120.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12120.1 (Glycine max), 5'ss of exon 10
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 10
ATGCCATTTTCCAAGTTTTGCAAACTAGGGAGTTGCCACCTACCTATTTCCGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGGgtgagcatcatactgttttccttttcctcattt--------------------tattcctttatttgtagttgtgtgtgtggaaagatgaggtttagt--tattgatattatgtgcagaata----------
   | |||||||| ||  |   ||| |  |||| |||||| || ||||| ||||||||||||||||||||| |  | || | |||| ||||  | ||||||| ||  || | |||      ||  |    |||                    ||  | || | || ||      ||||| | |   || | |||| |  | |     ||   |    | |           
GATCAATTTTCCAGGTCCTAAGAACCAAAGAGTCGCCACCAACTTATTTTCGCACAAACAAATTTACTTCTGCAATCCAGGAAATTGTTGATGCGTATGGgtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcag

upper sequence: GLYMA11G12120.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 5'ss of exon 10
ATGCCATTTTCCAAGTTTTGCAAACTAGGGAGTTGCCACCTACCTATTTCCGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGGgtgagcatcatactgttttccttttcctcattttattcctttatttgtagttgtgtgtgtggaaagatgaggtttagttattg--atattatgtgcagaata--
  ||||||||||| |||||||| || |  |||| |||||| || ||||||||||||||||||||||||||| ||||||| | |||| ||||  ||||||||| ||   ||  | | ||   ||| |  | | ||      ||| |    ||      | || |   || | |  |    ||    |||| | | | |  |    
GAGCCATTTTCCAGGTTTTGCATACGATAGAGTCGCCACCAACTTATTTCCGCACAAACAAATTTACTTCTGCTTTTCAGGAAATTGTTGATGCATATGGgttagttccactcagattgtttttactgcttctt----tattagtgaaggtaacaattatgcattaataatgcatgtgcatgagaatatcaggagtaccactac
















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|193586563|gb|FK543923.1|FK543923
EST:     CGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGG                         GGTTAAGCTAAGTATCAGGAG
genomic: CGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGGgtgagcatca ... aacatttcagGGTT--GCTAAGTATCAGGAG
EST: gi|193411199|gb|FK376822.1|FK376822
EST:     CGCACAAACAAATTTACTTCTTCTTT-CAAGGAATTATTGACTCATATGG                         GGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTT
genomic: CGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGGgtgagcatca ... aacatttcagGGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTT
EST: gi|193424034|gb|FK391129.1|FK391129
EST:     CGCACAAACAAATTTACTTCTTC-TTTCAAGGAATTATTGACTCATATGG                         GGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTT
genomic: CGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGGgtgagcatca ... aacatttcagGGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTT
EST: gi|207713390|gb|GD695779.1|GD695779
EST:     CGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGG                         GGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTT
genomic: CGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGGgtgagcatca ... aacatttcagGGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTT
EST: gi|193540033|gb|FK499017.1|FK499017
EST:     TTATTGACTCATATGG                         GGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTT
genomic: TTATTGACTCATATGGgtgagcatca ... aacatttcagGGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTT
EST: gi|193549644|gb|FK506401.1|FK506401
EST:     CGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGG                         GGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTT
genomic: CGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGGgtgagcatca ... aacatttcagGGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCCATTTTCCAAGTTTTGCAAACTAGGGAGTTGCCACCTACCTATTTCCGCACAAACAAATTTACTTCTTCTTTTCAAGGAATTATTGACTCATATGGgtgagcatcatactgttttccttttcctcattttattcctttatttgtagttgtgtgtgtggaaagatgaggtttagttattgatattatgtgcagaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttttcc