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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgatattctcttgttgtgactataaggaagttcttacacatttaattgtctattggggttaccttgggattgaattgaattcatattggcttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCGTTTTCTCTGACCCTTATAAAGTTTCTCAATATAATCGTTGTACTTCCCC

Basic information

species Glycine max
transcript GLYMA20G26580.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 2
ctgatattctcttgttgtgactataaggaagttcttacacatttaattgtcta-ttggggttaccttgg-gattgaattgaattcatattggcttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCGTTTTCTCTGACCCTTATAAAGTTTCTCAATATAATCGTTGTACTTCCCC
                       | |  |   ||  |   |||| |||  ||| |    |||| | ||  | ||| | ||| |   | |||  ||  || |||  ||||||||||||| ||||||||||||||| |  | || || || || || || || ||||| |||| ||||||   || ||||||||| ||||| ||
---------------------gttcaaaaccctcacatctattttatttactagtcaatgttatcgtgttgcttgtagtgagtgtcttttgtgtttgtgtagTAACCGAATTTTGTGGTAATGTGGAGTTATGCCGATTAACGGAGCAAGTTGTGTTTTCGGACCCATATAGAGTTTCCACATTTAATCGTTGGACTTCACC

upper sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0091g00080.t01 (Vitis vinifera), 3'ss of exon 2
ctgatattctcttgttgtgactataaggaagttcttacacatttaattgtctattggggttaccttg------ggattgaattgaattcatattg-gcttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCGTTTTCTCTGACCCTTATAAAGTTTCTCAATATAATCGTTGTACTTCCCC
    || |  || || |    ||  || || ||      || ||   | |||  ||  ||||   |        ||||||||    |||| |||| |||| |||||||||| ||||||||||| ||||||||||||||  |||||||||| || || || |||||||| || || ||||| ||||| || ||||| || ||||| ||
-gagtaattactggtagaatgtacgagaaaatt-----gcagtttgct-tctgatgaagttattctattgacaagattgaatcatgttcaaattgtgctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTGTGTTCTCTGATCCATACAAAGTATCTCAGTACAATCGGTGGACTTCTCC

upper sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0091g00100.t01 (Vitis vinifera), 3'ss of exon 2
ctgatattctcttgttgtgactataaggaagttcttacacatttaattgtctattggggttaccttg------ggattgaattgaattcatattg-gcttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCGTTTTCTCTGACCCTTATAAAGTTTCTCAATATAATCGTTGTACTTCCCC
    || |  || || |    ||  || || ||      || ||   | |||  ||  ||||   |          ||||||    |||| |||| |||| |||||||||| ||||||||||| ||||||||||||||  ||| |||||  || || ||||||||||| || || ||||| ||||| |||||| | || ||||||||
-gagtaattactggtagaatttaagagaaaatt-----gcagtttgct-tctgatgaagttattctattgacaaacttgaatcatgttcaaattgtgctttatgcagTTGCTGAATTTTGTGGAAATGTGGAGTTATGTCGGCACACTGGGCAAGTTGTTTTCTCTGATCCATACAAAGTATCTCAGTATAATTGGTGGACTTCCCC

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|105634567|gb|DW247599.1|DW247599
EST:     CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACG                         TTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
genomic: CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
EST: gi|151408064|gb|EV277872.1|EV277872
EST:     CTTCTTCGCGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACG                         TTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
genomic: CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
EST: gi|6567066|gb|AW234693.1|AW234693
EST:     CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACG                         TTGCCGAATTNTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
genomic: CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
EST: gi|18040792|gb|BM309086.1|BM309086
EST:     CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACG                         TTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
genomic: CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
EST: gi|192324081|gb|FK019372.1|FK019372
EST:     CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACG                         TTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
genomic: CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
EST: gi|254322009|gb|GR837423.1|GR837423
EST:     CACAAACGGGACG                         TTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
genomic: CACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
EST: gi|213594296|gb|DB969974.1|DB969974
EST:     CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACG-----                         TTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
genomic: CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
EST: gi|24205958|gb|BU965211.1|BU965211
EST:     CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACG                         TTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
genomic: CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
EST: gi|192298387|gb|FG988433.1|FG988433
EST:     CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACG                         TTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
genomic: CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
EST: gi|8825853|gb|BE209583.1|BE209583
EST:     CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACG                         TTGCCGAATGTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAAGTCG
genomic: CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
EST: gi|10232185|gb|BE801081.1|BE801081
EST:     CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACG                         TTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
genomic: CTTCTTCACGTCTCTGCTTTTCCGTTCCACTGCTGACCACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
EST: gi|254332676|gb|GR844046.1|GR844046
EST:     CACAAACGGGACG                         TTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG
genomic: CACAAACGGGACGgtataacctt ... cttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtctattggggttaccttgggattgaattgaattcatattggcttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCGTTTTCTCTGACCCTTATAAAGTTTCTCAATATAATCGTTGTACTTCCCC
 atttaat  putative branch site (score: 4)
                            aattgaattcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgatattctcttgttgtgactataaggaagttcttacacatttaattgtctattggggttaccttgggattgaattgaattcatattggcttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCGTTTTCTCTGACCCTTATAAAGTTTCTCAATATAATCGTTGTACTTCCCC

- - - - - cttgttg
- - - - - - - - - - - - - - - - -cttacac
- - - - - - - - - - - - - - - - - - - - - - - - - - attgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaattc