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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattaaatattttgttaagttttattgagattatcgctgactgtgcatactagtctgttttctctaatgcttgtgcgatctatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCATGGAAGCCCTGGCTGCTGGTGCTGATGTGAGCATGATTGGACAGTTTGG

Basic information

species Glycine max
transcript GLYMA02G47210.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G47210.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29061 (Selaginella moellendorffii), 3'ss of exon 2
gtaagattaaatattttgttaagttttattgagattatcgctgactgtgcatactagtctgttttctctaatgcttgtgcgatctatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCATGGAAGCCCTGGCTGCTGGTGCTGATGTGAGCATGATTGGACAGTTTGG
                             | || || | |||  | || | | |||| | |  ||||    ||  ||  |  |||   ||| |||| | ||||| |||||||| || ||||| |||||||| |||||||| |||||||||||| |||| ||||| || ||||||  |||||| || ||||||||
----------------------------gtaagtttctagcttccagttcttcctagccggagttcttacttgtatgctcattct---ttctagATCTCGTGAACAACCTCGGCACAATTGCCAGGTCTGGCACCAAGGAGTTCATGGAAGCCTTGGCCGCTGGCGCCGATGTGTCCATGATCGGTCAGTTTGG

upper sequence: GLYMA02G47210.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17594 (Selaginella moellendorffii), 3'ss of exon 2
gtaagattaaatattttgttaagttttattgagattatcgctgactgtgcatactagtctgttttctctaatgcttgtgcgatctatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCATGGAAGCCCTGGCTGCTGGTGCTGATGTGAGCATGATTGGACAGTTTGG
                             | || || | |||  | || | | |||| | |  ||||    ||  ||  |  |||    || |||| | ||||| |||||||| || ||||| |||||||| |||||||| |||||||||||| |||| ||||| || ||||||  |||||| || ||||||||
----------------------------gtaagtttctagcttccagttcttcctagccggagttcttacttgtatgctcattct---ctctagATCTCGTGAACAACCTCGGCACAATTGCCAGGTCTGGCACCAAGGAGTTCATGGAAGCCTTGGCCGCTGGCGCCGATGTGTCCATGATCGGTCAGTTTGG
















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|209706912|gb|BW653153.1|BW653153
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGAC
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGAC
EST: gi|209715369|gb|BW684678.1|BW684678
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|213608197|gb|DB963057.1|DB963057
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGTATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|213595973|gb|DB966276.1|DB966276
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|192324535|gb|FK016786.1|FK016786
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|11275146|gb|BF325469.1|BF325469
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|209722271|gb|BW651261.1|BW651261
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|192297661|gb|FG989580.1|FG989580
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|213616959|gb|DB959271.1|DB959271
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|4296389|gb|AI442468.1|AI442468
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|213589308|gb|DB961641.1|DB961641
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|213597221|gb|DB962067.1|DB962067
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|8826909|gb|BE210639.1|BE210639
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|6455834|gb|AW186517.1|AW186517
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|18735365|gb|BM528724.1|BM528724
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|209696909|gb|BW660474.1|BW660474
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|18040372|gb|BM308666.1|BM308666
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTCGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|298182250|gb|HO026425.1|HO026425
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCCGgtaagattaa ... tatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgactgtgcatactagtctgttttctctaatgcttgtgcgatctatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCATGGAAGCCCTGGCTGCTGGTGCTGATGTGAGCATGATTGGACAGTTTGG
                          ctctaat  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattaaatattttgttaagttttattgagattatcgctgactgtgcatactagtctgttttctctaatgcttgtgcgatctatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCATGGAAGCCCTGGCTGCTGGTGCTGATGTGAGCATGATTGGACAGTTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT